http://irefindex.vib.be/wiki/api.php?action=feedcontributions&user=Sabry&feedformat=atomirefindex - User contributions [en]2024-03-29T02:38:22ZUser contributionsMediaWiki 1.33.0http://irefindex.vib.be/wiki/index.php?title=iRefScape_1.0_Installation&diff=3669iRefScape 1.0 Installation2011-08-05T14:18:36Z<p>Sabry: /* Install from file */ An laternative method to install the plugin</p>
<hr />
<div>==Installation==<br />
<br />
=== Before You Begin ===<br />
<br />
* These instructions assume that you have downloaded and installed the Cytoscape application. See http://cytoscape.org/ for a manual and a set of tutorials which describe the installation and use of Cytoscape.<br />
* Make sure you have an active Internet connection. During installation the plugin will download files from the iRefIndex FTP site.<br />
* Make sure you have latest Java environment installed: Java 1.6 or later is required.<br />
* '''If you have a plugin called iRefIndex installed, it is recommended that you first delete it''', selecting the "Manage Plugins" option in the "Plugins" menu. This will only be the case for people who may have tried earlier development versions of the plugin.<br />
<br />
=== Using the Cytoscape Plugin menu ===<br />
<br />
[[Image:IRefIndex-Cytoscape-Manage-Plugins.png|thumb|300px|Manage Plugins]]<br />
<br />
# Start Cytoscape. You must start Cytoscape as a user that has write privileges to the target directory. <br />
# From the menu select "Plugins" -> "Manage Plugins". <br />
# Select "Manage plugins" from the plugin menu.<br />
# Locate "Available for Install" then "Network and Attribute I/O", verifying that iRefScape is listed in this category.<br />
# Select the iRefScape plugin and then click "Install" (in the bottom-right-hand corner of the window).<br />
# When you see the message "iRefScape v.x.x install complete" click "Close" to leave the "Manage Plugins" dialogue.<br />
# Close Cytoscape.<br />
# Go to the next section to complete the setup.<br />
<br />
<br />
<br clear="all" /><br />
<br />
=== Completing the Installation ===<br />
<br />
[[Image:IRefIndex-Cytoscape-Location.png|thumb|300px|Indicating the location of iRefIndex data]]<br />
<br />
[[Image:IRefIndex-Cytoscape-Download.png|thumb|300px|The download status dialogue]]<br />
<br />
# Restart Cytoscape.<br />
# Select iRefIndexx.x from Cytoscape's "Plugins" menu.<br />
# When the plugin is started for the first time, it will download the dataset.<br />
# You will be prompted to select an installation directory for the data and indices. The recommended place would be the plugin home directory which will appear as the recommended directory. The data and indices require a minimum disk space of 1 GB at this location. Using this default directory is strongly encouraged.<br />
# If the default directory is selected and is not accessible, you will be prompted to restart Cytoscape. If this message appears on second or subsequent attempts, this may mean that there is a problem accessing this directory. To avoid such problems, ensure that you have write access to the directory and at least 1GB of free space on the disk.<br />
# The downloading and installation of indices usually takes less than 5 minutes if you have a internet connection of 10Mb/sec or more. However installation may take between 15 and 30 minutes depending on your internet connection.<br />
# The installation process should now complete itself.<br />
# If the installation was successful, you will see a new iRefScape panel near the "Network" tab of Cytoscape as well as an iRefScape menu (blue) at the top of the Cytoscape interface. Also, you will see an Information frame with several tabs in it ("Messages", "Search history", "Query helper", and so on). This window can be closed.<br />
<br />
<br clear="all" /><br />
<br />
<br />
=== Using the iRefIndex Installation site ===<br />
<br />
In rare cases, the Cytoscape plugin site may be down. In this case, you have the option of using the iRefScape plugin site.<br />
<br />
# Start Cytoscape. You must start Cytoscape as a user that has write privileges to the target directory. <br />
# From the menu select "Plugins" -> "Manage Plugins".<br />
<br />
To use the iRefScape plugin site:<br />
<br />
# Click on "Settings" tab.<br />
# Click "Add" and for each of the following fields, enter the suggested values:<br />
#* Name: <tt>iRefScape</tt><br />
#* URL: <tt>ftp://ftp.no.embnet.org/irefindex/Cytoscape/plugin/current/plugins_irefindex.xml</tt><br />
<br />
<br />
To install the plugin:<br />
<br />
# Locate "Available for Install" then "Network and Attribute I/O", verifying that iRefScape is listed in this category.<br />
# Select the iRefScape plugin and then click "Install" (in the bottom-right-hand corner of the window).<br />
# Click "Close" to leave the "Manage Plugins" dialogue.<br />
# Restart Cytoscape.<br />
# Go to the "Completing the installation" step above.<br />
<br />
=== Install from file ===<br />
<br />
If the plug-in download manager fails to initialise or if you face a problem using it, the plugin can be manually downloaded from the following locations:<br />
*Cytoscape plugin repository: http://chianti.ucsd.edu/cyto_web/plugins/ (look for iRefScape under "Network and Attribute I/O"). Locate the link "Download Jar/zip: click here" and download the plugin to a easily locatable place (e.g. desktop).<br />
<br />
*irect link to iRefScape at Cytoscape site: http://chianti.ucsd.edu/cyto_web/plugins/displayplugininfo.php?name=iRefScape<br />
(The latest version is listed last). Locate the link "Download Jar/zip: click here" and download the plugin to a easily locatable place (e.g. desktop).<br />
<br />
*From iRefIndex ftp: <br />
ftp://ftp.no.embnet.org/irefindex/Cytoscape/plugin/current/iRefScape.jar<br />
<br />
After downloading the plugin can be installed by following the steps below.<br />
# Start Cytoscape<br />
# Make sure there are no other versions of the iRefScape plugin are already installed (if you see iRefScape please uninstall and restart Cytoscape, before proceeding)<br />
#Locate and select the Cytoscape menu "Plugins" -> "install plugin from file"<br />
#When the file open dialogue window appears, select the downloaded file (iRefScape.jar).<br />
# After installation is complete please restart Cytoscape (please do not try to activate the iRefScape plugin before restarting Cytoscape)<br />
# After restarting activate the plugin by selecting iRefScape from plugin menu of Cytoscape and follow instructions to download the dataset.<br />
<br />
Please note that this method do not solve firewall related issues.<br />
<br />
=== Manual Installation: if you have problems installing with the Cytoscape plugin manager ===<br />
<br />
If you are still having problems, you can try manually downloading and installing the files. This is especially useful if you are having firewall problems while getting the plugin or the data.<br />
<br />
# Before starting:<br />
#* Make sure that Cytoscape is not running.<br />
#* Remove any other installations of iRefScape (or iRefIndex) or directories created by those installations (such as <tt>.../Cytoscape_vx.x.x/plugins/iRefScape</tt>).<br />
#* Go to ftp://ftp.no.embnet.org/irefindex/Cytoscape/plugin/current/ (username: anonymous password:ftp if you use command line ftp to do this).<br />
#* Download iRefScape.jar<br />
#* Download iRefDATA_mmddyyyy.irfz (where mmddyyyy is the date stamp for the file)<br />
# Copy the <tt>iRefScape.jar</tt> file to the plugins directory of your Cytoscape installation. For example:<br />
On Unix: .../Cytoscape_v2.6.2/plugins/<br />
On Windows: ...\Cytoscape_v2.6.2\plugins\<br />
#* Copy the iRefDATA_mmddyyyy.irfz file to the same directory or anywhere else where you have permissions to write to.<br />
#* Start Cytoscape<br />
#* Select iRefIndex from the Plugins menu<br />
#* When prompted for an installation directory, select the directory where you placed the iRefDATA_mmddyyyy.irfz file.<br />
#* The plugin will complete the installation without having to first download the iRefDATA_mmddyyyy.irfz file.<br />
# Email the iRefIndex google group if you have problems. <br />
<br clear="all" /><br />
<br />
=== Uninstalling the Plugin===<br />
<br />
# From the Cytoscape Plugins menu, select "Currently Installed" -> "Network and Attribute I/O Plugins" and choose the iRefScape plugin.<br />
# Then, click the "Delete" button and confirm.<br />
# Click "Close" to leave the "Manage Plugins" dialogue and restart Cytoscape.<br />
# The plugin will be deleted when you restart Cytoscape.<br />
<br />
<br />
=== Increasing memory available to Cytoscape ===<br />
<br />
If the Cytoscape interface becomes unresponsive (especially when working with large graphs), take a look at this page to increase memory available to Cytoscape.<br />
<br />
[http://cytoscape.wodaklab.org/wiki/How_to_increase_memory_for_Cytoscape How_to_increase_memory_for_Cytoscape]<br />
<br />
== Troubleshooting Platform-Specific Issues ==<br />
<br />
=== Windows Vista and Windows XP ===<br />
<br />
You will require write privileges to the installation directory not only during installation but also during operation of the plugin. If the plugin disappears from the "Plugins" menu or it does not appear at all, then Cytoscape has to be started as an administrator. This could be done by right-clicking on the Cytoscape shortcut and selecting "Run as" option. When requesting help for such situations, please include a copy-paste of the Cytoscape error console ("Help" -> "Error console"). (To copy-paste, open the error console, click inside, press <tt>Ctrl-A</tt> (to select all) then <tt>Ctrl-C</tt> (to copy). The selection can then be pasted into a message using <tt>Ctrl-V</tt>.)<br />
<br />
=== Mac OS X ===<br />
<br />
* Please verify that Java 1.6 or later is available. ''The plugin will not work unless Java 1.5 or later is installed.''<br />
* Increase the <tt>Xmx</tt> setting to <tt>512m</tt> and the <tt>Xms</tt> setting to <tt>512m</tt> in <tt>cytoscape.sh</tt>.<br />
* This version of the plugin is not extensively tested on Mac OS and we are sorry that the support we could provide for Mac users is limited at this point. <br />
<br />
=== Unix/Linux ===<br />
<br />
* Please verify that Java 1.6 or later is available.<br />
** The "Java SE Development Kit (JDK)" from http://java.sun.com/javase/downloads/index.jsp is suitable. The Sun/Oracle version of Java may be available as a package for your distribution. For example, the <tt>sun-java6-bin</tt> package for Ubuntu provides a compatible version of Java.<br />
** The OpenJDK packages from http://openjdk.java.net/install/ may also be suitable and are often available via distributions. For example, OpenJDK 6 for [http://packages.debian.org/search?keywords=openjdk-6-jdk&searchon=names&suite=all&section=all Debian] and [http://packages.ubuntu.com/search?keywords=openjdk-6-jdk&searchon=names&suite=all&section=all Ubuntu].<br />
** After installing a new version of Java for Debian or Ubuntu, you may need to use the <tt>update-alternatives</tt> command to indicate that you would like to use this new version instead of any existing version, or you may need to add the precise location of the new <tt>java</tt> program to your <tt>PATH</tt>.<br />
* You will require write privileges to the installation directory not only during installation but also during operation.<br />
* The plugin behavior is proven to be very stable in Unix/Linux environments.<br />
* To improve font appearance, try adding the following environment variable definition to your configuration (in <tt>.bashrc</tt> or <tt>.bash_profile</tt>), as described in this [http://wiki.archlinux.org/index.php/Java_Fonts_-_Sun_JRE guide to Java fonts for Arch Linux]:<br />
<br />
export _JAVA_OPTIONS='-Dawt.useSystemAAFontSettings=lcd'<br />
<br />
== Troubleshooting Security Issues==<br />
<br />
The plugin has two components:<br />
<br />
* The Java executable file (<tt>iRefScape_x.x.jar</tt>) which is the software component providing the plugin functionality.<br />
* The data component containing protein-protein interaction data.<br />
<br />
Both these components are required for the functioning of the plugin. The installation section above explains how to install the executable components, and once this component is installed and the plugin is loaded, the data component will then be downloaded by the plugin itself. The downloaded file is compressed and has the extension <tt>.irfz</tt> and a size of around 200 MB. After the download is complete this file will be partially uncompressed (the indices and few other files required for immediate operation will be extracted from the complex file). However, the bulk of the data will remain compressed and will only be uncompressed when needed. Thus, the speed of query execution will increase with usage and the size of the <tt>iRefIndex</tt> directory will increase. Therefore, although 250MB of available free space is enough during installation, the plugin requires up to 1GB of space for its operation.<br />
<br />
If the plugin manager is used for the installation (as of Cytoscape 2.6.3 and later), the plugin will be placed in a directory under the home area and a record file is kept in a file named <tt>track_plugins.xml</tt>. The location of these would as follows:<br />
<br />
* Linux: <tt>~/.cytoscape/2.8</tt><br />
* Windows: <tt>''<user's home directory>''\.cytoscape\2.8</tt><br />
<br />
The entry corresponding to iRefScape plugin would looks like follows:<br />
<br />
<plugin><br />
<uniqueID>999</uniqueID><br />
<name>iRefScape</name><br />
<description>.&lt;br&gt;http://irefindex.uio.no/wiki/README_Cytoscape_plugin_0.8x&lt;p&gt;</description><br />
<cytoscapeVersion>2.6</cytoscapeVersion><br />
<url>ftp://ftp.no.embnet.org/irefindex/Cytoscape/plugin/archive/beta8/iRefScape_0_83.jar</url><br />
<downloadUrl>ftp://ftp.no.embnet.org/irefindex/Cytoscape/plugin/current/plugins_irefindex.xml</downloadUrl><br />
<category>Network and Attribute I/O</category><br />
<releaseDate>MAY 20, 2010</releaseDate><br />
<pluginVersion>0.83</pluginVersion><br />
<classname>cytoscape.no.uio.biotek.Main</classname><br />
<projectUrl>http://irefindex.uio.no</projectUrl><br />
<filetype>jar</filetype><br />
<installLocation>.../.cytoscape/2.6/plugins/iRefScape-0.83</installLocation><br />
<license><br />
<text /><br />
</license><br />
<filelist><br />
<file>.../.cytoscape/2.6/plugins/iRefScape-0.83/iRefScape.jar</file><br />
</filelist><br />
<authorlist><br />
<author><br />
<name>Ian Donaldson and Sabry Razick</name><br />
<institution>Biotechnology Centre of Oslo, University of Oslo</institution><br />
</author><br />
</authorlist><br />
</plugin><br />
<br />
'''Note:''' If you encounter an exception during Cytoscape's start-up process due to a plugin failure and there is no way of uninstalling it, you could remove the entry for the corresponding plugin from this file when Cytoscape is not running. First, take a backup of the file, then delete the plugin entry resembling that shown above for the plugin concerned. Finally, save the file and restart Cytoscape.<br />
<br />
The download and installation of the plugin executable is managed by the core functionality provided by Cytoscape, and if the plugin complies with the requirements defined for the plugin framework, the installation should proceed smoothly. However, some users have encountered problems when installing the data component; this is mainly due to privilege and security issues.<br />
<br />
* Privilege issues arise when a user does not have access to the place where the data component is to be installed. This directory should permit write access for that user.<br />
* Security issues are mainly encountered with Microsoft Windows-based operating systems. When software tries to perform a suspicious operation, the operation is blocked and the user is prompted to confirm that this is something they have chosen to do themselves. If the user selects "block", the iRefScape plugin installation fails and it may not be possible to attempt to install the plugin again until the blocking action is revoked manually. Although antivirus products are also known to interfere with software installers, the plugin installation process has been tested on systems running several popular antivirus products, but has not revealed any issues relating to them at the time of writing. If you encounter any such issues, please report to these to the [http://groups.google.com/group/irefindex?hl=en iRefIndex Google Group]. <br />
<br />
The behaviour of the plugin when installed using the plugin manager is different before and after Cytoscape is restarted. After the installation, the plugin will appear in the plugin manager and could be activated, however it is not aware of its environment: for example, it does not know its installation location. Therefore it is highly recommended that Cytoscape be restarted immediately after installing the plugin, and that the plugin is not activated before the first restart (do not click on the "iRefScape" menu entry). When a manual installation is performed, the plugin can be activated after starting Cytoscape for the first time, since Cytoscape is not running during the installation process.<br />
<br />
Some of the reasons behind distributing the data with the plugin rather than more popular approaches such as the use of Web services include the following:<br />
<br />
* Execution speed<br />
* No need for a fast internet connection after installation<br />
* Hosting restrictions applying to the iRefScape/iRefIndex download site<br />
* Privacy for the user: there is no monitoring of the types of searches the user performs; thus, the user's activities remain private <br />
<br />
<br clear="all" /><br />
<br />
== About the Installation Files ==<br />
<br />
During installation the plugin downloads protein-protein interaction data from iRefIndex (ftp://ftp.no.embnet.org/irefindex/Cytoscape/plugin/current/) in a compressed form. The downloaded files will reside in the <tt>iRefIndex</tt> directory under the Cytoscape plugin folder. It is recommended that the files in this directory '''not''' be modified as this may lead to unpredictable results. In particular, please do not open them in word-processing software (such as Microsoft Office). After successful installation you will also find some index files and serialized Java object files which will be used in the search and load operations.<br />
<br />
=== Brief Description of the Files ===<br />
<br />
* irft files: this file contains a ROG (Redundant Object Group) to PARAMETER mapping. This is a sort of index that maps identifiers like accessions and names to ROGs. The ROG is an integer representation of the ROGID. However, ROG is not stable like ROGID and it may be different from one version to another. However, from beta4 onwards the ROGID to ROG mapping will be propagated for backwards compatibility for live proteins (proteins which are not removed from original source). <br />
* Irfm files: These are index files containing information about partners of each interaction.<br />
* ROGS Directory: Contains protein attributes (Warning! Please do not try to open this directory in a file browser; the computer may crash) <br />
* RIGS Directory: Contains interaction attributes (Warning! Please do not try to open this directory in a file browser; the computer may crash) <br />
* Irfj files : these files contain the interaction and object data in a compressed form. When requested for the first time the information will be uncompressed to the RIGS or ROGS directory.<br />
<br />
[[Category:iRefIndex]]</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefScape_1.0_Installation&diff=3668iRefScape 1.0 Installation2011-08-05T14:17:46Z<p>Sabry: /* Install from file */</p>
<hr />
<div>==Installation==<br />
<br />
=== Before You Begin ===<br />
<br />
* These instructions assume that you have downloaded and installed the Cytoscape application. See http://cytoscape.org/ for a manual and a set of tutorials which describe the installation and use of Cytoscape.<br />
* Make sure you have an active Internet connection. During installation the plugin will download files from the iRefIndex FTP site.<br />
* Make sure you have latest Java environment installed: Java 1.6 or later is required.<br />
* '''If you have a plugin called iRefIndex installed, it is recommended that you first delete it''', selecting the "Manage Plugins" option in the "Plugins" menu. This will only be the case for people who may have tried earlier development versions of the plugin.<br />
<br />
=== Using the Cytoscape Plugin menu ===<br />
<br />
[[Image:IRefIndex-Cytoscape-Manage-Plugins.png|thumb|300px|Manage Plugins]]<br />
<br />
# Start Cytoscape. You must start Cytoscape as a user that has write privileges to the target directory. <br />
# From the menu select "Plugins" -> "Manage Plugins". <br />
# Select "Manage plugins" from the plugin menu.<br />
# Locate "Available for Install" then "Network and Attribute I/O", verifying that iRefScape is listed in this category.<br />
# Select the iRefScape plugin and then click "Install" (in the bottom-right-hand corner of the window).<br />
# When you see the message "iRefScape v.x.x install complete" click "Close" to leave the "Manage Plugins" dialogue.<br />
# Close Cytoscape.<br />
# Go to the next section to complete the setup.<br />
<br />
<br />
<br clear="all" /><br />
<br />
=== Completing the Installation ===<br />
<br />
[[Image:IRefIndex-Cytoscape-Location.png|thumb|300px|Indicating the location of iRefIndex data]]<br />
<br />
[[Image:IRefIndex-Cytoscape-Download.png|thumb|300px|The download status dialogue]]<br />
<br />
# Restart Cytoscape.<br />
# Select iRefIndexx.x from Cytoscape's "Plugins" menu.<br />
# When the plugin is started for the first time, it will download the dataset.<br />
# You will be prompted to select an installation directory for the data and indices. The recommended place would be the plugin home directory which will appear as the recommended directory. The data and indices require a minimum disk space of 1 GB at this location. Using this default directory is strongly encouraged.<br />
# If the default directory is selected and is not accessible, you will be prompted to restart Cytoscape. If this message appears on second or subsequent attempts, this may mean that there is a problem accessing this directory. To avoid such problems, ensure that you have write access to the directory and at least 1GB of free space on the disk.<br />
# The downloading and installation of indices usually takes less than 5 minutes if you have a internet connection of 10Mb/sec or more. However installation may take between 15 and 30 minutes depending on your internet connection.<br />
# The installation process should now complete itself.<br />
# If the installation was successful, you will see a new iRefScape panel near the "Network" tab of Cytoscape as well as an iRefScape menu (blue) at the top of the Cytoscape interface. Also, you will see an Information frame with several tabs in it ("Messages", "Search history", "Query helper", and so on). This window can be closed.<br />
<br />
<br clear="all" /><br />
<br />
<br />
=== Using the iRefIndex Installation site ===<br />
<br />
In rare cases, the Cytoscape plugin site may be down. In this case, you have the option of using the iRefScape plugin site.<br />
<br />
# Start Cytoscape. You must start Cytoscape as a user that has write privileges to the target directory. <br />
# From the menu select "Plugins" -> "Manage Plugins".<br />
<br />
To use the iRefScape plugin site:<br />
<br />
# Click on "Settings" tab.<br />
# Click "Add" and for each of the following fields, enter the suggested values:<br />
#* Name: <tt>iRefScape</tt><br />
#* URL: <tt>ftp://ftp.no.embnet.org/irefindex/Cytoscape/plugin/current/plugins_irefindex.xml</tt><br />
<br />
<br />
To install the plugin:<br />
<br />
# Locate "Available for Install" then "Network and Attribute I/O", verifying that iRefScape is listed in this category.<br />
# Select the iRefScape plugin and then click "Install" (in the bottom-right-hand corner of the window).<br />
# Click "Close" to leave the "Manage Plugins" dialogue.<br />
# Restart Cytoscape.<br />
# Go to the "Completing the installation" step above.<br />
<br />
=== Install from file ===<br />
<br />
If the plug-in download manager fails to initialise or if you face a problem using it, the plugin can be manually downloaded from the following locations:<br />
#Cytoscape plugin repository: http://chianti.ucsd.edu/cyto_web/plugins/ (look for iRefScape under "Network and Attribute I/O"). Locate the link "Download Jar/zip: click here" and download the plugin to a easily locatable place (e.g. desktop).<br />
<br />
#Direct link to iRefScape at Cytoscape site: http://chianti.ucsd.edu/cyto_web/plugins/displayplugininfo.php?name=iRefScape<br />
(The latest version is listed last). Locate the link "Download Jar/zip: click here" and download the plugin to a easily locatable place (e.g. desktop).<br />
<br />
#From iRefIndex ftp: <br />
ftp://ftp.no.embnet.org/irefindex/Cytoscape/plugin/current/iRefScape.jar<br />
<br />
After downloading the plugin can be installed by following the steps below.<br />
# Start Cytoscape<br />
# Make sure there are no other versions of the iRefScape plugin are already installed (if you see iRefScape please uninstall and restart Cytoscape, before proceeding)<br />
#Locate and select the Cytoscape menu "Plugins" -> "install plugin from file"<br />
#When the file open dialogue window appears, select the downloaded file (iRefScape.jar).<br />
# After installation is complete please restart Cytoscape (please do not try to activate the iRefScape plugin before restarting Cytoscape)<br />
# After restarting activate the plugin by selecting iRefScape from plugin menu of Cytoscape and follow instructions to download the dataset.<br />
<br />
Please note that this method do not solve firewall related issues.<br />
<br />
=== Manual Installation: if you have problems installing with the Cytoscape plugin manager ===<br />
<br />
If you are still having problems, you can try manually downloading and installing the files. This is especially useful if you are having firewall problems while getting the plugin or the data.<br />
<br />
# Before starting:<br />
#* Make sure that Cytoscape is not running.<br />
#* Remove any other installations of iRefScape (or iRefIndex) or directories created by those installations (such as <tt>.../Cytoscape_vx.x.x/plugins/iRefScape</tt>).<br />
#* Go to ftp://ftp.no.embnet.org/irefindex/Cytoscape/plugin/current/ (username: anonymous password:ftp if you use command line ftp to do this).<br />
#* Download iRefScape.jar<br />
#* Download iRefDATA_mmddyyyy.irfz (where mmddyyyy is the date stamp for the file)<br />
# Copy the <tt>iRefScape.jar</tt> file to the plugins directory of your Cytoscape installation. For example:<br />
On Unix: .../Cytoscape_v2.6.2/plugins/<br />
On Windows: ...\Cytoscape_v2.6.2\plugins\<br />
#* Copy the iRefDATA_mmddyyyy.irfz file to the same directory or anywhere else where you have permissions to write to.<br />
#* Start Cytoscape<br />
#* Select iRefIndex from the Plugins menu<br />
#* When prompted for an installation directory, select the directory where you placed the iRefDATA_mmddyyyy.irfz file.<br />
#* The plugin will complete the installation without having to first download the iRefDATA_mmddyyyy.irfz file.<br />
# Email the iRefIndex google group if you have problems. <br />
<br clear="all" /><br />
<br />
=== Uninstalling the Plugin===<br />
<br />
# From the Cytoscape Plugins menu, select "Currently Installed" -> "Network and Attribute I/O Plugins" and choose the iRefScape plugin.<br />
# Then, click the "Delete" button and confirm.<br />
# Click "Close" to leave the "Manage Plugins" dialogue and restart Cytoscape.<br />
# The plugin will be deleted when you restart Cytoscape.<br />
<br />
<br />
=== Increasing memory available to Cytoscape ===<br />
<br />
If the Cytoscape interface becomes unresponsive (especially when working with large graphs), take a look at this page to increase memory available to Cytoscape.<br />
<br />
[http://cytoscape.wodaklab.org/wiki/How_to_increase_memory_for_Cytoscape How_to_increase_memory_for_Cytoscape]<br />
<br />
== Troubleshooting Platform-Specific Issues ==<br />
<br />
=== Windows Vista and Windows XP ===<br />
<br />
You will require write privileges to the installation directory not only during installation but also during operation of the plugin. If the plugin disappears from the "Plugins" menu or it does not appear at all, then Cytoscape has to be started as an administrator. This could be done by right-clicking on the Cytoscape shortcut and selecting "Run as" option. When requesting help for such situations, please include a copy-paste of the Cytoscape error console ("Help" -> "Error console"). (To copy-paste, open the error console, click inside, press <tt>Ctrl-A</tt> (to select all) then <tt>Ctrl-C</tt> (to copy). The selection can then be pasted into a message using <tt>Ctrl-V</tt>.)<br />
<br />
=== Mac OS X ===<br />
<br />
* Please verify that Java 1.6 or later is available. ''The plugin will not work unless Java 1.5 or later is installed.''<br />
* Increase the <tt>Xmx</tt> setting to <tt>512m</tt> and the <tt>Xms</tt> setting to <tt>512m</tt> in <tt>cytoscape.sh</tt>.<br />
* This version of the plugin is not extensively tested on Mac OS and we are sorry that the support we could provide for Mac users is limited at this point. <br />
<br />
=== Unix/Linux ===<br />
<br />
* Please verify that Java 1.6 or later is available.<br />
** The "Java SE Development Kit (JDK)" from http://java.sun.com/javase/downloads/index.jsp is suitable. The Sun/Oracle version of Java may be available as a package for your distribution. For example, the <tt>sun-java6-bin</tt> package for Ubuntu provides a compatible version of Java.<br />
** The OpenJDK packages from http://openjdk.java.net/install/ may also be suitable and are often available via distributions. For example, OpenJDK 6 for [http://packages.debian.org/search?keywords=openjdk-6-jdk&searchon=names&suite=all&section=all Debian] and [http://packages.ubuntu.com/search?keywords=openjdk-6-jdk&searchon=names&suite=all&section=all Ubuntu].<br />
** After installing a new version of Java for Debian or Ubuntu, you may need to use the <tt>update-alternatives</tt> command to indicate that you would like to use this new version instead of any existing version, or you may need to add the precise location of the new <tt>java</tt> program to your <tt>PATH</tt>.<br />
* You will require write privileges to the installation directory not only during installation but also during operation.<br />
* The plugin behavior is proven to be very stable in Unix/Linux environments.<br />
* To improve font appearance, try adding the following environment variable definition to your configuration (in <tt>.bashrc</tt> or <tt>.bash_profile</tt>), as described in this [http://wiki.archlinux.org/index.php/Java_Fonts_-_Sun_JRE guide to Java fonts for Arch Linux]:<br />
<br />
export _JAVA_OPTIONS='-Dawt.useSystemAAFontSettings=lcd'<br />
<br />
== Troubleshooting Security Issues==<br />
<br />
The plugin has two components:<br />
<br />
* The Java executable file (<tt>iRefScape_x.x.jar</tt>) which is the software component providing the plugin functionality.<br />
* The data component containing protein-protein interaction data.<br />
<br />
Both these components are required for the functioning of the plugin. The installation section above explains how to install the executable components, and once this component is installed and the plugin is loaded, the data component will then be downloaded by the plugin itself. The downloaded file is compressed and has the extension <tt>.irfz</tt> and a size of around 200 MB. After the download is complete this file will be partially uncompressed (the indices and few other files required for immediate operation will be extracted from the complex file). However, the bulk of the data will remain compressed and will only be uncompressed when needed. Thus, the speed of query execution will increase with usage and the size of the <tt>iRefIndex</tt> directory will increase. Therefore, although 250MB of available free space is enough during installation, the plugin requires up to 1GB of space for its operation.<br />
<br />
If the plugin manager is used for the installation (as of Cytoscape 2.6.3 and later), the plugin will be placed in a directory under the home area and a record file is kept in a file named <tt>track_plugins.xml</tt>. The location of these would as follows:<br />
<br />
* Linux: <tt>~/.cytoscape/2.8</tt><br />
* Windows: <tt>''<user's home directory>''\.cytoscape\2.8</tt><br />
<br />
The entry corresponding to iRefScape plugin would looks like follows:<br />
<br />
<plugin><br />
<uniqueID>999</uniqueID><br />
<name>iRefScape</name><br />
<description>.&lt;br&gt;http://irefindex.uio.no/wiki/README_Cytoscape_plugin_0.8x&lt;p&gt;</description><br />
<cytoscapeVersion>2.6</cytoscapeVersion><br />
<url>ftp://ftp.no.embnet.org/irefindex/Cytoscape/plugin/archive/beta8/iRefScape_0_83.jar</url><br />
<downloadUrl>ftp://ftp.no.embnet.org/irefindex/Cytoscape/plugin/current/plugins_irefindex.xml</downloadUrl><br />
<category>Network and Attribute I/O</category><br />
<releaseDate>MAY 20, 2010</releaseDate><br />
<pluginVersion>0.83</pluginVersion><br />
<classname>cytoscape.no.uio.biotek.Main</classname><br />
<projectUrl>http://irefindex.uio.no</projectUrl><br />
<filetype>jar</filetype><br />
<installLocation>.../.cytoscape/2.6/plugins/iRefScape-0.83</installLocation><br />
<license><br />
<text /><br />
</license><br />
<filelist><br />
<file>.../.cytoscape/2.6/plugins/iRefScape-0.83/iRefScape.jar</file><br />
</filelist><br />
<authorlist><br />
<author><br />
<name>Ian Donaldson and Sabry Razick</name><br />
<institution>Biotechnology Centre of Oslo, University of Oslo</institution><br />
</author><br />
</authorlist><br />
</plugin><br />
<br />
'''Note:''' If you encounter an exception during Cytoscape's start-up process due to a plugin failure and there is no way of uninstalling it, you could remove the entry for the corresponding plugin from this file when Cytoscape is not running. First, take a backup of the file, then delete the plugin entry resembling that shown above for the plugin concerned. Finally, save the file and restart Cytoscape.<br />
<br />
The download and installation of the plugin executable is managed by the core functionality provided by Cytoscape, and if the plugin complies with the requirements defined for the plugin framework, the installation should proceed smoothly. However, some users have encountered problems when installing the data component; this is mainly due to privilege and security issues.<br />
<br />
* Privilege issues arise when a user does not have access to the place where the data component is to be installed. This directory should permit write access for that user.<br />
* Security issues are mainly encountered with Microsoft Windows-based operating systems. When software tries to perform a suspicious operation, the operation is blocked and the user is prompted to confirm that this is something they have chosen to do themselves. If the user selects "block", the iRefScape plugin installation fails and it may not be possible to attempt to install the plugin again until the blocking action is revoked manually. Although antivirus products are also known to interfere with software installers, the plugin installation process has been tested on systems running several popular antivirus products, but has not revealed any issues relating to them at the time of writing. If you encounter any such issues, please report to these to the [http://groups.google.com/group/irefindex?hl=en iRefIndex Google Group]. <br />
<br />
The behaviour of the plugin when installed using the plugin manager is different before and after Cytoscape is restarted. After the installation, the plugin will appear in the plugin manager and could be activated, however it is not aware of its environment: for example, it does not know its installation location. Therefore it is highly recommended that Cytoscape be restarted immediately after installing the plugin, and that the plugin is not activated before the first restart (do not click on the "iRefScape" menu entry). When a manual installation is performed, the plugin can be activated after starting Cytoscape for the first time, since Cytoscape is not running during the installation process.<br />
<br />
Some of the reasons behind distributing the data with the plugin rather than more popular approaches such as the use of Web services include the following:<br />
<br />
* Execution speed<br />
* No need for a fast internet connection after installation<br />
* Hosting restrictions applying to the iRefScape/iRefIndex download site<br />
* Privacy for the user: there is no monitoring of the types of searches the user performs; thus, the user's activities remain private <br />
<br />
<br clear="all" /><br />
<br />
== About the Installation Files ==<br />
<br />
During installation the plugin downloads protein-protein interaction data from iRefIndex (ftp://ftp.no.embnet.org/irefindex/Cytoscape/plugin/current/) in a compressed form. The downloaded files will reside in the <tt>iRefIndex</tt> directory under the Cytoscape plugin folder. It is recommended that the files in this directory '''not''' be modified as this may lead to unpredictable results. In particular, please do not open them in word-processing software (such as Microsoft Office). After successful installation you will also find some index files and serialized Java object files which will be used in the search and load operations.<br />
<br />
=== Brief Description of the Files ===<br />
<br />
* irft files: this file contains a ROG (Redundant Object Group) to PARAMETER mapping. This is a sort of index that maps identifiers like accessions and names to ROGs. The ROG is an integer representation of the ROGID. However, ROG is not stable like ROGID and it may be different from one version to another. However, from beta4 onwards the ROGID to ROG mapping will be propagated for backwards compatibility for live proteins (proteins which are not removed from original source). <br />
* Irfm files: These are index files containing information about partners of each interaction.<br />
* ROGS Directory: Contains protein attributes (Warning! Please do not try to open this directory in a file browser; the computer may crash) <br />
* RIGS Directory: Contains interaction attributes (Warning! Please do not try to open this directory in a file browser; the computer may crash) <br />
* Irfj files : these files contain the interaction and object data in a compressed form. When requested for the first time the information will be uncompressed to the RIGS or ROGS directory.<br />
<br />
[[Category:iRefIndex]]</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefScape_1.0_Installation&diff=3667iRefScape 1.0 Installation2011-08-05T14:04:33Z<p>Sabry: /* Manual Installation: if you have problems installing with the Cytoscape plugin manager */</p>
<hr />
<div>==Installation==<br />
<br />
=== Before You Begin ===<br />
<br />
* These instructions assume that you have downloaded and installed the Cytoscape application. See http://cytoscape.org/ for a manual and a set of tutorials which describe the installation and use of Cytoscape.<br />
* Make sure you have an active Internet connection. During installation the plugin will download files from the iRefIndex FTP site.<br />
* Make sure you have latest Java environment installed: Java 1.6 or later is required.<br />
* '''If you have a plugin called iRefIndex installed, it is recommended that you first delete it''', selecting the "Manage Plugins" option in the "Plugins" menu. This will only be the case for people who may have tried earlier development versions of the plugin.<br />
<br />
=== Using the Cytoscape Plugin menu ===<br />
<br />
[[Image:IRefIndex-Cytoscape-Manage-Plugins.png|thumb|300px|Manage Plugins]]<br />
<br />
# Start Cytoscape. You must start Cytoscape as a user that has write privileges to the target directory. <br />
# From the menu select "Plugins" -> "Manage Plugins". <br />
# Select "Manage plugins" from the plugin menu.<br />
# Locate "Available for Install" then "Network and Attribute I/O", verifying that iRefScape is listed in this category.<br />
# Select the iRefScape plugin and then click "Install" (in the bottom-right-hand corner of the window).<br />
# When you see the message "iRefScape v.x.x install complete" click "Close" to leave the "Manage Plugins" dialogue.<br />
# Close Cytoscape.<br />
# Go to the next section to complete the setup.<br />
<br />
<br />
<br clear="all" /><br />
<br />
=== Completing the Installation ===<br />
<br />
[[Image:IRefIndex-Cytoscape-Location.png|thumb|300px|Indicating the location of iRefIndex data]]<br />
<br />
[[Image:IRefIndex-Cytoscape-Download.png|thumb|300px|The download status dialogue]]<br />
<br />
# Restart Cytoscape.<br />
# Select iRefIndexx.x from Cytoscape's "Plugins" menu.<br />
# When the plugin is started for the first time, it will download the dataset.<br />
# You will be prompted to select an installation directory for the data and indices. The recommended place would be the plugin home directory which will appear as the recommended directory. The data and indices require a minimum disk space of 1 GB at this location. Using this default directory is strongly encouraged.<br />
# If the default directory is selected and is not accessible, you will be prompted to restart Cytoscape. If this message appears on second or subsequent attempts, this may mean that there is a problem accessing this directory. To avoid such problems, ensure that you have write access to the directory and at least 1GB of free space on the disk.<br />
# The downloading and installation of indices usually takes less than 5 minutes if you have a internet connection of 10Mb/sec or more. However installation may take between 15 and 30 minutes depending on your internet connection.<br />
# The installation process should now complete itself.<br />
# If the installation was successful, you will see a new iRefScape panel near the "Network" tab of Cytoscape as well as an iRefScape menu (blue) at the top of the Cytoscape interface. Also, you will see an Information frame with several tabs in it ("Messages", "Search history", "Query helper", and so on). This window can be closed.<br />
<br />
<br clear="all" /><br />
<br />
<br />
=== Using the iRefIndex Installation site ===<br />
<br />
In rare cases, the Cytoscape plugin site may be down. In this case, you have the option of using the iRefScape plugin site.<br />
<br />
# Start Cytoscape. You must start Cytoscape as a user that has write privileges to the target directory. <br />
# From the menu select "Plugins" -> "Manage Plugins".<br />
<br />
To use the iRefScape plugin site:<br />
<br />
# Click on "Settings" tab.<br />
# Click "Add" and for each of the following fields, enter the suggested values:<br />
#* Name: <tt>iRefScape</tt><br />
#* URL: <tt>ftp://ftp.no.embnet.org/irefindex/Cytoscape/plugin/current/plugins_irefindex.xml</tt><br />
<br />
<br />
To install the plugin:<br />
<br />
# Locate "Available for Install" then "Network and Attribute I/O", verifying that iRefScape is listed in this category.<br />
# Select the iRefScape plugin and then click "Install" (in the bottom-right-hand corner of the window).<br />
# Click "Close" to leave the "Manage Plugins" dialogue.<br />
# Restart Cytoscape.<br />
# Go to the "Completing the installation" step above.<br />
<br />
=== Install from file ===<br />
<br />
=== Manual Installation: if you have problems installing with the Cytoscape plugin manager ===<br />
<br />
If you are still having problems, you can try manually downloading and installing the files. This is especially useful if you are having firewall problems while getting the plugin or the data.<br />
<br />
# Before starting:<br />
#* Make sure that Cytoscape is not running.<br />
#* Remove any other installations of iRefScape (or iRefIndex) or directories created by those installations (such as <tt>.../Cytoscape_vx.x.x/plugins/iRefScape</tt>).<br />
#* Go to ftp://ftp.no.embnet.org/irefindex/Cytoscape/plugin/current/ (username: anonymous password:ftp if you use command line ftp to do this).<br />
#* Download iRefScape.jar<br />
#* Download iRefDATA_mmddyyyy.irfz (where mmddyyyy is the date stamp for the file)<br />
# Copy the <tt>iRefScape.jar</tt> file to the plugins directory of your Cytoscape installation. For example:<br />
On Unix: .../Cytoscape_v2.6.2/plugins/<br />
On Windows: ...\Cytoscape_v2.6.2\plugins\<br />
#* Copy the iRefDATA_mmddyyyy.irfz file to the same directory or anywhere else where you have permissions to write to.<br />
#* Start Cytoscape<br />
#* Select iRefIndex from the Plugins menu<br />
#* When prompted for an installation directory, select the directory where you placed the iRefDATA_mmddyyyy.irfz file.<br />
#* The plugin will complete the installation without having to first download the iRefDATA_mmddyyyy.irfz file.<br />
# Email the iRefIndex google group if you have problems. <br />
<br clear="all" /><br />
<br />
=== Uninstalling the Plugin===<br />
<br />
# From the Cytoscape Plugins menu, select "Currently Installed" -> "Network and Attribute I/O Plugins" and choose the iRefScape plugin.<br />
# Then, click the "Delete" button and confirm.<br />
# Click "Close" to leave the "Manage Plugins" dialogue and restart Cytoscape.<br />
# The plugin will be deleted when you restart Cytoscape.<br />
<br />
<br />
=== Increasing memory available to Cytoscape ===<br />
<br />
If the Cytoscape interface becomes unresponsive (especially when working with large graphs), take a look at this page to increase memory available to Cytoscape.<br />
<br />
[http://cytoscape.wodaklab.org/wiki/How_to_increase_memory_for_Cytoscape How_to_increase_memory_for_Cytoscape]<br />
<br />
== Troubleshooting Platform-Specific Issues ==<br />
<br />
=== Windows Vista and Windows XP ===<br />
<br />
You will require write privileges to the installation directory not only during installation but also during operation of the plugin. If the plugin disappears from the "Plugins" menu or it does not appear at all, then Cytoscape has to be started as an administrator. This could be done by right-clicking on the Cytoscape shortcut and selecting "Run as" option. When requesting help for such situations, please include a copy-paste of the Cytoscape error console ("Help" -> "Error console"). (To copy-paste, open the error console, click inside, press <tt>Ctrl-A</tt> (to select all) then <tt>Ctrl-C</tt> (to copy). The selection can then be pasted into a message using <tt>Ctrl-V</tt>.)<br />
<br />
=== Mac OS X ===<br />
<br />
* Please verify that Java 1.6 or later is available. ''The plugin will not work unless Java 1.5 or later is installed.''<br />
* Increase the <tt>Xmx</tt> setting to <tt>512m</tt> and the <tt>Xms</tt> setting to <tt>512m</tt> in <tt>cytoscape.sh</tt>.<br />
* This version of the plugin is not extensively tested on Mac OS and we are sorry that the support we could provide for Mac users is limited at this point. <br />
<br />
=== Unix/Linux ===<br />
<br />
* Please verify that Java 1.6 or later is available.<br />
** The "Java SE Development Kit (JDK)" from http://java.sun.com/javase/downloads/index.jsp is suitable. The Sun/Oracle version of Java may be available as a package for your distribution. For example, the <tt>sun-java6-bin</tt> package for Ubuntu provides a compatible version of Java.<br />
** The OpenJDK packages from http://openjdk.java.net/install/ may also be suitable and are often available via distributions. For example, OpenJDK 6 for [http://packages.debian.org/search?keywords=openjdk-6-jdk&searchon=names&suite=all&section=all Debian] and [http://packages.ubuntu.com/search?keywords=openjdk-6-jdk&searchon=names&suite=all&section=all Ubuntu].<br />
** After installing a new version of Java for Debian or Ubuntu, you may need to use the <tt>update-alternatives</tt> command to indicate that you would like to use this new version instead of any existing version, or you may need to add the precise location of the new <tt>java</tt> program to your <tt>PATH</tt>.<br />
* You will require write privileges to the installation directory not only during installation but also during operation.<br />
* The plugin behavior is proven to be very stable in Unix/Linux environments.<br />
* To improve font appearance, try adding the following environment variable definition to your configuration (in <tt>.bashrc</tt> or <tt>.bash_profile</tt>), as described in this [http://wiki.archlinux.org/index.php/Java_Fonts_-_Sun_JRE guide to Java fonts for Arch Linux]:<br />
<br />
export _JAVA_OPTIONS='-Dawt.useSystemAAFontSettings=lcd'<br />
<br />
== Troubleshooting Security Issues==<br />
<br />
The plugin has two components:<br />
<br />
* The Java executable file (<tt>iRefScape_x.x.jar</tt>) which is the software component providing the plugin functionality.<br />
* The data component containing protein-protein interaction data.<br />
<br />
Both these components are required for the functioning of the plugin. The installation section above explains how to install the executable components, and once this component is installed and the plugin is loaded, the data component will then be downloaded by the plugin itself. The downloaded file is compressed and has the extension <tt>.irfz</tt> and a size of around 200 MB. After the download is complete this file will be partially uncompressed (the indices and few other files required for immediate operation will be extracted from the complex file). However, the bulk of the data will remain compressed and will only be uncompressed when needed. Thus, the speed of query execution will increase with usage and the size of the <tt>iRefIndex</tt> directory will increase. Therefore, although 250MB of available free space is enough during installation, the plugin requires up to 1GB of space for its operation.<br />
<br />
If the plugin manager is used for the installation (as of Cytoscape 2.6.3 and later), the plugin will be placed in a directory under the home area and a record file is kept in a file named <tt>track_plugins.xml</tt>. The location of these would as follows:<br />
<br />
* Linux: <tt>~/.cytoscape/2.8</tt><br />
* Windows: <tt>''<user's home directory>''\.cytoscape\2.8</tt><br />
<br />
The entry corresponding to iRefScape plugin would looks like follows:<br />
<br />
<plugin><br />
<uniqueID>999</uniqueID><br />
<name>iRefScape</name><br />
<description>.&lt;br&gt;http://irefindex.uio.no/wiki/README_Cytoscape_plugin_0.8x&lt;p&gt;</description><br />
<cytoscapeVersion>2.6</cytoscapeVersion><br />
<url>ftp://ftp.no.embnet.org/irefindex/Cytoscape/plugin/archive/beta8/iRefScape_0_83.jar</url><br />
<downloadUrl>ftp://ftp.no.embnet.org/irefindex/Cytoscape/plugin/current/plugins_irefindex.xml</downloadUrl><br />
<category>Network and Attribute I/O</category><br />
<releaseDate>MAY 20, 2010</releaseDate><br />
<pluginVersion>0.83</pluginVersion><br />
<classname>cytoscape.no.uio.biotek.Main</classname><br />
<projectUrl>http://irefindex.uio.no</projectUrl><br />
<filetype>jar</filetype><br />
<installLocation>.../.cytoscape/2.6/plugins/iRefScape-0.83</installLocation><br />
<license><br />
<text /><br />
</license><br />
<filelist><br />
<file>.../.cytoscape/2.6/plugins/iRefScape-0.83/iRefScape.jar</file><br />
</filelist><br />
<authorlist><br />
<author><br />
<name>Ian Donaldson and Sabry Razick</name><br />
<institution>Biotechnology Centre of Oslo, University of Oslo</institution><br />
</author><br />
</authorlist><br />
</plugin><br />
<br />
'''Note:''' If you encounter an exception during Cytoscape's start-up process due to a plugin failure and there is no way of uninstalling it, you could remove the entry for the corresponding plugin from this file when Cytoscape is not running. First, take a backup of the file, then delete the plugin entry resembling that shown above for the plugin concerned. Finally, save the file and restart Cytoscape.<br />
<br />
The download and installation of the plugin executable is managed by the core functionality provided by Cytoscape, and if the plugin complies with the requirements defined for the plugin framework, the installation should proceed smoothly. However, some users have encountered problems when installing the data component; this is mainly due to privilege and security issues.<br />
<br />
* Privilege issues arise when a user does not have access to the place where the data component is to be installed. This directory should permit write access for that user.<br />
* Security issues are mainly encountered with Microsoft Windows-based operating systems. When software tries to perform a suspicious operation, the operation is blocked and the user is prompted to confirm that this is something they have chosen to do themselves. If the user selects "block", the iRefScape plugin installation fails and it may not be possible to attempt to install the plugin again until the blocking action is revoked manually. Although antivirus products are also known to interfere with software installers, the plugin installation process has been tested on systems running several popular antivirus products, but has not revealed any issues relating to them at the time of writing. If you encounter any such issues, please report to these to the [http://groups.google.com/group/irefindex?hl=en iRefIndex Google Group]. <br />
<br />
The behaviour of the plugin when installed using the plugin manager is different before and after Cytoscape is restarted. After the installation, the plugin will appear in the plugin manager and could be activated, however it is not aware of its environment: for example, it does not know its installation location. Therefore it is highly recommended that Cytoscape be restarted immediately after installing the plugin, and that the plugin is not activated before the first restart (do not click on the "iRefScape" menu entry). When a manual installation is performed, the plugin can be activated after starting Cytoscape for the first time, since Cytoscape is not running during the installation process.<br />
<br />
Some of the reasons behind distributing the data with the plugin rather than more popular approaches such as the use of Web services include the following:<br />
<br />
* Execution speed<br />
* No need for a fast internet connection after installation<br />
* Hosting restrictions applying to the iRefScape/iRefIndex download site<br />
* Privacy for the user: there is no monitoring of the types of searches the user performs; thus, the user's activities remain private <br />
<br />
<br clear="all" /><br />
<br />
== About the Installation Files ==<br />
<br />
During installation the plugin downloads protein-protein interaction data from iRefIndex (ftp://ftp.no.embnet.org/irefindex/Cytoscape/plugin/current/) in a compressed form. The downloaded files will reside in the <tt>iRefIndex</tt> directory under the Cytoscape plugin folder. It is recommended that the files in this directory '''not''' be modified as this may lead to unpredictable results. In particular, please do not open them in word-processing software (such as Microsoft Office). After successful installation you will also find some index files and serialized Java object files which will be used in the search and load operations.<br />
<br />
=== Brief Description of the Files ===<br />
<br />
* irft files: this file contains a ROG (Redundant Object Group) to PARAMETER mapping. This is a sort of index that maps identifiers like accessions and names to ROGs. The ROG is an integer representation of the ROGID. However, ROG is not stable like ROGID and it may be different from one version to another. However, from beta4 onwards the ROGID to ROG mapping will be propagated for backwards compatibility for live proteins (proteins which are not removed from original source). <br />
* Irfm files: These are index files containing information about partners of each interaction.<br />
* ROGS Directory: Contains protein attributes (Warning! Please do not try to open this directory in a file browser; the computer may crash) <br />
* RIGS Directory: Contains interaction attributes (Warning! Please do not try to open this directory in a file browser; the computer may crash) <br />
* Irfj files : these files contain the interaction and object data in a compressed form. When requested for the first time the information will be uncompressed to the RIGS or ROGS directory.<br />
<br />
[[Category:iRefIndex]]</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefScape_1.0&diff=3648iRefScape 1.02011-07-14T11:41:42Z<p>Sabry: /* Questions and answers about list comparison */</p>
<hr />
<div>Last edited: {{REVISIONYEAR}}-{{padleft:{{REVISIONMONTH}}|2}}-{{REVISIONDAY2}}<br />
<br />
Release date: 2011-07-13<br />
<br />
This page describes the iRefScape 1.0 plug-in for Cytoscape 2.8.1. See the following table for more detailed iRefScape compatibility information.<br />
<br />
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"<br />
! align="center" style="background:#f0f0f0;"|Cytoscape<br />
! align="center" style="background:#f0f0f0;"|iRefScape<br />
|-<br />
| 2.8.1<br />
| iRefScape 1.0 (described on this page)<br />
|-<br />
| 2.7.0<br />
| [[iRefScape 0.9]]<br />
|-<br />
| 2.6.3<br />
| [[iRefScape 0.8]]<br />
|}<br />
<br />
Join the [http://groups.google.com/group/irefindex?hl=en iRefIndex Google Group] to be informed of updates. See also the [[iRefScape|latest release of iRefScape]] which may differ from the release described here.<br />
<br />
==Installation==<br />
<br />
The plugin can be installed using Cytoscape's plugin menu. Select...<br />
<br />
# "Manage plugins"<br />
# "Available for Install"<br />
# "Network and Attribute I/O"<br />
# "iRefScape" (where the precise version will provide a specific version such as "iRefScape 1.0")<br />
<br />
Then follow the on-screen instructions.<br />
<br />
More detailed instructions, troubleshooting tips and alternative methods are available in the [[iRefScape 1.0 Installation|installation guide]].<br />
<br />
After, installation, select the "iRefScape" entry from Cytoscape's plugin menu.<br />
<br />
When the plugin is started for the first time, it will download the publicly available data set.<br />
<br />
=== Tested systems ===<br />
This version of the iRefScape plugin has been tested with the following system configurations:<br />
<br />
{| cellspacing="0" cellpadding="10" border="1" style="margin: 2em"<br />
! Operating System<br />
! Java Version<br />
|-<br />
| Red Hat Enterprise Linux 5 (32-bit) (kernel 2.6.18)<br />
| 1.6.0_01 (32-bit)<br />
|-<br />
| Microsoft Windows 7 (64-bit)<br />
| 1.6.0_25 (64-bit)<br />
|-<br />
| Microsoft Windows Vista (32-bit)<br />
| 1.6.0 (32-bit)<br />
|-<br />
| Ubuntu Linux 8.04 (32-bit)<br />
| 1.6 (32-bit)<br />
|-<br />
| Mac OS X 10.6 (64-bit)<br />
| 1.6.0_15 (32-bit)<br />
|}<br />
<br />
Please refer to the [[iRefScape 1.0 Installation|installation guide]] for more details on system configuration issues.<br />
<br />
== Using the Wizard - an example search ==<br />
<br />
Click the "Wizard" button - a pop-up window will appear. <br />
<br />
Follow the prompts. Here is an example search:<br />
<br />
# Select "Search protein-protein interactions for a protein".<br />
# Select "UniProt identifier".<br />
# For "Taxonomy identifier", select "9606 (Human)" <br />
# Type <tt>QCR2_HUMAN</tt> in the provided space. Click "Next".<br />
# Click "Search & load".<br />
<br />
<br />
<!-- commenting these out since they are outdated<br />
The images below show each of the steps in the wizard.<br />
<br />
<gallery perrow="5"><br />
Image:IRefIndex-Cytoscape-Wizard.png|The iRefIndex wizard<br />
Image:IRefIndex-Cytoscape-Wizard-step2.png|Choosing a result type<br />
Image:IRefIndex-Cytoscape-Wizard-step3.png|Choosing a taxonomy type<br />
Image:IRefIndex-Cytoscape-Wizard-step4.png|Specifying the search term<br />
Image:IRefIndex-Cytoscape-Wizard-step5.png|Additional options<br />
</gallery><br />
--><br />
<br />
== Using the Search Panel ==<br />
<br />
To perform a search, the following steps are involved:<br />
<br />
# Enter query term(s)<br />
# Select a search type<br />
# Select taxonomy/organism<br />
# Adjust search options (iterations, new view, canonical expansion) - this is optional<br />
# Start the search<br />
<br />
=== Enter query term(s) ===<br />
<br />
Queries may be loaded from a file or by pasting the query into the text box (one query per line). Multiple queries can also be separated by pipe characters (<tt>|</tt>) or by tab characters. Queries with spaces in them should be enclosed in double quotes.<br />
<br />
=== Select a search type ===<br />
<br />
Example searches are listed below.<br />
<br />
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"<br />
! align="center" style="background:#f0f0f0;"|Search Type<br />
! align="center" style="background:#f0f0f0;"|Example<br />
! align="center" style="background:#f0f0f0;"|Notes<br />
|-<br />
| <tt>RefSeq_Ac</tt>||<tt>NP_996224</tt>||See http://www.ncbi.nlm.nih.gov/protein/221379660<br />
|-<br />
| <tt>UniProt_Ac</tt>||<tt>Q7KSF4</tt>||See http://www.uniprot.org/uniprot/Q7KSF4<br />
|-<br />
| <tt>UniProt_ID</tt>||<tt>Q7KSF4_DROME</tt>||See http://www.uniprot.org/uniprot/Q7KSF4<br />
|-<br />
| <tt>geneID</tt>||<tt>42066</tt>||See http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=42066<br />
|-<br />
| <tt>geneSymbol</tt>||<tt>cher</tt>||See http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=42066<br />
|-<br />
| <tt>mass</tt>||<tt>72854<-->72866</tt>||Search protein interactors for a range of molecular mass (in Da).<br />
|-<br />
| <tt>rog</tt>||<tt>10121899</tt>||Redundant object group: iRefIndex's internal identifier for a protein. See note feature i.rog.<br />
|-<br />
| <tt>PMID</tt>||<tt>14605208</tt>||PubMed Identifier where an interaction is described. See http://www.ncbi.nlm.nih.gov/pubmed. Iterations and "Use canonical expansion" have no effect on this search type. This search will return all protein interactors in the given PMID and will automatically draw all interactions known between these proteins (even if these interactions are supported by different PMIDs). Select edges in the resulting graph, and see the i.PMID attribute in the Edge Attribute Browser.<br />
|-<br />
| <tt>src_intxn_id</tt>||<tt>EBI-212627</tt>||Source interaction database identifier. Iterations and "Use canonical expansion" have no effect on this search type. Caution: multiple databases may have overlapping interaction record identifiers (e.g. <tt>147805</tt> returns records from both BIND and BioGrid) and there is no way to limit this search to a specific database at this time.<br />
Equivalent interactions from other databases will be automatically retrieved using this search type (see provided example).<br />
|-<br />
| <tt>omim</tt>||<tt>227650</tt>||OMIM identifier. See http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=227650<br />
|-<br />
| <tt>digid</tt>||<tt>449</tt>||Internal identifier for a group of phenotypically related diseases. See [[DiG: Disease groups]]. A digid can be found by first performing a search for some omim identifier - the digid will then appear as the i.digid node attribute.<br />
|-<br />
|style="background:#f0f0f0;" colspan="3" align="center"| Additional search types: first select from Advanced features/Preferences.<br />
|-<br />
| <tt>dig_title</tt>||<tt>fanconi</tt>||Non-exact text search of OMIM titles. Select matching titles from the Query Helper and press return to copy titles to search box. Then hit "Search and load". See [[DiG: Disease groups]].<br />
|-<br />
| <tt>ROGID</tt>||<tt>5IrM14EfdlehbVJ0WAcAoQM3pFw9606</tt>||Exact search results for ROGID of a protein. This searches the i.rogid_TOP node feature. Users can also generate a ROGID for an amino acid sequence and taxon identifier pair using the Wizard/Create SEGUID/ROGID for sequence tool. See PMID 18823568.<br />
|-<br />
| <tt>RIGID</tt>||<tt>cXAoT7JjMde7J+CN/2tOR6gETyA</tt>||Exact search results for RIGID of an interaction. This searches the i.rigid edge feature. See PMID 18823568.<br />
|-<br />
|}<br />
<br />
=== Select taxonomy/organism ===<br />
<br />
This will limit the search results to a particular organism. An organism can be selected from the list, or a taxonomy identifier can be entered into the field itself. See [http://www.ncbi.nlm.nih.gov/taxonomy Entrez Taxonomy] for more details on taxonomy identifiers. For most search types, it is acceptable to leave this field set to <tt>Any</tt>.<br />
<br />
=== Adjust search options ===<br />
<br />
The following optional adjustments can be made:<br />
<br />
==== Iterations ====<br />
<br />
A distance from the query list's members can be specified:<br />
<br />
* Selecting <tt>0</tt> will return only interactions between nodes found by the query list<br />
* Selecting <tt>1</tt> will return immediate neighbours of nodes in the query list<br />
<br />
==== Create new view ====<br />
<br />
A new view will be opened for the search results if this option is selected. Otherwise, the results will be added to the current view.<br />
<br />
==== Use canonical expansion ====<br />
<br />
Selecting this option will expand the search to include all proteins that are related to the query protein (for example, splice isoforms). See [[Canonicalization]] for technical details.<br />
<br />
=== Start the search ===<br />
<br />
Press the "Search and load" button to perform the search.<br />
<br />
{{Note|<br />
See the [[iRefScape Batch Files]] document for information on using text files to describe searches, annotate result nodes and to define new search types using user-supplied data.<br />
}}<br />
<br />
== Viewing the Results ==<br />
<br />
=== Colours and Shapes ===<br />
<br />
* Blue nodes corresponds to proteins found by your query<br />
* Green nodes are interacting partners for your query protein<br />
* Purple hexagons are complex-nodes (also called pseudo-nodes); they keep partners of a complex together (i.e. QCR6_HUMAN is found in two complexes also involving "QCR2_HUMAN")<br />
* Orange-yellow edges indicate protein-protein interactions and pink edges represent membership of some protein in a complex<br />
<br />
=== Toggling Edges ===<br />
<br />
Multiple edges may appear between two nodes. These represent separate interaction records that support this link. Details on each original record can be viewed using the edge attribute viewer (below). You can toggle this multi-view on and off by selecting "Toggle selected multi-edges" in the iRefScape/View Tools menu. Only one of the edges will be shown in the collapsed view.<br />
<br />
=== iRefScape Menu ===<br />
<br />
The iRefScape menu in the Cytoscape menu bar contains a number of other functions that may help with searching and viewing interaction data. These are described in more detail in the [[iRefScape plugin menu]] document.<br />
<br />
=== Expanding the Interaction Map ===<br />
<br />
You can search for additional interactions by right-clicking on a node and selecting "iRefIndex -- Retrieve interactions".<br />
<br />
Some example result displays are shown below.<br />
<br />
<gallery widths="500px" heights="300px"><br />
Image:QCR2_HUMAN_initial.png|Results<br />
Image:QCR2_HUMAN.png|Results (tidied)<br />
</gallery><br />
<br />
== Attributes ==<br />
<br />
[[Image:iRefIndex-0.83-node-attributes-close-up-closed.png|right|The node attributes menu]]<br />
<br />
There are two types of attributes available from iRefIndex: node attributes and edge attributes. These may be used to view information about selected nodes or edges (like <tt>i.taxid</tt>). Some features may allow the user to link out to additional data sources through the "right-click" menu (like <tt>i.geneID</tt>). Features may also be used to sort and select nodes and edges with specific attributes (like <tt>i.order</tt>). The <tt>i.query</tt> feature shows the user's query that is responsible for returning the node or edge.<br />
<br />
Brief descriptions and examples of each attribute are provided below. <br />
<br />
The user must first select the attributes that are to be displayed. This can be done by clicking on the "attribute" icon at the top of the node or edge attribute browser, as shown in the illustrative images.<br />
<br />
<div style="clear: right"></div><br />
=== Node Attributes ===<br />
<br />
[[Image:iRefIndex-0.83-node-attributes-close-up-open.png|right|The open node attributes menu]]<br />
<br />
Each node represents a distinct amino acid sequence (protein) from a distinct organism (taxonomy identifier). Each of the attributes below, provide additional information about the node. Although each node is distinct, a graph produced by iRefIndex may contain multiple nodes that are related proteins (such as splice isoform products from the same gene). These nodes will all have the same <tt>i.canonical_rog</tt> and <tt>i.canonical_rogid</tt> feature values. See the notes below.<br />
<br />
Node attributes that can be lists of items (like <tt>i.UniProt</tt>) will have a corresponding attribute called <tt>i.''attribute name''_TOP</tt> (for example, <tt>i.UniProt_TOP</tt>) which provides the first item of the associated list.<br />
<br />
<div style="clear: right"></div><br />
<br />
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"<br />
! align="center" style="background:#f0f0f0;"|Attribute name<br />
! align="center" style="background:#f0f0f0;"|Data type<br />
! align="center" style="background:#f0f0f0;"|Example value<br />
! align="center" style="background:#f0f0f0;"|Description<br />
|-<br />
| <tt>ID</tt>||Integer||<tt>10121899</tt>||This is a unique identifier for the node assigned by iRefIndex (no two nodes will have the same ID). Each node corresponds to a distinct amino acid sequence from a distinct taxonomy identifier. See also <tt>i.rog</tt> and <tt>i.rogid</tt>.<br />
|-<br />
| <tt>canonicalName</tt>||Integer||<tt>10121899</tt>||This is the same as <tt>ID</tt>. This attribute is set by Cytoscape and is unrelated to the <tt>i.canonical_rog</tt> or <tt>i.canonical_rogid</tt> used by iRefIndex<br />
|-<br />
| <tt>i.RefSeq_Ac</tt>||List||<tt>[NP_996224]</tt> ||All RefSeq accessions with an amino acid sequence and taxon identifier identical to the protein represented by this node. Right click on this entry and select "Search ''[RefSeq_Ac]'' on the web -- Entrez -- Protein" for more information. See also <tt>i.RefSeq_TOP</tt> for the first entry in this list of accessions.<br />
|-<br />
| <tt>i.UniProt_Ac</tt>||List||<tt>[Q7KSF4]</tt>||All UniProt accessions with an amino acid sequence and taxonomy identifier identical to the protein represented by this node. Right click on this entry and select "Search ''[UniProt_Ac]'' on the web -- UniProt -- KB Beta" for more information. See also <tt>i.UniProt_Ac_TOP</tt> for the first entry in this list of accessions.<br />
|-<br />
| <tt>i.UniProt_ID</tt>||List||<tt>[Q7KSF4_DROME]</tt> ||All UniProt identifers with an amino acid sequence and taxonomy identifier identical to the protein represented by this node. Right click on this entry and select "Search ''[UniProt_ID]'' on the web -- UniProt -- KB Beta" for more information. See also <tt>i.UniProt_ID_TOP</tt> for the first entry in this list of IDs.<br />
|-<br />
| <tt>i.canonical_rog</tt>||Integer||<tt>10121899</tt>||Related proteins (say splice isoforms from the same gene) will all belong to the same canonical group. One member of this group is assigned as the canonical representative of this group. The <tt>i.canonical_rog</tt> attribute lists the identifier of the protein's canonical group identifier. For example, all products of Entrez Gene 42066 have the same <tt>i.canonical_rog</tt> (<tt>10121899</tt>). Each of these gene products has its own identifier (because they each have a distinct amino acid sequence). One of the splice isoforms (<tt>NP_996224</tt>) was chosen as the canonical representative of this group. See the [http://irefindex.uio.no/wiki/Canonicalization canonicalization document] for more details on how canonical groups are constructed and how canonical representatives are chosen.<br />
|-<br />
| <tt>i.canonical_rogid</tt>||String||<tt>1ZFb1WlW0OgOlhiAPtkJTdb6oOg7227</tt>||This is a unique alphanumeric key for the canonical representative of the canonical group to which this node belongs. Briefly, an SHA-1 digest of the amino acid sequence is used to generate a unique 27 character key and this is prepended to the taxonomy identifier for the protein's source organism in order to make the rogid. See PMID 18823568 for details on how this key can be generated. This is a string equivalent of the <tt>i.canonical_rog</tt> attribute. All <tt>i.canonical_rog</tt> instances (each being an integer) have one corresponding <tt>i.canonical_rogid</tt>. See the [http://irefindex.uio.no/wiki/Canonicalization canonicalization document] for more details on how canonical groups are constructed and how canonical representatives are chosen. Note that the rogid for the protein represented by this specific node is listed under <tt>i.rogid</tt>.<br />
|-<br />
| <tt>i.dataset</tt>||Integer||<tt>0</tt>||In the batch query mode this can be used to locate the query batch (i.e. which group of queries were responsible for the node). In single query mode, when a sequence of queries are issued one after another this variable can be used to distinguish the results from each step. All nodes with a i.dataset value higher than 999 can be found using more than one batch of queries. <br />
|-<br />
| <tt>i.digid</tt>||List||<tt>449</tt>||This is an integer identifier that is shared by a group of disease entries in OMIM that are related by their titles. See [[DiG: Disease groups]] for more details. Also see <tt>i.omim</tt> and <tt>i.dig_title</tt>.<br />
|-<br />
| <tt>i.dig_title</tt>||List||<tt>[Fanconi anemia, complementation group B, 300514 (3), VACTERL association with hydrocephalus, X-linked, 314390 (3)]</tt>||These are entries from OMIM's Morbid Map that are all part of the same disease group. See [[DiG: Disease groups]] for more details. Also see <tt>i.omim</tt> and <tt>i.digid</tt>.<br />
|-<br />
| <tt>i.displayLabel</tt>||List||<tt>[Q7KSF4_DROME]</tt> ||This is a list of short labels chosen by iRefIndex to label the node using the VizMapper. The UniProt identifier is preferentially chosen (if one is available) followed by the Entrez Gene Symbol. See also <tt>i.displayLabel_TOP</tt> for the first entry in this list.<br />
|-<br />
| <tt>i.geneID</tt>||List||<tt>[42066]</tt>||All NCBI Entrez Gene identifiers that encode a protein sequence identical to that of this node. Right click on this entry and select "Search ''[geneID]'' on the web -- Entrez -- Gene" for more information. See also <tt>i.geneID_TOP</tt> for the first entry in this list.<br />
|-<br />
| <tt>i.geneSymbol</tt>||List||<tt>[CHER]</tt>||All NCBI Entrez Gene official symbols that encode a protein sequence identical to that of this node. Right click on this entry and select "Search ''[geneSymbol]'' on the web -- Entrez -- Gene" for more information. See also <tt>i.geneSymbol_TOP</tt> for the first entry in this list.<br />
|-<br />
| <tt>i.interactor_description</tt>||List||<tt>[Q7KSF4_DROME, CHER, DMEL_CG3937, SKO, DMEL CG3937, FLN, CG3937, CHER, DMEL\\CG3937, FLN, SKO, CHER, NAME=CHER, DMEL_CG3937]</tt>||A collection of all the names in their short form as given by the original interaction databases. See also <tt>i.interactor_description_TOP</tt> for the first entry in this list.<br />
|-<br />
| <tt>i.mass</tt>||Integer|| <tt>259142</tt> ||Mass associated with the protein sequence for this node. From UniProt, if available. You can search for nodes inside a mass range using the <tt>mass</tt> search type in the iRefIndex plugin.<br />
|-<br />
| <tt>i.omim</tt>||List||<tt>[608053]</tt>||List of OMIM disease identifiers associated with this protein. Right click on the entry and select "Search for ''[omim]'' on the web -- Entrez -- OMIM" for more information. <br />
|-<br />
| <tt>i.order</tt>||Integer|| <tt>0</tt> || The distance of this node from the query node (query node has distance <tt>0</tt>, nodes that are returned by a query because they are a part of the same canonical group have a value of <tt>10</tt>, direct neighbours have a value of<tt>1</tt>). Pseudonodes have negative values (<tt>-1</tt> is a complex holder, <tt>-2</tt> is a collapsed instance).<br />
|-<br />
| <tt>i.overall_degree_TOP</tt>||Integer|| <tt>42</tt> ||The total number of interactions described for this node in the iRefIndex database. Not all of these edges will be necessarily shown in the current view. This is the node degree in the full iRefIndex interactome. When calculating the value of this all proteins in iRefIndex (not only the ones currently loaded) will be used<br />
|-<br />
| <tt>i.popularity</tt>||List|| <tt>42</tt> || '''TO BE DESCRIBED'''<br />
|-<br />
| <tt>i.pseudonode</tt>||Boolean|| <tt>false</tt> || This is set to true is the node represents a "complex" or n-ary interaction record. Protein nodes with edges incident to a pseudonode are member interactors from the interaction record where specific interactions between pairs of interactors is unknown. Pseudonodes appear as hexagons when using the iRefIndex VizMapper style. <br />
|-<br />
| <tt>i.query</tt>||String||<tt>NP_996224</tt>||The user query used to retrieve this specific node. Neighbours of "query" nodes will not have an <tt>i.query</tt> value. Nodes returned by queries are coloured blue when using the iRefIndex VizMapper style.<br />
|-<br />
| <tt>i.rog</tt>||Integer||<tt>10121899</tt>||This is a unique identifier for the node assigned by iRefIndex (no two nodes will have the same ID). Each node corresponds to a distinct amino acid sequence associated with a distinct taxonomy identifier. <tt>i.rog</tt> also appears as the <tt>ID</tt> attribute. Each <tt>i.rog</tt> has a corresponding <tt>i.rogid</tt> - see below.<br />
|-<br />
| <tt>i.rogid</tt>||String||<tt>2mL9oLZ9g/SSPyK0nOz97RmOzPg3702</tt>||This is a unique alphanumeric key for the protein represented by this node. Briefly, an SHA-1 digest of the amino acid sequence is used to generate a unique 27 character key and this is prepended to the taxonomy identifier for the protein's source organism in order to make the rogid. See PMID 18823568 for details on how this key can be generated. This is a string equivalent of the <tt>i.rog</tt> attribute. All <tt>i.rog</tt> instances (each being an integer) have one corresponding <tt>i.rogid</tt>.<br />
|-<br />
| <tt>i.taxid</tt>||Integer||<tt>7227</tt>||The NCBI taxonomy identifier for this protein's source organism. See http://www.ncbi.nlm.nih.gov/taxonomy?term=7227 for more details of this example value for <tt>i.taxid</tt>.<br />
|-<br />
| <tt>i.xref</tt>||List||<tt>[AAF70826.1,Q9M6R5]</tt> ||All the accessions as given by the original interaction database records to describe this protein. See also <tt>i.xref_TOP</tt> for the first entry in this list.<br />
|-<br />
| <tt>i.alive</tt>||Boolean||<tt>true or false</tt> ||This is true for all nodes after a search operation. This variable is used by the iRefScape filter and after a filter is applied, all nodes matching the filter criteria will have a true value for this variable (all other nodes will have false).<br />
|-<br />
| <tt>i.alive_degree</tt>||Integer||<tt>0,1,2-...</tt> ||This is will give the node degree after a search. When an iRefScape filter is applied this will give the number of nodes with "i.alive=true" connected to a particular node(How many nodes matching the filter criteria has connections with a particular node). <br />
|-<br />
|}<br />
<br />
===Edge Attributes===<br />
<br />
Each edge represents a distinct primary database record that supports some relationship between the two incident nodes. So, if an interaction between two proteins has been annotated by two databases (or twice by the same database) then two edges will appear between those two protein nodes.<br />
<br />
<br />
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"<br />
! align="center" style="background:#f0f0f0;"|Attribute name<br />
! align="center" style="background:#f0f0f0;"|Data type<br />
! align="center" style="background:#f0f0f0;"|Example value<br />
! align="center" style="background:#f0f0f0;"|Description<br />
|-<br />
| <tt>ID</tt>||String||<tt>10121899 (2771704(40952)) 13911416</tt>||This is a unique identifier for the edge assigned by Cytoscape (no two edges will have same <tt>ID</tt>). See <tt>i.rig</tt> and <tt>i.rigid</tt> for unique identifiers for the edge assigned by iRefIndex.<br />
|-<br />
| <tt>i.PMID</tt>||Integer||<tt>14605208</tt>||Publication identifier of the publication where the interaction represented by the edge mentioned. Right click on this entry and select "Search ''[PMID]'' on the web -- Entrez -- Pubmed" for more details on the publication.<br />
|-<br />
| <tt>i.bait</tt>||Integer||<tt>13911416</tt>||Node ID for the protein that was used as a bait in this experiment. Only applicable where the experimental system (see <tt>i.method_name</tt>) used to support this relationship was a bait-prey system (for example, two hybrid).<br />
|-<br />
| <tt>i.canonical_rig</tt>||Integer||<tt>27799</tt>||See notes for the <tt>i.rig</tt> edge feature. This is the rig constructed for the interaction using its canonical rogs. Use a web browser to query http://wodaklab.org/iRefWeb/interaction/show/27799 (where <tt>27799</tt> is the <tt>i.canonical_rig</tt> value) to retrieve more information on this interaction and equivalent source interaction records.<br />
|-<br />
| <tt>i.experiment</tt>||String||<tt>Giot L [2003]</tt>||A short label for the experiment where this interaction was found (usually contains authors names).<br />
|-<br />
| <tt>i.flag</tt>||Integer||<tt>1</tt>||Used by iRefIndex plugin to control display of edges (<tt>0</tt> being the representative edge, used in edge toggle; <tt>1</tt> being an edge which will disappear during edge toggle; <tt>2</tt> being a complex holder edge; <tt>6</tt> being a path; <tt>7</tt> being an edge from or to a collapsed node).<br />
|-<br />
| <tt>i.host_taxid</tt>||Integer||<tt>7227</tt>||Indicates the organism taxonomy identifier where the interaction was experimentally demonstrated.<br />
|-<br />
| <tt>i.isLoop</tt>||Integer||<tt>1</tt>||Indicates whether the interaction is a self interaction (such as a dimer or possibly multimer of the same protein type). See the source interaction record for details.<br />
|-<br />
| <tt>i.method_cv</tt>||String||<tt>MI:0018</tt>||PSI-MI controlled vocabulary term identifier for the method used to provide evidence for this interaction. See http://www.ebi.ac.uk/ontology-lookup/ for more details. The name of the method is also given in the <tt>i.method_name</tt> feature.<br />
|-<br />
| <tt>i.method_name</tt>||String||<tt>two hybrid</tt>||PSI-MI controlled vocabulary term name for the method used to provide evidence for this interaction. See http://www.ebi.ac.uk/ontology-lookup/ for more details. The term identifer is also given in the <tt>i.method_cv</tt> feature.<br />
|-<br />
| <tt>i.participant_identification</tt>||String||<tt>predetermined participant</tt>||PSI-MI controlled vocabulary term for the participant identification method used to provide evidence for this interaction. See http://www.ebi.ac.uk/ontology-lookup/ for more details. The identifier for the term is also given in the <tt>i.participant_cv</tt> feature.<br />
|-<br />
| <tt>i.participant_cv</tt>||String||<tt>predetermined participant</tt>||PSI-MI controlled vocabulary term identifier for the participant identification method used to provide evidence for this interaction. See http://www.ebi.ac.uk/ontology-lookup/ for more details. The term itself is also given in the <tt>i.participant_identification</tt> feature.<br />
|-<br />
| <tt>i.query</tt>||String||<tt>NP_996224</tt>||The user's query that is responsible for returning this edge.<br />
|-<br />
| <tt>i.rig</tt>||Integer||<tt>27799</tt>||Redundant interaction group identifier for the interaction. <br />
This is an integer equivalent of <tt>i.rigid</tt>. Every rig has one corresponding rigid.<br />
|-<br />
| <tt>i.rigid</tt>||String||<tt>TAabV6yJ1XzUvEhYwZLpu5reBU0</tt>||Redundant interaction group identifier for the interaction. This is a universal key generated for the interaction by ordering according to ASCII value and concatentating the rogids participating in the interaction and then generating a Base-64 representation of an SHA-1 digest of the resulting string. See PMID 18823568 for details on how this key can be generated.<br />
|-<br />
| <tt>i.score_hpr</tt>||Integer||<tt>15</tt>||The hpr score (highest pmid re-use) is the highest number of interactions that any one PMID (supporting this interaction) is used to support. See PMID 18823568 for details. See also <tt>i.score_np</tt> and <tt>i.score_lpr</tt>.<br />
|-<br />
| <tt>i.score_lpr</tt>||Integer||<tt>11</tt>||The lpr score (lowest pmid re-use) is the lowest number of distinct interactions that any one PMID (supporting this interaction) is used to support. An lpr of greater than 20 is considered to be a high-throughput experiment. See PMID 18823568 for details. See also <tt>i.score_np</tt> and <tt>i.score_lpr</tt>.<br />
|-<br />
| <tt>i.score_np</tt>||Integer||<tt>2</tt>||Number of PubMed Identifiers (PMIDs) pointing to literature where this interaction is supported. See PMID 18823568 for details. See also <tt>i.score_lpr</tt>.<br />
|-<br />
| <tt>i.source_protein</tt>||Integer||<tt>-1</tt>||'''TO BE DESCRIBED'''<br />
|-<br />
| <tt>i.src_intxn_db</tt>||String||<tt>grid</tt>||Original interaction database where this interaction record was obtained.<br />
|-<br />
| <tt>i.src_intxn_id</tt>||String||<tt>38677</tt>||Original interaction database where this interaction record was obtained. <br />
In some case, it may be possible to right click and "Search ''[src_intxn_id]'' on the web -- Interaction databases -- the database" to see the original record.<br />
|-<br />
| <tt>i.type_cv</tt>||String||<tt>MI:0407</tt>||PSI-MI controlled vocabulary term identifier for the interaction type that occurs between the two proteins. See http://www.ebi.ac.uk/ontology-lookup/ for more details. The term itself is also given in the <tt>i.type_name</tt> feature.<br />
|-<br />
| <tt>i.type_name</tt>||String||<tt>direct interaction</tt>||PSI-MI controlled vocabulary term identifier for the interaction type that occurs between the two proteins. See http://www.ebi.ac.uk/ontology-lookup/ for more details. The term itself is also given in the <tt>i.type_name</tt> feature.<br />
|-<br />
| <tt>i.target_protein</tt>||Integer||<tt>-1</tt>||'''TO BE DESCRIBED'''<br />
|-<br />
|}<br />
<br />
=== User Attributes ===<br />
<br />
See [[iRefScape Batch Files]] for information on adding attributes to search results.<br />
<br />
== Obtaining Updates to the Data ==<br />
<br />
You can check for and download updates to the dataset used by your plugin using the Wizard (see "Check for iRefIndex updates").<br />
<br />
iRefIndex updates are announced through the [http://groups.google.com/group/irefindex?hl=en iRefIndex Google Group]<br />
<br />
==Obtaining Updates to the Plugin==<br />
<br />
If you already have a plugin called iRefScape (a menu entry "iRefScape" under the plugin menu of Cytoscape) and you want to make sure you have the latest version, use "Update plugins" from the "Plugins" menu. However, if you want to reinstall the plugin, you should uninstall any previous version of the plugin first.<br />
<br />
Plugin updates are announced through the [http://groups.google.com/group/irefindex?hl=en iRefIndex Google Group]<br />
<br />
<!--<br />
<br />
==Integrating User Data into the Plugin==<br />
<br />
===How to create node and edge attributes ===<br />
<br />
Example: Attaching [[DiG: Disease groups]] identifiers to nodes<br />
<br />
==Updating==<br />
# From Cytoscape updater<br />
# Using plugins update feature<br />
<br />
== Log Files, Search Details and Errors ==<br />
# How to interpret log messages and save them for later reference. <br />
<br />
==Using the plugin as a search tool ==<br />
The plugin could also be used to search the current network. However, there is a better search option in Cytoscape with Google suggest which may be more convenient to use. The reason for including the search function was that the Cytoscape search filed remained inactive on some occasions for networks crated using the plugin. The reason for this is still unknown and deleting a node on the network seems to activate it, when this bug will be fixed the users are encouraged to use the Cytoscape search option.<br />
Currently, if a user performs a search with a term and if the corresponding protein is already loaded, the loaded protein (corresponding node) would be highlighted with Cytoscape default highlight colors. <br />
<br />
<br />
== Exit plugin and force terminate operations ==<br />
The exit button performs two functions. <br />
# First one is to exit iRefIndex plugin, where the outcome is to detach the plugin from Cytoscape. <br />
# The second function "FORCE STOP" (only available during a active task) is to terminate current operation. The "FORCE STOP" is useful when the search query or a subsequent operation takes too long to finish or none-responding. When a force stop is performed the out come is unpredictable and behavior was undefined, therefore results after such operation could not be trusted. <br />
<br />
--><br />
<br />
==Advanced features==<br />
<br />
The advanced features panel holds a number of tabbed panels, most of which expose settings which can be adjusted to change the behaviour of the normal search operations. Many panels offer contextual help via the iRefScape help system, but a brief description of each panel is also given here.<br />
<br />
{| cellpadding="10" cellspacing="0" border="1"<br />
! Preferences<br />
| This panel configures the range of search types (such as <tt>UniProt_Ac</tt>) presented in the main query interface. More search types can be added, and existing search types can be removed.<br />
|-<br />
! Statistics<br />
| A selection of statistics measures for the current network can be calculated and displayed using this panel.<br />
|-<br />
! Compare<br />
| This panel configures the <tt>COMPARE</tt> search operation and the equivalent functionality in the "Grouping" submenu of the iRefScape menu.<br />
|-<br />
! Summary<br />
| This panel generates node-by-node summaries where the attributes of each selected node (or of all nodes in the current network, if no nodes are selected) are presented in a separate table in the help viewer.<br />
|-<br />
! Filter<br />
| As an alternative to the manual selection of nodes and edges using the graphical user interface, this panel permits the selection of nodes and edges according to certain criteria based on node and edge attributes.<br />
|-<br />
! Path parameters<br />
| This pane provides options that configure the path-finding functionality described below.<br />
|-<br />
! Loading options<br />
| The options presented here affect the retrieval of data in search operations, including or excluding certain kinds of data (such as lists of values for certain attributes) in order to either simplify the results or speed up each search operation.<br />
|-<br />
! Import<br />
| The import panel provides the ability to import a generic Cytoscape network into iRefScape by interpreting node attributes as iRefScape queries.<br />
|-<br />
! Export<br />
| The export panel provides the ability to export an iRefScape network in such a way that other Cytoscape plugins may be able to access and manipulate the network's essential information.<br />
|}<br />
<br />
===Path-finding===<br />
[[Image:iRefIndex-0.83-path-original.png|thumb|500px|The path in the results, highlighted in green. Solid green lines indicate presence of evidence for this step of the path in the direction specified by the query OR the presence of evidence that has no directionality. A dashed green line indicates there is evidence for this step of the path but only in the direction that is opposite to that specified in the query.]]<br />
<br />
iRefScape can be used to find interaction events connecting two proteins or a sequence of events involving several proteins. <br />
<br />
This process intakes two terminal nodes as input and returns all reasonable paths connecting these two. The results returned here are pathway independent. In other words, the sequences of interactions connecting the nodes are not constructed using currently published pathways. However, the paths returned may contain pathway centric information.<br />
<br />
The query format is as follows:<br />
<br />
NP_004976 <==> NP_002871<br />
<br />
Additional type and taxonomy parameters were also supplied as required:<br />
<br />
* '''Search type:''' <tt>RefSeq_Ac</tt><br />
* '''Taxonomy:''' <tt>9606 (Homo sapiens)</tt><br />
<br />
This query located all reasonable paths between <tt>NP_004976</tt> and <tt>NP_002871</tt> and the returned path also contains the shortest path between them. The results of the path finding was sorted in the ascending order of path length and the maximum path length was restricted to a default value of 6; this value can be modified by changing the value of "Maximum distance" from the "Path parameters" tab in the advanced options panel. The paths found in this way were "reasonable paths", this concept is different from finding the shortest path or finding all the paths. A "reasonable path" from A to B is a path extending from A to B where none of the intermediate points can be reached from A with fewer steps by a path that extends from A via B (in other words, when evaluating a path from A to B, nodes beyond B are not considered).<br />
<br />
<div style="clear: right"></div><br />
<br />
=== Reversing the Path ===<br />
<br />
[[Image:iRefIndex-0.83-path.png|thumb|500px|The path in the results, highlighted in green]]<br />
<br />
Due to the way the algorithm works, when the opposite search was performed...<br />
<br />
NP_002871 <==> NP_004976<br />
<br />
...it took 120 seconds and returned 3 paths. The reason for this is that <tt>NP_002871</tt> is directly connected to many hubs and therefore, the initial seed-list size was larger than when starting with <tt>NP_004976</tt>. The algorithm first tries the direction requested by the user and after that considers the opposite direction when creating the sub-network to look for the path. The time consuming step in the opposite search (<tt>NP_002871<==>NP_004976</tt>) is thus the initial evaluation step. When constructing the query for path-finding we used the attribute <tt>i.overall_degree_TOP</tt> and it provided the overall connectivity of the proteins within iRefIndex. The <tt>i.overall_degree_TOP</tt> value of <tt>RAF1</tt> was found to be 443 and for the <tt>KRAS</tt> isoform was found to be 2. Therefore, although not shown in the graph, <tt>RAF</tt> is connected to more than 400 other proteins than <tt>RAS1</tt>.<br />
<br />
In the image shown here, the green arrow shows the path.<br />
<br />
<div style="clear: right"></div><br />
=== Path Selection ===<br />
<br />
[[Image:iRefIndex-0.83-path-selector.png|thumb|500px|The path selector for the results]]<br />
<br />
After the path-finding is completed the "Path selection" panel can be used to selectively load the paths. In order to make the selection easier, the paths found can be described by a particular attribute type: by selecting a value from the list for "Convert pop-up type to" (such as <tt>RefSeq_Ac</tt>) and pressing the "Convert" button, a tooltip appearing over each path description will show the requested attribute values for each component of the path. Thus, a path description such as...<br />
<br />
321631 -> 2229473 -> 4410739 -> 4531114<br />
<br />
...will provide a tooltip showing the following identifiers:<br />
<br />
NP_002871 -> NP_001123914 -> NP_036979 -> NP_004976<br />
<br />
===List Comparison===<br />
This feature is available with version 0.91 and later.<br />
<br />
This feature provides a way to compare two lists of proteins. When a <tt>COMPARE{<List1>,<List2>}</tt> format query is issued with default settings an interaction network is loaded with interactions involving only the proteins of the list and proteins which are not in the list but interacts with at least two proteins from each list (intermediate components). At the end of the operation, in addition to the Cytoscape network a adjacency cube (adjacency matrix with colours as the third dimension) is also created. This adjacency cube is synchronized with the network and can be used examine the results easily. A summary report function is provided to list the overall summary of each protein in the list sorted order so that the most connected protein appear first. The identifiers used to display the proteins in the adjacency cube are either iROGID or the ROGID of complexes. The user has the option to visualize these in popular identifier types using convert feature.<br />
<br />
An example query (from PMID:20670417):<br />
<br />
COMPARE{P08588,P16671|P07550,P13945}<br />
<br />
This query compares two groups:<br />
<br />
# P08588,P16671<br />
# P07550,P13945<br />
<br />
Members within the group are separated with a comma (<tt>,</tt>); groups are separated by a pipe (<tt>|</tt>).<br />
<br />
====Questions and answers about list comparison====<br />
<br />
''What is the maximum number of members a group can have?''<br />
<br />
You could have any number of members. The more members there are, the more time it will take for the operation, and the more memory it will need. For instance the above example search will complete comfortably in 1 minute with 256MB of allocated memory. If you have more than 100 members we recommend having at least 1GB dedicated memory for Cytoscape. <br />
<br />
''Can I compare more than two groups?''<br />
No. Only two groups could be compared in the current version. If a protein appearers in both groups being compared these proteins will be treated as a third group. But this third group is defined after the execution. <br />
<br />
''What if a protein or protein resulting from query appears in more than one group?''<br />
<br />
All proteins found in more than one group are treated as a new group (group 3).<br />
<br />
==Troubleshooting==<br />
<br />
* See http://cytoscape.org/ for a manual and a set of tutorials which describe the installation and use of Cytoscape.<br />
* For problems with Cytoscape installation or use, try the [http://groups-beta.google.com/group/cytoscape-helpdesk Cytoscape Help Desk].<br />
* If you have problems with installation or use, please share your experience with us through the [http://groups.google.com/group/irefindex?hl=en iRefIndex Google Group].<br />
* When updating data on Microsoft Windows XP and Vista, a "Failed to find resources message" may appear in the log message window. If this happens please run the update again and the plugin will check and correct the problem during the second attempt.<br />
* If you are working with large graphs, make sure Cytoscape has at least 128MB memory. See the [http://cytoscape.org/cgi-bin/moin.cgi/How_to_increase_memory_for_Cytoscape Cytoscape documentation] for more information on setting up memory allowances.<br />
<br />
<br />
==Internal Testing==<br />
Our internal test results for this release of the plugin can be found on the [[iRefScape Test Cases 1.0]] page.<br />
<br />
== All iRefIndex Pages ==<br />
<br />
Follow this link for a listing of all iRefIndex related pages (archived and current).<br />
<br />
[[Category:iRefIndex]]</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=README_Cytoscape_plugin_menu_1.0x&diff=3550README Cytoscape plugin menu 1.0x2011-06-28T15:01:09Z<p>Sabry: /* Grouping and adjacency matrix */</p>
<hr />
<div> Content of this page will be transferred to :[[README_Cytoscape_plugin_1.0x]]<br />
<br />
=iRefScape=<br />
A new menu called "iRefScape" will be created when the plugin is activated.<br />
<br />
==Search tools==<br />
This sub menu contain search related operations.<br />
<br />
===Retrieve interactions for the selected nodes===<br />
This option will load interactions involving the selected nodes. Nodes could be selected using the mouse or using an operation such as applying a filter.<br />
<br />
===Expand one level===<br />
This will load interactions involving all the nodes in the current network.<br />
<br />
===Load interactions between neighbours===<br />
<br />
<br />
===Clear load history (Reload everything next time)===<br />
===Reset node degree===<br />
===Load user variables===<br />
<br />
==View tools==<br />
===Toggle selected multi-edges===<br />
===Zoom to selected===<br />
===Select last iRefScape selection===<br />
===Select nodes with different taxid than query node===<br />
===Select between nodes===<br />
===Select between nodes with originals===<br />
===Show spoke-represented complexes===<br />
=== (Currently hidden, used for debuging) Show live details of nodes and edges===<br />
<br />
==Grouping==<br />
===Reset Group===<br />
===Set group=1 for selection===<br />
===Set group=2 for selection===<br />
===Create comparison table===<br />
<br />
==Hide/Un-hide==<br />
===Hide selected nodes===<br />
===Hide nodes (except pseudonodes)===<br />
===Hide nodes not selected===<br />
===Hide nodes not selected (except pseudonodes)===<br />
===Un-hide all===<br />
<br />
= Grouping and adjacency matrix =<br />
This feature provides a way to examine the Cytoscape node-link diagram using a adjacency matrix. <br />
<br />
== Create groups ==<br />
The first step in using the matrix_view feature is group the nodes in the current network into two groups.The grouping could be achieved as a result of another operation or done manually.<br />
<br />
=== Manual grouping===<br />
#Select one or more nodes using the mouse (first group)<br />
#Select the menu: iRefScape -> Grouping -> set group=1 for selection<br />
#Select one or more nodes which were not in the first group* using the mouse (second group)<br />
#Select the menu: iRefScape -> Grouping -> set group=2 for selection<br />
#Select the menu: iRefScape -> Grouping -> Create comparison table<br />
<br />
*If a node is selected both as in group 1 and group 2, this is considered as an especial case. These nodes will appear in both as column headings and as row heading.<br />
<br />
<br />
=== Grouping as part of a filter ===<br />
<br />
<br />
=== Interpreting results from a grouping operation ===</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=README_Cytoscape_plugin_menu_1.0x&diff=3549README Cytoscape plugin menu 1.0x2011-06-28T15:00:18Z<p>Sabry: /* Grouping and adjacency matrix */</p>
<hr />
<div> Content of this page will be transferred to :[[README_Cytoscape_plugin_1.0x]]<br />
<br />
=iRefScape=<br />
A new menu called "iRefScape" will be created when the plugin is activated.<br />
<br />
==Search tools==<br />
This sub menu contain search related operations.<br />
<br />
===Retrieve interactions for the selected nodes===<br />
This option will load interactions involving the selected nodes. Nodes could be selected using the mouse or using an operation such as applying a filter.<br />
<br />
===Expand one level===<br />
This will load interactions involving all the nodes in the current network.<br />
<br />
===Load interactions between neighbours===<br />
<br />
<br />
===Clear load history (Reload everything next time)===<br />
===Reset node degree===<br />
===Load user variables===<br />
<br />
==View tools==<br />
===Toggle selected multi-edges===<br />
===Zoom to selected===<br />
===Select last iRefScape selection===<br />
===Select nodes with different taxid than query node===<br />
===Select between nodes===<br />
===Select between nodes with originals===<br />
===Show spoke-represented complexes===<br />
=== (Currently hidden, used for debuging) Show live details of nodes and edges===<br />
<br />
==Grouping==<br />
===Reset Group===<br />
===Set group=1 for selection===<br />
===Set group=2 for selection===<br />
===Create comparison table===<br />
<br />
==Hide/Un-hide==<br />
===Hide selected nodes===<br />
===Hide nodes (except pseudonodes)===<br />
===Hide nodes not selected===<br />
===Hide nodes not selected (except pseudonodes)===<br />
===Un-hide all===<br />
<br />
= Grouping and adjacency matrix =<br />
This feature provides a way to examine the Cytoscape node-link diagram using a adjacency matrix. <br />
<br />
== Create groups ==<br />
The first step in using the matrix_view feature is group the nodes in the current network into two groups.The grouping could be achieved as a result of another operation or done manually.<br />
<br />
=== Manual grouping===<br />
#Select one or more nodes using the mouse (first group)<br />
#Select the menu: iRefScape -> Grouping -> set group=1 for selection<br />
#Select one or more nodes which were not in the first group* using the mouse (second group)<br />
#Select the menu: iRefScape -> Grouping -> set group=2 for selection<br />
#Select the menu: iRefScape -> Grouping -> Create comparison table<br />
<br />
*If a node is selected both as in group 1 and group 2, this is considered as an especial case. These nodes will appear in both as column headings and as row heading.<br />
<br />
<br />
=== Grouping as part of a filter ===</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=README_Cytoscape_plugin_menu_1.0x&diff=3548README Cytoscape plugin menu 1.0x2011-06-28T13:44:26Z<p>Sabry: </p>
<hr />
<div> Content of this page will be transferred to :[[README_Cytoscape_plugin_1.0x]]<br />
<br />
=iRefScape=<br />
A new menu called "iRefScape" will be created when the plugin is activated.<br />
<br />
==Search tools==<br />
This sub menu contain search related operations.<br />
<br />
===Retrieve interactions for the selected nodes===<br />
This option will load interactions involving the selected nodes. Nodes could be selected using the mouse or using an operation such as applying a filter.<br />
<br />
===Expand one level===<br />
This will load interactions involving all the nodes in the current network.<br />
<br />
===Load interactions between neighbours===<br />
<br />
<br />
===Clear load history (Reload everything next time)===<br />
===Reset node degree===<br />
===Load user variables===<br />
<br />
==View tools==<br />
===Toggle selected multi-edges===<br />
===Zoom to selected===<br />
===Select last iRefScape selection===<br />
===Select nodes with different taxid than query node===<br />
===Select between nodes===<br />
===Select between nodes with originals===<br />
===Show spoke-represented complexes===<br />
=== (Currently hidden, used for debuging) Show live details of nodes and edges===<br />
<br />
==Grouping==<br />
===Reset Group===<br />
===Set group=1 for selection===<br />
===Set group=2 for selection===<br />
===Create comparison table===<br />
<br />
==Hide/Un-hide==<br />
===Hide selected nodes===<br />
===Hide nodes (except pseudonodes)===<br />
===Hide nodes not selected===<br />
===Hide nodes not selected (except pseudonodes)===<br />
===Un-hide all===<br />
<br />
=Grouping and adjacency matrix=</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=README_Cytoscape_plugin_menu_1.0x&diff=3547README Cytoscape plugin menu 1.0x2011-06-28T13:43:26Z<p>Sabry: /* iRefScape */</p>
<hr />
<div> Content of this page will be transferred to :[[README_Cytoscape_plugin_1.0x]]<br />
<br />
=iRefScape=<br />
A new menu called "iRefScape" will be created when the plugin is activated.<br />
<br />
==Search tools==<br />
This sub menu contain search related operations.<br />
<br />
===Retrieve interactions for the selected nodes===<br />
This option will load interactions involving the selected nodes. Nodes could be selected using the mouse or using an operation such as applying a filter.<br />
<br />
===Expand one level===<br />
This will load interactions involving all the nodes in the current network.<br />
<br />
===Load interactions between neighbours===<br />
<br />
<br />
===Clear load history (Reload everything next time)===<br />
===Reset node degree===<br />
===Load user variables===<br />
<br />
==View tools==<br />
===Toggle selected multi-edges===<br />
===Zoom to selected===<br />
===Select last iRefScape selection===<br />
===Select nodes with different taxid than query node===<br />
===Select between nodes===<br />
===Select between nodes with originals===<br />
===Show spoke-represented complexes===<br />
=== (Currently hidden, used for debuging) Show live details of nodes and edges===<br />
<br />
==Grouping==<br />
===Reset Group===<br />
===Set group=1 for selection===<br />
===Set group=2 for selection===<br />
===Create comparison table===<br />
<br />
==Hide/Un-hide==<br />
===Hide selected nodes===<br />
===Hide nodes (except pseudonodes)===<br />
===Hide nodes not selected===<br />
===Hide nodes not selected (except pseudonodes)===<br />
===Un-hide all===</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=README_Cytoscape_plugin_menu_1.0x&diff=3543README Cytoscape plugin menu 1.0x2011-06-27T15:52:59Z<p>Sabry: </p>
<hr />
<div> Content of this page will be transferred to :[[README_Cytoscape_plugin_1.0x]]<br />
<br />
=iRefScape=<br />
<br />
==Search tools==<br />
===Retrieve interactions for the selected nodes===<br />
===Expand one level===<br />
===Load interactions between neighbours===<br />
===Clear load history (Reload everything next time)===<br />
===Reset node degree===<br />
===Load user variables===<br />
<br />
==View tools==<br />
===Toggle selected multi-edges===<br />
===Zoom to selected===<br />
===Select last iRefScape selection===<br />
===Select nodes with different taxid than query node===<br />
===Select between nodes===<br />
===Select between nodes with originals===<br />
===Show spoke-represented complexes===<br />
=== (Currently hidden, used for debuging) Show live details of nodes and edges===<br />
<br />
==Grouping==<br />
===Reset Group===<br />
===Set group=1 for selection===<br />
===Set group=2 for selection===<br />
===Create comparison table===<br />
<br />
==Hide/Un-hide==<br />
===Hide selected nodes===<br />
===Hide nodes (except pseudonodes)===<br />
===Hide nodes not selected===<br />
===Hide nodes not selected (except pseudonodes)===<br />
===Un-hide all===</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=README_Cytoscape_plugin_menu_1.0x&diff=3542README Cytoscape plugin menu 1.0x2011-06-27T15:05:28Z<p>Sabry: Created page with " Content of this page will be transferred to :README_Cytoscape_plugin_1.0x"</p>
<hr />
<div> Content of this page will be transferred to :[[README_Cytoscape_plugin_1.0x]]</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefScape_1.0&diff=3521iRefScape 1.02011-06-23T12:06:33Z<p>Sabry: /* Tested systems */</p>
<hr />
<div>Last edited: {{REVISIONYEAR}}-{{padleft:{{REVISIONMONTH}}|2}}-{{REVISIONDAY2}}<br />
<br />
Release date: To be announced<br />
<br />
This page describes the iRefScape 1.0 plug-in for Cytoscape 2.8.1. See the following table for more detailed iRefScape compatibility information.<br />
<br />
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"<br />
! align="center" style="background:#f0f0f0;"|Cytoscape<br />
! align="center" style="background:#f0f0f0;"|iRefScape<br />
|-<br />
| 2.8.1<br />
| iRefScape 1.0 (described on this page)<br />
|-<br />
| 2.7.0<br />
| [[README_Cytoscape_plugin_0.9x|iRefScape 0.9]]<br />
|-<br />
| 2.6.3<br />
| [[README_Cytoscape_plugin_0.8x|iRefScape 0.8]]<br />
|}<br />
<br />
Join the [http://groups.google.com/group/irefindex?hl=en iRefIndex Google Group] to be informed of updates. See also the [[README_Cytoscape_plugin|latest release of iRefScape]] which may differ from the release described here.<br />
<br />
==Installation==<br />
<br />
The plugin can be installed using Cytoscape's plugin menu. Select "Manage plugins" and then "Available for Install" and then "Network and Attribute I/O" and finally the "iRefScape" entry (where the precise version will provide a specific version such as "iRefScape v.1.0").<br />
<br />
Follow the on-screen instructions.<br />
<br />
More detailed instructions, troubleshooting tips and alternative methods are available on the [[README_Cytoscape_plugin_1.0x_Installation|iRefIndex Cytoscape Plugin 1.0 installation page]] and this can be followed for subsequent releases of iRefScape as well, until replaced by a newer document.<br />
<br />
After, installation, select the "iRefScape" entry from Cytoscape's plugin menu.<br />
<br />
When the plugin is started for the first time, it will download the publicly available data set.<br />
<br />
<br />
=== Tested systems ===<br />
This version of the iRefScape plugin has been tested and works on the following operating systems.<br />
<br />
# Redhat Linux el5 (32 bit) (kernel 2.6.18) with JAVA 32 bit versions 1.6.0_01 <br />
# Microsoft Windows 7 (64 bit) with JAVA 64 bit versions 1.6.0_25<br />
# Microsoft Windows Vista (32 bit) with JAVA 32 bit versions 1.6.0<br />
# Ubuntu (32 bit)(version 8.04) with JAVA 32 bit versions 1.6.<br />
# Mac OS X Version 10.6 (64 bit) with Java 32 bit 1.6.0_15<br />
<br />
Please refer [http://irefindex.uio.no/wiki/README_Cytoscape_plugin_1.0x_Installation '''README_Cytoscape_plugin_1.0x_Installation'''] for more details on OS specific issues.<br />
<br />
== Using the Wizard - an example search ==<br />
<br />
Click the "Wizard" button - a pop-up window will appear. <br />
<br />
Follow these steps<br />
<br />
# Select "Search protein-protein interactions for a protein".<br />
# Select "UniProt identifier".<br />
# For "Taxonomy identifier", select "9606 (Human)" <br />
# Type <tt>QCR2_HUMAN</tt> in the provided space. Click "Next".<br />
# Click "Search & load".<br />
<br />
The images below show each of the steps in the wizard.<br />
<br />
<gallery perrow="5"><br />
Image:IRefIndex-Cytoscape-Wizard.png|The iRefIndex wizard<br />
Image:IRefIndex-Cytoscape-Wizard-step2.png|Choosing a result type<br />
Image:IRefIndex-Cytoscape-Wizard-step3.png|Choosing a taxonomy type<br />
Image:IRefIndex-Cytoscape-Wizard-step4.png|Specifying the search term<br />
Image:IRefIndex-Cytoscape-Wizard-step5.png|Additional options<br />
</gallery><br />
<br />
== Using the Search Panel ==<br />
<br />
To perform a search, the following steps are involved:<br />
<br />
# Enter query term(s)<br />
# Select a search type<br />
# Select taxonomy/organism<br />
# Adjust search options (iterations, new view, canonical expansion) - this is optional<br />
# Start the search<br />
<br />
=== Enter query term(s) ===<br />
<br />
Queries may be loaded from a file or by pasting the query into the text box (one query per line). Multiple queries can also be separated by pipe characters (<tt>|</tt>) or by tab characters. Queries with spaces in them should be enclosed in double quotes.<br />
<br />
=== Select a search type ===<br />
<br />
Example searches are listed below.<br />
<br />
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"<br />
! align="center" style="background:#f0f0f0;"|Search Type<br />
! align="center" style="background:#f0f0f0;"|Example<br />
! align="center" style="background:#f0f0f0;"|Notes<br />
|-<br />
| <tt>RefSeq_Ac</tt>||<tt>NP_996224</tt>||See http://www.ncbi.nlm.nih.gov/protein/221379660<br />
|-<br />
| <tt>UniProt_Ac</tt>||<tt>Q7KSF4</tt>||See http://www.uniprot.org/uniprot/Q7KSF4<br />
|-<br />
| <tt>UniProt_ID</tt>||<tt>Q7KSF4_DROME</tt>||See http://www.uniprot.org/uniprot/Q7KSF4<br />
|-<br />
| <tt>geneID</tt>||<tt>42066</tt>||See http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=42066<br />
|-<br />
| <tt>geneSymbol</tt>||<tt>cher</tt>||See http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=42066<br />
|-<br />
| <tt>mass</tt>||<tt>72854<-->72866</tt>||Search protein interactors for a range of molecular mass (in Da).<br />
|-<br />
| <tt>rog</tt>||<tt>10121899</tt>||Redundant object group: iRefIndex's internal identifier for a protein<br />
|-<br />
| <tt>PMID</tt>||<tt>14605208</tt>||PubMed Identifier where an interaction is described. See http://www.ncbi.nlm.nih.gov/pubmed. Iterations and "Use canonical expansion" have no effect on this search type. This search will return all protein interactors in the given PMID and will automatically draw all interactions known between these proteins (even if these interactions are supported by different PMIDs). Select edges in the resulting graph, and see the i.PMID attribute in the Edge Attribute Browser.<br />
|-<br />
| <tt>src_intxn_id</tt>||<tt>EBI-212627</tt>||Source interaction database identifier. Iterations and "Use canonical expansion" have no effect on this search type. Caution: multiple databases may have overlapping interaction record identifiers (e.g. <tt>147805</tt> returns records from both BIND and BioGrid) and there is no way to limit this search to a specific database at this time.<br />
Equivalent interactions from other databases will be automatically retrieved using this search type (see provided example).<br />
|-<br />
| <tt>omim</tt>||<tt>227650</tt>||OMIM identifier. See http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=227650<br />
|-<br />
| <tt>digid</tt>||<tt>449</tt>||Internal identifier for a group of phenotypically related diseases. See http://donaldson.uio.no/wiki/DiG:_Disease_groups. A digid can be found by first performing a search for some omim identifier - the digid will then appear as the i.digid node attribute.<br />
<!--<br />
|-<br />
| <tt>dig_title</tt>||<tt>fanconi</tt>||Text search for a group of phenotypically related diseases. See http://donaldson.uio.no/wiki/DiG:_Disease_groups<br />
|-<br />
--><br />
|}<br />
<br />
=== Select taxonomy/organism ===<br />
<br />
This will limit the search results to a particular organism. An organism can be selected from the list, or a taxonomy identifier can be entered into the field itself. See [http://www.ncbi.nlm.nih.gov/taxonomy Entrez Taxonomy] for more details on taxonomy identifiers. For most search types, it is acceptable to leave this field set to <tt>Any</tt>.<br />
<br />
=== Adjust search options ===<br />
<br />
The following optional adjustments can be made:<br />
<br />
==== Iterations ====<br />
<br />
A distance from the query list's members can be specified:<br />
<br />
* Selecting <tt>0</tt> will return only interactions between nodes found by the query list<br />
* Selecting <tt>1</tt> will return immediate neighbours of nodes in the query list<br />
<br />
==== Create new view ====<br />
<br />
A new view will be opened for the search results if this option is selected. Otherwise, the results will be added to the current view.<br />
<br />
==== Use canonical expansion ====<br />
<br />
Selecting this option will expand the search to include all proteins that are related to the query protein (for example, splice isoforms). See [[Canonicalization]] for technical details.<br />
<br />
=== Start the search ===<br />
<br />
Press the "Search and load" button to perform the search.<br />
<br />
== Viewing the Results ==<br />
<br />
=== Colours and Shapes ===<br />
<br />
* Blue nodes corresponds to proteins found by your query<br />
* Green nodes are interacting partners for your query protein<br />
* Purple hexagons are complex-nodes (also called pseudo-nodes); they keep partners of a complex together (i.e. QCR6_HUMAN is found in two complexes also involving "QCR2_HUMAN")<br />
* Orange-yellow edges indicate protein-protein interactions and pink edges represent membership of some protein in a complex<br />
<br />
=== Toggling Edges ===<br />
<br />
Multiple edges may appear between two nodes. These represent separate interaction records that support this link. Details on each original record can be viewed using the edge attribute viewer (below). You can toggle this multi-view on and off by selecting "Toggle selected multi-edges" in the iRefScape/View Tools menu. Only one of the edges will be shown in the collapsed view.<br />
<br />
<br />
=== iRefScape Menu ===<br />
<br />
The iRefScape menu in the CytoScape menu bar contains a number of other functions that may help with searching and viewing interaction data. These are described in more detail on a separate page [[README_Cytoscape_plugin_menu]].<br />
<br />
=== Expanding the Interaction Map ===<br />
<br />
You can search for additional interactions by right-clicking on a node and selecting "iRefIndex -- Retrieve interactions".<br />
<br />
Some example result displays are shown below.<br />
<br />
<gallery widths="500px" heights="300px"><br />
Image:QCR2_HUMAN_initial.png|Results<br />
Image:QCR2_HUMAN.png|Results (tidied)<br />
</gallery><br />
<br />
== Attributes ==<br />
<br />
[[Image:iRefIndex-0.83-node-attributes-close-up-closed.png|right|The node attributes menu]]<br />
<br />
There are two types of attributes available from iRefIndex: node attributes and edge attributes. These may be used to view information about selected nodes or edges (like <tt>i.taxid</tt>). Some features may allow the user to link out to additional data sources through the "right-click" menu (like <tt>i.geneID</tt>). Features may also be used to sort and select nodes and edges with specific attributes (like <tt>i.order</tt>). The <tt>i.query</tt> feature shows the user's query that is responsible for returning the node or edge.<br />
<br />
Brief descriptions and examples of each attribute are provided below. <br />
<br />
The user must first select the attributes that are to be displayed. This can be done by clicking on the "attribute" icon at the top of the node or edge attribute browser, as shown in the illustrative images.<br />
<br />
<div style="clear: right"></div><br />
=== Node Attributes ===<br />
<br />
[[Image:iRefIndex-0.83-node-attributes-close-up-open.png|right|The open node attributes menu]]<br />
<br />
Each node represents a distinct amino acid sequence (protein) from a distinct organism (taxonomy identifier). Each of the attributes below, provide additional information about the node. Although each node is distinct, a graph produced by iRefIndex may contain multiple nodes that are related proteins (such as splice isoform products from the same gene). These nodes will all have the same <tt>i.canonical_rog</tt> and <tt>i.canonical_rogid</tt> feature values. See the notes below.<br />
<br />
Node attributes that can be lists of items (like <tt>i.UniProt</tt>) will have a corresponding attribute called <tt>i.''attribute name''_TOP</tt> (for example, <tt>i.UniProt_TOP</tt>) which provides the first item of the associated list.<br />
<br />
<div style="clear: right"></div><br />
<br />
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"<br />
! align="center" style="background:#f0f0f0;"|Attribute name<br />
! align="center" style="background:#f0f0f0;"|Data type<br />
! align="center" style="background:#f0f0f0;"|Example value<br />
! align="center" style="background:#f0f0f0;"|Description<br />
|-<br />
| <tt>ID</tt>||Integer||<tt>10121899</tt>||This is a unique identifier for the node assigned by iRefIndex (no two nodes will have the same ID). Each node corresponds to a distinct amino acid sequence from a distinct taxonomy identifier. See also <tt>i.rog</tt> and <tt>i.rogid</tt>.<br />
|-<br />
| <tt>canonicalName</tt>||Integer||<tt>10121899</tt>||This is the same as <tt>ID</tt>. This attribute is set by Cytoscape and is unrelated to the <tt>i.canonical_rog</tt> or <tt>i.canonical_rogid</tt> used by iRefIndex<br />
|-<br />
| <tt>i.RefSeq_Ac</tt>||List||<tt>[NP_996224]</tt> ||All RefSeq accessions with an amino acid sequence and taxon identifier identical to the protein represented by this node. Right click on this entry and select "Search ''[RefSeq_Ac]'' on the web -- Entrez -- Protein" for more information. See also <tt>i.RefSeq_TOP</tt> for the first entry in this list of accessions.<br />
|-<br />
| <tt>i.UniProt_Ac</tt>||List||<tt>[Q7KSF4]</tt>||All UniProt accessions with an amino acid sequence and taxonomy identifier identical to the protein represented by this node. Right click on this entry and select "Search ''[UniProt_Ac]'' on the web -- UniProt -- KB Beta" for more information. See also <tt>i.UniProt_Ac_TOP</tt> for the first entry in this list of accessions.<br />
|-<br />
| <tt>i.UniProt_ID</tt>||List||<tt>[Q7KSF4_DROME]</tt> ||All UniProt identifers with an amino acid sequence and taxonomy identifier identical to the protein represented by this node. Right click on this entry and select "Search ''[UniProt_ID]'' on the web -- UniProt -- KB Beta" for more information. See also <tt>i.UniProt_ID_TOP</tt> for the first entry in this list of IDs.<br />
|-<br />
| <tt>i.canonical_rog</tt>||Integer||<tt>10121899</tt>||Related proteins (say splice isoforms from the same gene) will all belong to the same canonical group. One member of this group is assigned as the canonical representative of this group. The <tt>i.canonical_rog</tt> attribute lists the identifier of the protein's canonical group identifier. For example, all products of Entrez Gene 42066 have the same <tt>i.canonical_rog</tt> (<tt>10121899</tt>). Each of these gene products has its own identifier (because they each have a distinct amino acid sequence). One of the splice isoforms (<tt>NP_996224</tt>) was chosen as the canonical representative of this group. See the [http://irefindex.uio.no/wiki/Canonicalization canonicalization document] for more details on how canonical groups are constructed and how canonical representatives are chosen.<br />
|-<br />
| <tt>i.canonical_rogid</tt>||String||<tt>1ZFb1WlW0OgOlhiAPtkJTdb6oOg7227</tt>||This is a unique alphanumeric key for the canonical representative of the canonical group to which this node belongs. Briefly, an SHA-1 digest of the amino acid sequence is used to generate a unique 27 character key and this is prepended to the taxonomy identifier for the protein's source organism in order to make the rogid. See PMID 18823568 for details on how this key can be generated. This is a string equivalent of the <tt>i.canonical_rog</tt> attribute. All <tt>i.canonical_rog</tt> instances (each being an integer) have one corresponding <tt>i.canonical_rogid</tt>. See the [http://irefindex.uio.no/wiki/Canonicalization canonicalization document] for more details on how canonical groups are constructed and how canonical representatives are chosen. Note that the rogid for the protein represented by this specific node is listed under <tt>i.rogid</tt>.<br />
|-<br />
| <tt>i.dataset</tt>||Integer||<tt>0</tt>||In the batch query mode this can be used to locate the query batch (i.e. which group of queries were responsible for the node). In single query mode, when a sequence of queries are issued one after another this variable can be used to distinguish the results from each step. All nodes with a i.dataset value higher than 999 can be found using more than one batch of queries. <br />
|-<br />
| <tt>i.digid</tt>||List||<tt>449</tt>||This is an integer identifier that is shared by a group of disease entries in OMIM that are related by their titles. See the [http://donaldson.uio.no/wiki/DiG:_Disease_groups disease groups document] for more details. Also see <tt>i.omim</tt> and <tt>i.dig_title</tt>.<br />
|-<br />
<!--<br />
| <tt>i.dig_title</tt>||List||<tt>[Fanconi anemia, complementation group B, 300514 (3), VACTERL association with hydrocephalus, X-linked, 314390 (3)]</tt>||These are entries from OMIM's Morbid Map that are all part of the same disease group. See the [http://donaldson.uio.no/wiki/DiG:_Disease_groups disease groups document] for more details. Also see <tt>i.omim</tt> and <tt>i.digid</tt>.<br />
--><br />
|-<br />
| <tt>i.displayLabel</tt>||List||<tt>[Q7KSF4_DROME]</tt> ||This is a list of short labels chosen by iRefIndex to label the node using the VizMapper. The UniProt identifier is preferentially chosen (if one is available) followed by the Entrez Gene Symbol. See also <tt>i.displayLabel_TOP</tt> for the first entry in this list.<br />
|-<br />
| <tt>i.geneID</tt>||List||<tt>[42066]</tt>||All NCBI Entrez Gene identifiers that encode a protein sequence identical to that of this node. Right click on this entry and select "Search ''[geneID]'' on the web -- Entrez -- Gene" for more information. See also <tt>i.geneID_TOP</tt> for the first entry in this list.<br />
|-<br />
| <tt>i.geneSymbol</tt>||List||<tt>[CHER]</tt>||All NCBI Entrez Gene official symbols that encode a protein sequence identical to that of this node. Right click on this entry and select "Search ''[geneSymbol]'' on the web -- Entrez -- Gene" for more information. See also <tt>i.geneSymbol_TOP</tt> for the first entry in this list.<br />
|-<br />
| <tt>i.interactor_description</tt>||List||<tt>[Q7KSF4_DROME, CHER, DMEL_CG3937, SKO, DMEL CG3937, FLN, CG3937, CHER, DMEL\\CG3937, FLN, SKO, CHER, NAME=CHER, DMEL_CG3937]</tt>||A collection of all the names in their short form as given by the original interaction databases. See also <tt>i.interactor_description_TOP</tt> for the first entry in this list.<br />
|-<br />
| <tt>i.mass</tt>||Integer|| <tt>259142</tt> ||Mass associated with the protein sequence for this node. From UniProt, if available. You can search for nodes inside a mass range using the <tt>mass</tt> search type in the iRefIndex plugin.<br />
|-<br />
| <tt>i.omim</tt>||List||<tt>[608053]</tt>||List of OMIM disease identifiers associated with this protein. Right click on the entry and select "Search for ''[omim]'' on the web -- Entrez -- OMIM" for more information. <br />
|-<br />
| <tt>i.order</tt>||Integer|| <tt>0</tt> || The distance of this node from the query node (query node has distance <tt>0</tt>, nodes that are returned by a query because they are a part of the same canonical group have a value of <tt>10</tt>, direct neighbours have a value of<tt>1</tt>). Pseudonodes have negative values (<tt>-1</tt> is a complex holder, <tt>-2</tt> is a collapsed instance).<br />
|-<br />
| <tt>i.overall_degree_TOP</tt>||Integer|| <tt>42</tt> ||The total number of interactions described for this node in the iRefIndex database. Not all of these edges will be necessarily shown in the current view. This is the node degree in the full iRefIndex interactome. When calculating the value of this all proteins in iRefIndex (not only the ones currently loaded) will be used<br />
|-<br />
| <tt>i.popularity</tt>||List|| <tt>42</tt> || '''TO BE DESCRIBED'''<br />
|-<br />
| <tt>i.pseudonode</tt>||Boolean|| <tt>false</tt> || This is set to true is the node represents a "complex" or n-ary interaction record. Protein nodes with edges incident to a pseudonode are member interactors from the interaction record where specific interactions between pairs of interactors is unknown. Pseudonodes appear as hexagons when using the iRefIndex VizMapper style. <br />
|-<br />
| <tt>i.query</tt>||String||<tt>NP_996224</tt>||The user query used to retrieve this specific node. Neighbours of "query" nodes will not have an <tt>i.query</tt> value. Nodes returned by queries are coloured blue when using the iRefIndex VizMapper style.<br />
|-<br />
| <tt>i.rog</tt>||Integer||<tt>10121899</tt>||This is a unique identifier for the node assigned by iRefIndex (no two nodes will have the same ID). Each node corresponds to a distinct amino acid sequence associated with a distinct taxonomy identifier. <tt>i.rog</tt> also appears as the <tt>ID</tt> attribute. Each <tt>i.rog</tt> has a corresponding <tt>i.rogid</tt> - see below.<br />
|-<br />
| <tt>i.rogid</tt>||String||<tt>2mL9oLZ9g/SSPyK0nOz97RmOzPg3702</tt>||This is a unique alphanumeric key for the protein represented by this node. Briefly, an SHA-1 digest of the amino acid sequence is used to generate a unique 27 character key and this is prepended to the taxonomy identifier for the protein's source organism in order to make the rogid. See PMID 18823568 for details on how this key can be generated. This is a string equivalent of the <tt>i.rog</tt> attribute. All <tt>i.rog</tt> instances (each being an integer) have one corresponding <tt>i.rogid</tt>.<br />
|-<br />
| <tt>i.taxid</tt>||Integer||<tt>7227</tt>||The NCBI taxonomy identifier for this protein's source organism. See http://www.ncbi.nlm.nih.gov/taxonomy?term=7227 for more details of this example value for <tt>i.taxid</tt>.<br />
|-<br />
| <tt>i.xref</tt>||List||<tt>[AAF70826.1,Q9M6R5]</tt> ||All the accessions as given by the original interaction database records to describe this protein. See also <tt>i.xref_TOP</tt> for the first entry in this list.<br />
|-<br />
| <tt>i.alive</tt>||Boolean||<tt>true or false</tt> ||This is true for all nodes after a search operation. This variable is used by the iRefScape filter and after a filter is applied, all nodes matching the filter criteria will have a true value for this variable (all other nodes will have false).<br />
|-<br />
| <tt>i.alive_degree</tt>||Integer||<tt>0,1,2-...</tt> ||This is will give the node degree after a search. When an iRefScape filter is applied this will give the number of nodes with "i.alive=true" connected to a particular node(How many nodes matching the filter criteria has connections with a particular node). <br />
|-<br />
|}<br />
<br />
===Edge Attributes===<br />
<br />
Each edge represents a distinct primary database record that supports some relationship between the two incident nodes. So, if an interaction between two proteins has been annotated by two databases (or twice by the same database) then two edges will appear between those two protein nodes.<br />
<br />
<br />
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"<br />
! align="center" style="background:#f0f0f0;"|Attribute name<br />
! align="center" style="background:#f0f0f0;"|Data type<br />
! align="center" style="background:#f0f0f0;"|Example value<br />
! align="center" style="background:#f0f0f0;"|Description<br />
|-<br />
| <tt>ID</tt>||String||<tt>10121899 (2771704(40952)) 13911416</tt>||This is a unique identifier for the edge assigned by Cytoscape (no two edges will have same <tt>ID</tt>). See <tt>i.rig</tt> and <tt>i.rigid</tt> for unique identifiers for the edge assigned by iRefIndex.<br />
|-<br />
| <tt>i.PMID</tt>||Integer||<tt>14605208</tt>||Publication identifier of the publication where the interaction represented by the edge mentioned. Right click on this entry and select "Search ''[PMID]'' on the web -- Entrez -- Pubmed" for more details on the publication.<br />
|-<br />
| <tt>i.bait</tt>||Integer||<tt>13911416</tt>||Node ID for the protein that was used as a bait in this experiment. Only applicable where the experimental system (see <tt>i.method_name</tt>) used to support this relationship was a bait-prey system (for example, two hybrid).<br />
|-<br />
| <tt>i.canonical_rig</tt>||Integer||<tt>27799</tt>||See notes for the <tt>i.rig</tt> edge feature. This is the rig constructed for the interaction using its canonical rogs. Use a web browser to query http://wodaklab.org/iRefWeb/interaction/show/27799 (where <tt>27799</tt> is the <tt>i.canonical_rig</tt> value) to retrieve more information on this interaction and equivalent source interaction records.<br />
|-<br />
| <tt>i.experiment</tt>||String||<tt>Giot L [2003]</tt>||A short label for the experiment where this interaction was found (usually contains authors names).<br />
|-<br />
| <tt>i.flag</tt>||Integer||<tt>1</tt>||Used by iRefIndex plugin to control display of edges (<tt>0</tt> being the representative edge, used in edge toggle; <tt>1</tt> being an edge which will disappear during edge toggle; <tt>2</tt> being a complex holder edge; <tt>6</tt> being a path; <tt>7</tt> being an edge from or to a collapsed node).<br />
|-<br />
| <tt>i.host_taxid</tt>||Integer||<tt>7227</tt>||Indicates the organism taxonomy identifier where the interaction was experimentally demonstrated.<br />
|-<br />
| <tt>i.isLoop</tt>||Integer||<tt>1</tt>||Indicates whether the interaction is a self interaction (such as a dimer or possibly multimer of the same protein type). See the source interaction record for details.<br />
|-<br />
| <tt>i.method_cv</tt>||String||<tt>MI:0018</tt>||PSI-MI controlled vocabulary term identifier for the method used to provide evidence for this interaction. See http://www.ebi.ac.uk/ontology-lookup/ for more details. The name of the method is also given in the <tt>i.method_name</tt> feature.<br />
|-<br />
| <tt>i.method_name</tt>||String||<tt>two hybrid</tt>||PSI-MI controlled vocabulary term name for the method used to provide evidence for this interaction. See http://www.ebi.ac.uk/ontology-lookup/ for more details. The term identifer is also given in the <tt>i.method_cv</tt> feature.<br />
|-<br />
| <tt>i.participant_identification</tt>||String||<tt>predetermined participant</tt>||PSI-MI controlled vocabulary term for the participant identification method used to provide evidence for this interaction. See http://www.ebi.ac.uk/ontology-lookup/ for more details. The identifier for the term is also given in the <tt>i.participant_cv</tt> feature.<br />
|-<br />
| <tt>i.participant_cv</tt>||String||<tt>predetermined participant</tt>||PSI-MI controlled vocabulary term identifier for the participant identification method used to provide evidence for this interaction. See http://www.ebi.ac.uk/ontology-lookup/ for more details. The term itself is also given in the <tt>i.participant_identification</tt> feature.<br />
|-<br />
| <tt>i.query</tt>||String||<tt>NP_996224</tt>||The user's query that is responsible for returning this edge.<br />
|-<br />
| <tt>i.rig</tt>||Integer||<tt>27799</tt>||Redundant interaction group identifier for the interaction. <br />
This is an integer equivalent of <tt>i.rigid</tt>. Every rig has one corresponding rigid.<br />
|-<br />
| <tt>i.rigid</tt>||String||<tt>TAabV6yJ1XzUvEhYwZLpu5reBU0</tt>||Redundant interaction group identifier for the interaction. This is a universal key generated for the interaction by ordering according to ASCII value and concatentating the rogids participating in the interaction and then generating a Base-64 representation of an SHA-1 digest of the resulting string. See PMID 18823568 for details on how this key can be generated.<br />
|-<br />
| <tt>i.score_hpr</tt>||Integer||<tt>15</tt>||The hpr score (highest pmid re-use) is the highest number of interactions that any one PMID (supporting this interaction) is used to support. See PMID 18823568 for details. See also <tt>i.score_np</tt> and <tt>i.score_lpr</tt>.<br />
|-<br />
| <tt>i.score_lpr</tt>||Integer||<tt>11</tt>||The lpr score (lowest pmid re-use) is the lowest number of distinct interactions that any one PMID (supporting this interaction) is used to support. An lpr of greater than 20 is considered to be a high-throughput experiment. See PMID 18823568 for details. See also <tt>i.score_np</tt> and <tt>i.score_lpr</tt>.<br />
|-<br />
| <tt>i.score_np</tt>||Integer||<tt>2</tt>||Number of PubMed Identifiers (PMIDs) pointing to literature where this interaction is supported. See PMID 18823568 for details. See also <tt>i.score_lpr</tt>.<br />
|-<br />
| <tt>i.source_protein</tt>||Integer||<tt>-1</tt>||'''TO BE DESCRIBED'''<br />
|-<br />
| <tt>i.src_intxn_db</tt>||String||<tt>grid</tt>||Original interaction database where this interaction record was obtained.<br />
|-<br />
| <tt>i.src_intxn_id</tt>||String||<tt>38677</tt>||Original interaction database where this interaction record was obtained. <br />
In some case, it may be possible to right click and "Search ''[src_intxn_id]'' on the web -- Interaction databases -- the database" to see the original record.<br />
|-<br />
| <tt>i.type_cv</tt>||String||<tt>MI:0407</tt>||PSI-MI controlled vocabulary term identifier for the interaction type that occurs between the two proteins. See http://www.ebi.ac.uk/ontology-lookup/ for more details. The term itself is also given in the <tt>i.type_name</tt> feature.<br />
|-<br />
| <tt>i.type_name</tt>||String||<tt>direct interaction</tt>||PSI-MI controlled vocabulary term identifier for the interaction type that occurs between the two proteins. See http://www.ebi.ac.uk/ontology-lookup/ for more details. The term itself is also given in the <tt>i.type_name</tt> feature.<br />
|-<br />
| <tt>i.target_protein</tt>||Integer||<tt>-1</tt>||'''TO BE DESCRIBED'''<br />
|-<br />
|}<br />
<br />
=== User Attributes ===<br />
Importing - TBD<br />
<br />
Searching on - TBD<br />
<br />
== Obtaining CORUM, DIP and HPRD Data ==<br />
<br />
Due to licensing issues, we are unable to distribute these data with the plugin. CORUM data and free IMex data from DIP will be included in the next public release of iRefIndex.<br />
<br />
You can request these data under a collaborative agreement by emailing ian.donaldson@biotek.uio.no<br />
<br />
Under the agreement you agree to<br />
<br />
# Not redistribute the data outside your research group.<br />
# Provide us with feedback on your use of the data (problems and requests).<br />
<br />
We do not require authorship on any related publications.<br />
<br />
== Obtaining Updates to the Data ==<br />
<br />
You can check for and download updates to the dataset used by your plugin using the Wizard (see "Check for iRefIndex updates").<br />
<br />
iRefIndex updates are announced through the [http://groups.google.com/group/irefindex?hl=en iRefIndex Google Group]<br />
<br />
==Obtaining Updates to the Plugin==<br />
<br />
If you already have a plugin called iRefScape (a menu entry "iRefScape" under the plugin menu of Cytoscape) and you want to make sure you have the latest version, use "Update plugins" from the "Plugins" menu. However, if you want to reinstall the plugin, you should uninstall any previous version of the plugin first.<br />
<br />
Plugin updates are announced through the [http://groups.google.com/group/irefindex?hl=en iRefIndex Google Group]<br />
<br />
<!--<br />
<br />
== How to load batch query from file ==<br />
1. Create a text file with the following format:<br />
<p><type><NCBI_taxonomy_identifier></p><br />
<p>query_text_1</p><br />
<p>query_text_2</p><br />
<p>query_text_3</p><br />
<br />
<p>The first line of the file starts with a hash ("#") and then the type. The type could be</P><br />
*ACCESSION<br />
*NAME<br />
*GENID<br />
<br />
The query_text is your query (e.g.Q39009). Each query line has to be terminated by a new line character (press enter after each line) <br />
<p>[Sample batch file: [http://irefindex.uio.no/wikifiles//images/b/b1/Sample_batch_accessions.txt.zip]]</p><br />
<br />
==Integrating User Data into the Plugin==<br />
<br />
<br />
===How to create your own file to use as index===<br />
<br />
'''TO BE DESCRIBED'''<br />
<br />
===How to create node and edge attributes ===<br />
<br />
Example: Attaching [http://irefindex.uio.no/wiki/DiG:_Disease_groups disease group] identifiers to nodes<br />
<br />
==Updating==<br />
# From Cytoscape updater<br />
# Using plugins update feature<br />
<br />
== Log Files, Search Details and Errors ==<br />
# How to interpret log messages and save them for later reference. <br />
<br />
==Using the plugin as a search tool ==<br />
The plugin could also be used to search the current network. However, there is a better search option in Cytoscape with Google suggest which may be more convenient to use. The reason for including the search function was that the Cytoscape search filed remained inactive on some occasions for networks crated using the plugin. The reason for this is still unknown and deleting a node on the network seems to activate it, when this bug will be fixed the users are encouraged to use the Cytoscape search option.<br />
Currently, if a user performs a search with a term and if the corresponding protein is already loaded, the loaded protein (corresponding node) would be highlighted with Cytoscape default highlight colors. <br />
<br />
<br />
== Exit plugin and force terminate operations ==<br />
The exit button performs two functions. <br />
# First one is to exit iRefIndex plugin, where the outcome is to detach the plugin from Cytoscape. <br />
# The second function "FORCE STOP" (only available during a active task) is to terminate current operation. The "FORCE STOP" is useful when the search query or a subsequent operation takes too long to finish or none-responding. When a force stop is performed the out come is unpredictable and behavior was undefined, therefore results after such operation could not be trusted. <br />
<br />
--><br />
<br />
==Advanced search options==<br />
===Path-Finding===<br />
[[Image:iRefIndex-0.83-path-original.png|thumb|500px|The path in the results, highlighted in green. Solid green lines indicate presence of evidence for this step of the path in the direction specified by the query OR the presence of evidence that has no directionality. A dashed green line indicates there is evidence for this step of the path but only in the direction that is opposite to that specified in the query.]]<br />
<br />
iRefScape can be used to find interaction events connecting two proteins or a sequence of events involving several proteins. <br />
<br />
This process intakes two terminal nodes as input and returns all reasonable paths connecting these two. The results returned here are pathway independent. In other words, the sequences of interactions connecting the nodes are not constructed using currently published pathways. However, the paths returned may contain pathway centric information.<br />
<br />
The query format is as follows:<br />
<br />
NP_004976 <==> NP_002871<br />
<br />
Additional type and taxonomy parameters were also supplied as required:<br />
<br />
* '''Search type:''' <tt>RefSeq_Ac</tt><br />
* '''Taxonomy:''' <tt>9606 (Homo sapiens)</tt><br />
<br />
This query located all reasonable paths between <tt>NP_004976</tt> and <tt>NP_002871</tt> and the returned path also contains the shortest path between them. The results of the path finding was sorted in the ascending order of path length and the maximum path length was restricted to a default value of 6; this value can be modified by changing the value of "Maximum distance" from the "Path parameters" tab in the advanced options panel. The paths found in this way were "reasonable paths", this concept is different from finding the shortest path or finding all the paths. A "reasonable path" from A to B is a path extending from A to B where none of the intermediate points can be reached from A with fewer steps by a path that extends from A via B (in other words, when evaluating a path from A to B, nodes beyond B are not considered).<br />
<br />
<div style="clear: right"></div><br />
<br />
=== Reversing the Path ===<br />
<br />
[[Image:iRefIndex-0.83-path.png|thumb|500px|The path in the results, highlighted in green]]<br />
<br />
Due to the way the algorithm works, when the opposite search was performed...<br />
<br />
NP_002871 <==> NP_004976<br />
<br />
...it took 120 seconds and returned 3 paths. The reason for this is that <tt>NP_002871</tt> is directly connected to many hubs and therefore, the initial seed-list size was larger than when starting with <tt>NP_004976</tt>. The algorithm first tries the direction requested by the user and after that considers the opposite direction when creating the sub-network to look for the path. The time consuming step in the opposite search (<tt>NP_002871<==>NP_004976</tt>) is thus the initial evaluation step. When constructing the query for path-finding we used the attribute <tt>i.overall_degree_TOP</tt> and it provided the overall connectivity of the proteins within iRefIndex. The <tt>i.overall_degree_TOP</tt> value of <tt>RAF1</tt> was found to be 443 and for the <tt>KRAS</tt> isoform was found to be 2. Therefore, although not shown in the graph, <tt>RAF</tt> is connected to more than 400 other proteins than <tt>RAS1</tt>.<br />
<br />
In the image shown here, the green arrow shows the path.<br />
<br />
<div style="clear: right"></div><br />
=== Path Selection ===<br />
<br />
[[Image:iRefIndex-0.83-path-selector.png|thumb|500px|The path selector for the results]]<br />
<br />
After the path-finding is completed the "Path selection" panel can be used to selectively load the paths. In order to make the selection easier, the paths found can be described by a particular attribute type: by selecting a value from the list for "Convert pop-up type to" (such as <tt>RefSeq_Ac</tt>) and pressing the "Convert" button, a tooltip appearing over each path description will show the requested attribute values for each component of the path. Thus, a path description such as...<br />
<br />
321631 -> 2229473 -> 4410739 -> 4531114<br />
<br />
...will provide a tooltip showing the following identifiers:<br />
<br />
NP_002871 -> NP_001123914 -> NP_036979 -> NP_004976<br />
<br />
===List comparison===<br />
This feature is available with version 0.91 and later.<br />
<br />
This feature provides a way to compare two lists of proteins. When a <tt>COMPARE{<List1>,<List2>}</tt> format query is issued with default settings an interaction network is loaded with interactions involving only the proteins of the list and proteins which are not in the list but interacts with at least two proteins from each list (intermediate components). At the end of the operation, in addition to the Cytoscape network a adjacency cube (adjacency matrix with colours as the third dimension) is also created. This adjacency cube is synchronized with the network and can be used examine the results easily. A summary report function is provided to list the overall summary of each protein in the list sorted order so that the most connected protein appear first. The identifiers used to display the proteins in the adjacency cube are either iROGID or the ROGID of complexes. The user has the option to visualize these in popular identifier types using convert feature.<br />
<br />
Example query.<br />
<br />
COMPARE{P08588,P16671|P07550,P13945} (Example from PMID:20670417)<br />
<br />
This query compares two groups:<br />
<br />
# P08588,P16671<br />
# P07550,P13945<br />
<br />
Members within the group are separated with a comma (<tt>,</tt>); groups are separated by a pipe (<tt>|</tt>).<br />
<br />
====Questions and answers about list comparison====<br />
<br />
''What is the maximum number of members a group can have?''<br />
<br />
You could have any number of members, more members there are more time it will take for the operation and more memory it will need. For instance the above example search will complete comfortably in 1 minute with 256MB of allocated memory. If you have more than 100 members we recommend having at least 1GB dedicated memory for Cytoscape. <br />
<br />
''Can I compare more than two groups?''<br />
<br />
Yes, each group should be separated with a pipe character. The maximum number of recommended group count is 255.<br />
<br />
''What if a protein or protein resulting from query appears in more than one group?''<br />
<br />
All proteins found in more than one group is treated as a new group.<br />
<br />
''Can I compare members of already grouped identifiers?''<br />
<br />
Yes. As an example if you want to compare interactions among the disease group 141, the following query could be used:<br />
<br />
COMPARE{141}<br />
<br />
==Troubleshooting==<br />
<br />
* See http://cytoscape.org/ for a manual and a set of tutorials which describe the installation and use of Cytoscape.<br />
* For problems with Cytoscape installation or use, try the [http://groups-beta.google.com/group/cytoscape-helpdesk Cytoscape Help Desk].<br />
* If you have problems with installation or use, please share your experience with us through the [http://groups.google.com/group/irefindex?hl=en iRefIndex Google Group].<br />
* When updating data on Microsoft Windows XP and Vista, a "Failed to find resources message" may appear in the log message window. If this happens please run the update again and the plugin will check and correct the problem during the second attempt.<br />
* If you are working with large graphs, make sure Cytoscape has at least 128MB memory. See the [http://cytoscape.org/cgi-bin/moin.cgi/How_to_increase_memory_for_Cytoscape Cytoscape documentation] for more information on setting up memory allowances.<br />
<br />
== All iRefIndex Pages ==<br />
<br />
Follow this link for a listing of all iRefIndex related pages (archived and current).<br />
<br />
[[Category:iRefIndex]]</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefScape_Test_Cases_1.0&diff=3518iRefScape Test Cases 1.02011-06-22T14:56:06Z<p>Sabry: /* Search cases */</p>
<hr />
<div>Last edited: {{REVISIONYEAR}}-{{padleft:{{REVISIONMONTH}}|2}}-{{REVISIONDAY2}}<br />
<br />
All tests have been performed against iRefIndex 8.1 data.<br />
<br />
==Search cases==<br />
<br />
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"<br />
! align="center" style="background:#f0f0f0;" | Query<br />
! align="center" style="background:#f0f0f0;" | Search Type<br />
! align="center" style="background:#f0f0f0;" | Options<br />
! align="center" style="background:#f0f0f0;" | Expected Result<br />
! align="center" style="background:#f0f0f0;" | Pass/Fail<br />
|-<br />
| rowspan="10" valign="top" | <pre>Q39009<br />
Q9ZNV8</pre><br />
| rowspan="12" valign="top" | <pre>UniProt_Ac</pre><br />
| rowspan="9" valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: no<br />
Use canonical expansion: no<br />
Add edges between neighbours: no</pre><br />
| 33 nodes, 94 edges. 2 queried nodes are blue (DMC_ARATH and AHP2_ARATH)<br />
| Pass<br />
|-<br />
| Node AHP2_ARATH linkout from i.RefSeq_Ac_TOP attribute (NP_189581) to Entrez Protein gives http://www.ncbi.nlm.nih.gov/protein/NP_189581?report=GenPept<br />
| Pass<br />
|-<br />
| i.taxid is 3702 and i.geneID is 822593<br />
| Pass<br />
|-<br />
| Node AHP2_ARATH linkout from i.UniProt_Ac_TOP attribute (Q9ZNV8) to UniProt/KB beta gives http://www.uniprot.org/uniprot/Q9ZNV8<br />
| Pass<br />
|-<br />
| UniProt record agrees with iRefScape on iRefSeq_Ac_TOP (see "Sequence databases"), i.taxid, i.geneID (see "Genome annotation databases")<br />
| Pass<br />
|-<br />
| Two edges between query nodes are EBI-1555390, EBI-1555417<br />
| Pass<br />
|-<br />
| Linkouts for query node edges (i.src_intxn_id) to Intact ("Interaction databases") provide PubMed #17937504 which should match i.PMID, and an interaction detection method of "anti tag coip" which should match i.method_name<br />
| Pass<br />
|-<br />
| The molecule names are DMC1 and ATHP1 in IntAct and these names should be available under the i.interactor_alias node attribute<br />
| Pass<br />
|-<br />
| Both interactions should have http://wodaklab.org/iRefWeb/interaction/show/102203 as i.iRefWEB<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: no<br />
Use canonical expansion: no<br />
Add edges between neighbours: no</pre><br />
| 2 nodes, 3 edges; 2 queried nodes are blue (DMC_ARATH and AHP2_ARATH) and are connected by two edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Q39009-1<br />
Q9ZNV8-2</pre><br />
| rowspan="2" valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: no<br />
Use canonical expansion: no<br />
Add edges between neighbours: no</pre><br />
| Return the same results as for UniProtKB: the isoform information is ignored when searching<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Q39009.1<br />
Q9ZNV8.2</pre><br />
| Returns no results. Version information is not a valid annotation for UniProtKB.<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| rowspan="5" valign="top" | <pre>RefSeq_Ac</pre><br />
| rowspan="11" valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 11 nodes, 29 edges. i.RefSeq_Ac = NP_188928 was returned; edges returned include EBI-1555390, EBI-1555417 between DMC1_ARATH and AHP2_ARATH<br />
| Pass<br />
|-<br />
| <pre>NP_188928</pre><br />
| The same results are returned<br />
| Pass<br />
|-<br />
| <pre>NP_188928.567</pre><br />
| The same results are returned<br />
| Pass<br />
|-<br />
| <pre>188928</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| <pre>NP 188928</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>geneID</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>ipi</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>mass</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>rog</pre><br />
| No results are returned<br />
| Pass (''Modified to give a warning'')<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH</pre><br />
| valign="top" rowspan="6" | <pre>UniProt_ID</pre><br />
| valign="top" rowspan="10" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 26 nodes, 67 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2 ARATH</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>ARATH</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AH2_ARATH</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH.2</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH</pre><br />
| valign="top" | <pre>geneID</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH</pre><br />
| valign="top" | <pre>ipi</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>821860<br />
822593</pre><br />
| valign="top" | <pre>geneID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 33 nodes and 94 edges. (Should return the same result as a UniProt_Ac query for Q39009 and Q9ZNV8.)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>821860</pre><br />
| valign="top" | <pre>geneID</pre><br />
| valign="top" rowspan="4"| <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 1 node<br />
| Pass<br />
|-<br />
| valign="top" | <pre>821860</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>821860</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>821860</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>1234</pre><br />
| valign="top" | <pre>geneID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 47 nodes and 158 edges<br />
| Pass<br />
|-<br />
| valign="top" | All geneIds from a search for <pre>1234</pre> (45 values producing 44 unique gene identifiers)<br />
| valign="top" | <pre>geneID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 80 nodes and 733 edges (upon last attempt)<br />
|<br />
|-<br />
| colspan="5" | '''Note:''' This test is made incredibly difficult by the apparently unreliability of the export function (what Paul is talking about here is the Cytoscape export,not the iRefScape export).<br />
|-<br />
| valign="top" | <pre>CXCR4</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 2 nodes<br />
| Pass<br />
|-<br />
| valign="top" | <pre>P61073-2</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| valign="top" rowspan="2" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 2 nodes (CXCR4 and CXCR4_HUMAN)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>P61073</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| 1 node (CXCR4_HUMAN)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>P61073-2</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| valign="top" rowspan="2" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
| 2 nodes (CXCR4 and CXCR4_HUMAN)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>P61073</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| 2 nodes (CXCR4 and CXCR4_HUMAN)<br />
| Pass<br />
|-<br />
| colspan="5" | '''Note:''' P61073-2 and P61073 are isoforms of CXCR4. Searching for P61073-2 actually results in the removal of the "-2" and a search for all isoforms, under the assumption that the user is unsure which isoform should be retrieved; as a result, all isoforms are returned, even though a specific isoform was requested. In contrast, the search without a "-" character results in just one protein with that exact name being returned.<br />
|-<br />
| valign="top" | <pre>CXCR</pre><br />
| valign="top" rowspan="4" | <pre>geneSymbol</pre><br />
| valign="top" rowspan="4" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>CXCR4</pre><br />
| rowspan="3"| 2 nodes with i.UniProt_Ac_TOP set to P61073 and P61073-2<br />
| Pass<br />
|-<br />
| valign="top" | <pre>cxcR4</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>CXC<br />
CXCR<br />
CXCR4</pre><br />
| Pass<br />
|-<br />
| colspan="5" | '''Note:''' no indication is given that CXC and CXCR failed to provide matches when the successfully used CXCR4 term is present. Maybe some feedback could be given about this.<br />
|-<br />
| valign="top" | <pre>CXCR5</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| valign="top" rowspan="3" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 3 nodes<br />
| Pass<br />
|-<br />
| valign="top" | <pre>CXCR5</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>PTK2</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| 6 nodes (involving 5 taxons)<br />
| Pass<br />
|-<br />
| valign="top" rowspan="3" | <pre>RPB1</pre><br />
| valign="top" rowspan="3" | <pre>geneSymbol</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 1 node (RPB1_SCHPO)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Taxon id: 4932<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| No results returned (even though an alias for yeast RPO21, gene identifier 851415, is RPB1, this search only searches on official gene symbols from Entrez<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Taxon id: 9606<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| No results returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>5366033</pre><br />
| valign="top" | <pre>rog</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: no<br />
Use canonical expansion: no</pre><br />
| 2 nodes (POL_HV1H2 and POL_HV1B1 interacting with it)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>IPI00543858<br />
IPI00517160</pre><br />
| valign="top" rowspan="4" | <pre>ipi</pre><br />
| valign="top" rowspan="4" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: no<br />
Use canonical expansion: no</pre><br />
| rowspan="3" | 33 nodes, 94 edges. 2 queried nodes are blue (DMC_ARATH and AHP2_ARATH)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>IPI00543858.1<br />
IPI00517160.1</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>00543858<br />
00517160</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>00543858<br />
0051716</pre><br />
| 33 nodes, 94 edges, but only after IPI00517160 has been chosen from the query helper<br />
| Pass<br />
|-<br />
| colspan="5" | '''Note:''' the transfer of the search term from the query helper and the augmentation of results from the term isn't particularly easy to accomplish, or it isn't obvious how to accomplish this successfully, because the iRefScape panel is hidden in the main window (a Cytoscape bug which appears to switch the visible panel all the time) and because a new search is required (without a new view being created, which is potentially how the original search might be set up).<br />
|-<br />
| valign="top" | <pre>IPI</pre><br />
| valign="top" rowspan="2" | <pre>ipi</pre><br />
| valign="top" rowspan="2" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: no<br />
Use canonical expansion: no</pre><br />
| Initiates query helper<br />
| Pass<br />
|-<br />
| valign="top" | <pre>IPI00543858</pre><br />
| 26 nodes, 67 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>72854<-->72866</pre><br />
| valign="top" | <pre>mass</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| The query helper is shown. Upon transferring the 4 suggestions into the query box and searching again, 5 nodes are retrieved.<br />
| Pass<br />
|-<br />
| colspan="5" | '''Note:''' the nodes are not laid out in a nice way, probably because no edges connect them.<br />
|-<br />
| valign="top" | <pre>72854 kda</pre><br />
| valign="top" | <pre>mass</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>72854<-->72856 kda</pre><br />
| valign="top" | <pre>mass</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| Query helper with 3 possible results<br />
| Pass<br />
|-<br />
| valign="top" | <pre>11401546</pre><br />
| valign="top" rowspan="12" | <pre>PMID</pre><br />
| valign="top" rowspan="12" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 4 nodes and 7 edges are returned. Three edges have PMID 11401546 and these involve the 4 nodes shown. All other edges (from different PMIDs) involve these proteins.<br />
|<br />
|-<br />
| valign="top" | <pre>11401546.1</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>1140154</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>SPTAN1</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>11401546<br />
SPTAN1</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10551855<br />
11401546</pre><br />
| 6 nodes and 27 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10551855|11401546</pre><br />
| 6 nodes and 27 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10551855| 11401546</pre><br />
| 6 nodes and 27 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10551855 | 11401546</pre><br />
| 6 nodes and 27 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10551855 [tab] 11401546</pre><br />
| 6 nodes and 27 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10551855, 11401546</pre><br />
| 6 nodes and 27 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10551855 11401546</pre><br />
| No results are returned (since space-delimited queries are not supported)<br />
| Pass<br />
|-<br />
| colspan="5" | The following example searches are listed in the [[README_Cytoscape_plugin_0.8x#Using_the_Search_Panel|Using the Search Panel]] documentation.<br />
|-<br />
| valign="top" | <pre>Q7KSF4</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
| 69 nodes, 213 edges, with the 4 query nodes having i.query = Q7KSF4, one of the query nodes having i.order = 0 (Q7KSF4_DROME) and the others having i.order = 10 (as canonical group members)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Q7KSF4</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 1 node (Q7KSF4_DROME) verifying the attributes in the previous search<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_996224</pre><br />
| valign="top" | <pre>RefSeq_Ac</pre><br />
| valign="top" rowspan="3" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
| rowspan="2" | 69 nodes, 213 edges (same as the above query for Q7KSF4)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Q7KSF4_DROME</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>42066</pre><br />
| valign="top" | <pre>geneID</pre><br />
| rowspan="3" | 69 nodes, 213 edges, with the 4 query nodes having i.order = 0 since all also have i.geneID = 42066<br />
| Pass<br />
|-<br />
| valign="top" | <pre>42066</pre><br />
| valign="top" | <pre>geneID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>cher</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| valign="top" rowspan="4" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>72854<-->72866</pre><br />
| valign="top" | <pre>mass</pre><br />
| 44 nodes, 140 edges, with 8 query nodes, 5 of which with i.mass in (72854, 72855, 72856, 72861) having i.order = 0 and the remaining 3 query nodes with i.mass outside the given range having i.order = 10<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10121899</pre><br />
| valign="top" | <pre>rog</pre><br />
| 69 nodes, 213 edges (same as the above query for Q7KSF4), but with one of the query nodes having i.order = 0 and i.query = 10121899 and the remaining 3 query nodes having i.order = 10<br />
| Pass<br />
|-<br />
| valign="top" | <pre>14605208</pre><br />
| valign="top" | <pre>PMID</pre><br />
| rowspan="3" | 929 nodes and 1605 edges returned all with PMID of 14605208<br />
|<br />
|-<br />
| valign="top" | <pre>14605208</pre><br />
| valign="top" | <pre>PMID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
|<br />
|-<br />
| valign="top" | <pre>14605208</pre><br />
| valign="top" | <pre>PMID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
|<br />
|-<br />
| valign="top" | <pre>47513</pre><br />
| valign="top" | <pre>src_intxn_id</pre><br />
| valign="top" rowspan="7" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
| 2 nodes and 1 edge returned (one query node, Q7KSF4_DROME)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>EBI-212627</pre><br />
| valign="top" | <pre>src_intxn_id</pre><br />
| 2 nodes and 5 edges returned (from bind, dip, intact, mint and BIND_Translation), with 2 query nodes (CRBN_DROME and Q9W279_DROME)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>147805</pre><br />
| valign="top" | <pre>src_intxn_id</pre><br />
| Returns 4 nodes and 4 interactions because the BIND/BIND_Translation and BioGRID interaction identifier spaces overlap (so 147805 refers to completely different interactions in different databases)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>227650</pre><br />
| valign="top" | <pre>omim</pre><br />
| 96 nodes (including 18 complex nodes) and 498 edges returned, with the query node having i.geneID = 2175 and i.digid = 460<br />
| Pass<br />
|-<br />
| valign="top" | <pre>449</pre><br />
| valign="top" | <pre>digid</pre><br />
| 321 nodes and 1010 edges returned, with the 3 query nodes having i.omim = 612219<br />
| Pass<br />
|-<br />
| valign="top" | <pre>460</pre><br />
| valign="top" | <pre>digid</pre><br />
| 668 nodes and 17554 edges returned, with the 16 query nodes having i.digid = 460<br />
| Pass<br />
|-<br />
| valign="top" | <pre>fanconi</pre><br />
| valign="top" | <pre>dig_title</pre><br />
| ''Query helper invoked, now the dig_title is a non-exact match''<br />
| Pass <br />
|}<br />
<br />
=== Invalid input tests ===<br />
<br />
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"<br />
! align="center" style="background:#f0f0f0;" | Query<br />
! align="center" style="background:#f0f0f0;" | Search Type<br />
! align="center" style="background:#f0f0f0;" | Options<br />
! align="center" style="background:#f0f0f0;" | Expected Result<br />
! align="center" style="background:#f0f0f0;" | Pass/Fail<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>RefSeq_Ac</pre><br />
|<br />
| No results are returned<br />
|Pass<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
|<br />
| No results are returned<br />
|Pass<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
|<br />
| No results are returned<br />
|Pass<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>geneID</pre><br />
|<br />
| No results are returned<br />
|Pass<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>mass</pre><br />
|<br />
| No results are returned<br />
|Pass<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>pmid</pre><br />
|<br />
| No results are returned<br />
|Pass<br />
|-<br />
| valign="top" | <pre>23</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
|<br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>-1</pre><br />
| valign="top" | <pre>mass</pre><br />
|<br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>-1</pre><br />
| valign="top" | <pre>pmid</pre><br />
|<br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>0000</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
|<br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>00001</pre><br />
| valign="top" | <pre>geneID</pre><br />
|<br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>12345</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
|<br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>abcd</pre><br />
| valign="top" | <pre>ipi</pre><br />
|<br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>abcde</pre><br />
| valign="top" | <pre>RefSeq_Ac</pre><br />
|<br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>abcde</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
|<br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>abcde</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
|<br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>abcde</pre><br />
| valign="top" | <pre>geneID</pre><br />
|<br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>abcdes</pre><br />
| valign="top" | <pre>geneID</pre><br />
|<br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>MW</pre><br />
| valign="top" | <pre>mass</pre><br />
|<br />
| No results are returned<br />
| Pass<br />
|-<br />
|}<br />
<br />
=== Not currently tested ===<br />
<br />
* src_intxn_id search 1<br />
* omim search 1<br />
* digid search 1<br />
* audit against external database - Intact<br />
* audit against external database - MINT<br />
* audit against external database - BioGRID<br />
* iterations 1<br />
* use canonical expansion 1<br />
<br />
=== User interface notes ===<br />
<br />
Many search types such as UniProt_ID now lead to exact-only searches. The production of results should not be allowed for imprecise protein names, for example, since the user might have entered gene names, selected UniProt_ID by mistake and would not be aware of their mistake because their search returned results. Also, since the first few characters of UniProt_ID search terms may be shared by multiple proteins from different organisms, an inexact match would need to trigger the query helper.<br />
<br />
Generally, searches should provide predictable outcomes without resorting to the attribute browsers to discover which search terms produced which results. For example, AH2_ARATH which returns no results from an exact match search, should not encourage similar terms to be used for searching. Previously AH2_ARATH returned CAH2_ARATH. Imagine if the user accidentally had such a query term embedded in a long list. They would never detect this search error!<br />
<br />
Where the taxonomy field is set to <tt>Any</tt>, a warning will be given. It is envisaged that the user will most frequently be working with a single organism's proteins or would at least tolerate being reminded that potentially irrelevant proteins might be searched for due to naming coincidences.<br />
<br />
The iterations setting resets to 1 after a query, even one which led to the query helper being shown, where the query will be completed by trying the search again.<br />
<br />
The i.query attribute on nodes will collect queries as they are performed. Thus, nodes will appear blue in a graph even if the current query had no direct relationship with the node.<br />
<br />
Exporting lists of attribute values should be as simple as selecting the values in the attribute browser and opening a context menu and copying the selection. However, it is also possible (when the context menus don't work) to use the "File" -> "Export" -> "Node Attributes" menu entry and to choose "i.geneID", then saving and processing the saved file to get a list. This seems to be rather unreliable, however.<br />
<br />
== Export cases ==<br />
<br />
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"<br />
! align="center" style="background:#f0f0f0;" | Query/Search Type/Options<br />
! align="center" style="background:#f0f0f0;" | Export Type<br />
! align="center" style="background:#f0f0f0;" | Expected Result<br />
! align="center" style="background:#f0f0f0;" | Pass/Fail<br />
|-<br />
| valign="top" rowspan="2" | <pre>CXCR4<br />
<br />
geneSymbol<br />
<br />
Taxon id: Any<br />
Iterations: 0<br />
Create new view: no<br />
Use canonical expansion: no</pre><br />
| valign="top" | <pre>i.UniProt_Ac_TOP</pre><br />
| 1 node showing P61073<br />
| Pass<br />
|-<br />
| valign="top" | <pre>i.canonical_rog_TOP</pre><br />
| 1 node showing 107322<br />
| Pass<br />
|}<br />
<br />
== Currently untested areas ==<br />
<br />
* Preferences<br />
* iRefScape menu<br />
* Right-click menu<br />
* Node attributes<br />
* Edge attributes<br />
* Wizard<br />
* Installation<br />
* Help system<br />
* Windows and sessions<br />
* Loading from file<br />
<br />
==To be corrected==<br />
*Remove the non-proprietary flag/check for current data<br />
*Handle the neighbourhood completion when expanding network (do not use all the nodes)<br />
*show_inxc dynamic index behaviour change not working<br />
*Scaling GUI at low resolution, maximise button may get hidden<br />
*Path finding cancelling time<br />
*focus progress when path finding<br />
*Ending with collapsed node error<br />
*unselect all nodes before edge filtering<br />
<br />
==List of GeneIDs to test the new canonical expansion==<br />
<br />
Available in data version 8.4:<br />
<br />
*945577 http://www.ncbi.nlm.nih.gov/gene/?term=945577<br />
*947704 http://www.ncbi.nlm.nih.gov/gene/?term=947704<br />
*2765365 http://www.ncbi.nlm.nih.gov/gene/?term=2765365<br />
*944797 http://www.ncbi.nlm.nih.gov/gene/?term=944797<br />
*29924 http://www.ncbi.nlm.nih.gov/gene/?term=29924 <br />
*948517 http://www.ncbi.nlm.nih.gov/gene/?term=948517<br />
*3673 http://www.ncbi.nlm.nih.gov/gene/?term=3673 <br />
*946848 http://www.ncbi.nlm.nih.gov/gene/?term=946848<br />
*653361 http://www.ncbi.nlm.nih.gov/gene/?term=653361<br />
*5657 http://www.ncbi.nlm.nih.gov/gene/?term=5657<br />
<br />
== All iRefIndex Pages ==<br />
<br />
[[Category:iRefIndex]]</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefScape_Test_Cases_1.0&diff=3517iRefScape Test Cases 1.02011-06-22T13:59:56Z<p>Sabry: /* Invalid input tests */</p>
<hr />
<div>Last edited: {{REVISIONYEAR}}-{{padleft:{{REVISIONMONTH}}|2}}-{{REVISIONDAY2}}<br />
<br />
All tests have been performed against iRefIndex 8.1 data.<br />
<br />
==Search cases==<br />
<br />
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"<br />
! align="center" style="background:#f0f0f0;" | Query<br />
! align="center" style="background:#f0f0f0;" | Search Type<br />
! align="center" style="background:#f0f0f0;" | Options<br />
! align="center" style="background:#f0f0f0;" | Expected Result<br />
! align="center" style="background:#f0f0f0;" | Pass/Fail<br />
|-<br />
| rowspan="10" valign="top" | <pre>Q39009<br />
Q9ZNV8</pre><br />
| rowspan="12" valign="top" | <pre>UniProt_Ac</pre><br />
| rowspan="9" valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: no<br />
Use canonical expansion: no<br />
Add edges between neighbours: no</pre><br />
| 33 nodes, 94 edges. 2 queried nodes are blue (DMC_ARATH and AHP2_ARATH)<br />
| Pass<br />
|-<br />
| Node AHP2_ARATH linkout from i.RefSeq_Ac_TOP attribute (NP_189581) to Entrez Protein gives http://www.ncbi.nlm.nih.gov/protein/NP_189581?report=GenPept<br />
| Pass<br />
|-<br />
| i.taxid is 3702 and i.geneID is 822593<br />
| Pass<br />
|-<br />
| Node AHP2_ARATH linkout from i.UniProt_Ac_TOP attribute (Q9ZNV8) to UniProt/KB beta gives http://www.uniprot.org/uniprot/Q9ZNV8<br />
| Pass<br />
|-<br />
| UniProt record agrees with iRefScape on iRefSeq_Ac_TOP (see "Sequence databases"), i.taxid, i.geneID (see "Genome annotation databases")<br />
| Pass<br />
|-<br />
| Two edges between query nodes are EBI-1555390, EBI-1555417<br />
| Pass<br />
|-<br />
| Linkouts for query node edges (i.src_intxn_id) to Intact ("Interaction databases") provide PubMed #17937504 which should match i.PMID, and an interaction detection method of "anti tag coip" which should match i.method_name<br />
| Pass<br />
|-<br />
| The molecule names are DMC1 and ATHP1 in IntAct and these names should be available under the i.interactor_alias node attribute<br />
| Pass<br />
|-<br />
| Both interactions should have http://wodaklab.org/iRefWeb/interaction/show/102203 as i.iRefWEB<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: no<br />
Use canonical expansion: no<br />
Add edges between neighbours: no</pre><br />
| 2 nodes, 3 edges; 2 queried nodes are blue (DMC_ARATH and AHP2_ARATH) and are connected by two edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Q39009-1<br />
Q9ZNV8-2</pre><br />
| rowspan="2" valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: no<br />
Use canonical expansion: no<br />
Add edges between neighbours: no</pre><br />
| Return the same results as for UniProtKB: the isoform information is ignored when searching<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Q39009.1<br />
Q9ZNV8.2</pre><br />
| Returns no results. Version information is not a valid annotation for UniProtKB.<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| rowspan="5" valign="top" | <pre>RefSeq_Ac</pre><br />
| rowspan="11" valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 11 nodes, 29 edges. i.RefSeq_Ac = NP_188928 was returned; edges returned include EBI-1555390, EBI-1555417 between DMC1_ARATH and AHP2_ARATH<br />
| Pass<br />
|-<br />
| <pre>NP_188928</pre><br />
| The same results are returned<br />
| Pass<br />
|-<br />
| <pre>NP_188928.567</pre><br />
| The same results are returned<br />
| Pass<br />
|-<br />
| <pre>188928</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| <pre>NP 188928</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>geneID</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>ipi</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>mass</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>rog</pre><br />
| No results are returned<br />
| Pass (''no error given, though'')<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH</pre><br />
| valign="top" rowspan="6" | <pre>UniProt_ID</pre><br />
| valign="top" rowspan="10" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 26 nodes, 67 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2 ARATH</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>ARATH</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AH2_ARATH</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH.2</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH</pre><br />
| valign="top" | <pre>geneID</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH</pre><br />
| valign="top" | <pre>ipi</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>821860<br />
822593</pre><br />
| valign="top" | <pre>geneID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 33 nodes and 94 edges. (Should return the same result as a UniProt_Ac query for Q39009 and Q9ZNV8.)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>821860</pre><br />
| valign="top" | <pre>geneID</pre><br />
| valign="top" rowspan="4"| <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 1 node<br />
| Pass<br />
|-<br />
| valign="top" | <pre>821860</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>821860</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>821860</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>1234</pre><br />
| valign="top" | <pre>geneID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 47 nodes and 158 edges<br />
| Pass<br />
|-<br />
| valign="top" | All geneIds from a search for <pre>1234</pre> (45 values producing 44 unique gene identifiers)<br />
| valign="top" | <pre>geneID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 80 nodes and 733 edges (upon last attempt)<br />
|<br />
|-<br />
| colspan="5" | '''Note:''' This test is made incredibly difficult by the apparently unreliability of the export function (what Paul is talking about here is the Cytoscape export,not the iRefScape export).<br />
|-<br />
| valign="top" | <pre>CXCR4</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 2 nodes<br />
| Pass<br />
|-<br />
| valign="top" | <pre>P61073-2</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| valign="top" rowspan="2" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 2 nodes (CXCR4 and CXCR4_HUMAN)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>P61073</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| 1 node (CXCR4_HUMAN)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>P61073-2</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| valign="top" rowspan="2" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
| 2 nodes (CXCR4 and CXCR4_HUMAN)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>P61073</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| 2 nodes (CXCR4 and CXCR4_HUMAN)<br />
| Pass<br />
|-<br />
| colspan="5" | '''Note:''' P61073-2 and P61073 are isoforms of CXCR4. Searching for P61073-2 actually results in the removal of the "-2" and a search for all isoforms, under the assumption that the user is unsure which isoform should be retrieved; as a result, all isoforms are returned, even though a specific isoform was requested. In contrast, the search without a "-" character results in just one protein with that exact name being returned.<br />
|-<br />
| valign="top" | <pre>CXCR</pre><br />
| valign="top" rowspan="4" | <pre>geneSymbol</pre><br />
| valign="top" rowspan="4" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>CXCR4</pre><br />
| rowspan="3"| 2 nodes with i.UniProt_Ac_TOP set to P61073 and P61073-2<br />
| Pass<br />
|-<br />
| valign="top" | <pre>cxcR4</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>CXC<br />
CXCR<br />
CXCR4</pre><br />
| Pass<br />
|-<br />
| colspan="5" | '''Note:''' no indication is given that CXC and CXCR failed to provide matches when the successfully used CXCR4 term is present. Maybe some feedback could be given about this.<br />
|-<br />
| valign="top" | <pre>CXCR5</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| valign="top" rowspan="3" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 3 nodes<br />
| Pass<br />
|-<br />
| valign="top" | <pre>CXCR5</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>PTK2</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| 6 nodes (involving 5 taxons)<br />
| Pass<br />
|-<br />
| valign="top" rowspan="3" | <pre>RPB1</pre><br />
| valign="top" rowspan="3" | <pre>geneSymbol</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 1 node (RPB1_SCHPO)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Taxon id: 4932<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| No results returned (even though an alias for yeast RPO21, gene identifier 851415, is RPB1, this search only searches on official gene symbols from Entrez<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Taxon id: 9606<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| No results returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>5366033</pre><br />
| valign="top" | <pre>rog</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: no<br />
Use canonical expansion: no</pre><br />
| 2 nodes (POL_HV1H2 and POL_HV1B1 interacting with it)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>IPI00543858<br />
IPI00517160</pre><br />
| valign="top" rowspan="4" | <pre>ipi</pre><br />
| valign="top" rowspan="4" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: no<br />
Use canonical expansion: no</pre><br />
| rowspan="3" | 33 nodes, 94 edges. 2 queried nodes are blue (DMC_ARATH and AHP2_ARATH)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>IPI00543858.1<br />
IPI00517160.1</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>00543858<br />
00517160</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>00543858<br />
0051716</pre><br />
| 33 nodes, 94 edges, but only after IPI00517160 has been chosen from the query helper<br />
| Pass<br />
|-<br />
| colspan="5" | '''Note:''' the transfer of the search term from the query helper and the augmentation of results from the term isn't particularly easy to accomplish, or it isn't obvious how to accomplish this successfully, because the iRefScape panel is hidden in the main window (a Cytoscape bug which appears to switch the visible panel all the time) and because a new search is required (without a new view being created, which is potentially how the original search might be set up).<br />
|-<br />
| valign="top" | <pre>IPI</pre><br />
| valign="top" rowspan="2" | <pre>ipi</pre><br />
| valign="top" rowspan="2" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: no<br />
Use canonical expansion: no</pre><br />
| Initiates query helper<br />
| Pass<br />
|-<br />
| valign="top" | <pre>IPI00543858</pre><br />
| 26 nodes, 67 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>72854<-->72866</pre><br />
| valign="top" | <pre>mass</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| The query helper is shown. Upon transferring the 4 suggestions into the query box and searching again, 5 nodes are retrieved.<br />
| Pass<br />
|-<br />
| colspan="5" | '''Note:''' the nodes are not laid out in a nice way, probably because no edges connect them.<br />
|-<br />
| valign="top" | <pre>72854 kda</pre><br />
| valign="top" | <pre>mass</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>72854<-->72856 kda</pre><br />
| valign="top" | <pre>mass</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| Query helper with 3 possible results<br />
| Pass<br />
|-<br />
| valign="top" | <pre>11401546</pre><br />
| valign="top" rowspan="12" | <pre>PMID</pre><br />
| valign="top" rowspan="12" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 4 nodes and 7 edges are returned. Three edges have PMID 11401546 and these involve the 4 nodes shown. All other edges (from different PMIDs) involve these proteins.<br />
|<br />
|-<br />
| valign="top" | <pre>11401546.1</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>1140154</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>SPTAN1</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>11401546<br />
SPTAN1</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10551855<br />
11401546</pre><br />
| 6 nodes and 27 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10551855|11401546</pre><br />
| 6 nodes and 27 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10551855| 11401546</pre><br />
| 6 nodes and 27 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10551855 | 11401546</pre><br />
| 6 nodes and 27 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10551855 [tab] 11401546</pre><br />
| 6 nodes and 27 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10551855, 11401546</pre><br />
| 6 nodes and 27 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10551855 11401546</pre><br />
| No results are returned (since space-delimited queries are not supported)<br />
| Pass<br />
|-<br />
| colspan="5" | The following example searches are listed in the [[README_Cytoscape_plugin_0.8x#Using_the_Search_Panel|Using the Search Panel]] documentation.<br />
|-<br />
| valign="top" | <pre>Q7KSF4</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
| 69 nodes, 213 edges, with the 4 query nodes having i.query = Q7KSF4, one of the query nodes having i.order = 0 (Q7KSF4_DROME) and the others having i.order = 10 (as canonical group members)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Q7KSF4</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 1 node (Q7KSF4_DROME) verifying the attributes in the previous search<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_996224</pre><br />
| valign="top" | <pre>RefSeq_Ac</pre><br />
| valign="top" rowspan="3" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
| rowspan="2" | 69 nodes, 213 edges (same as the above query for Q7KSF4)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Q7KSF4_DROME</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>42066</pre><br />
| valign="top" | <pre>geneID</pre><br />
| rowspan="3" | 69 nodes, 213 edges, with the 4 query nodes having i.order = 0 since all also have i.geneID = 42066<br />
| Pass<br />
|-<br />
| valign="top" | <pre>42066</pre><br />
| valign="top" | <pre>geneID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>cher</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| valign="top" rowspan="4" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>72854<-->72866</pre><br />
| valign="top" | <pre>mass</pre><br />
| 44 nodes, 140 edges, with 8 query nodes, 5 of which with i.mass in (72854, 72855, 72856, 72861) having i.order = 0 and the remaining 3 query nodes with i.mass outside the given range having i.order = 10<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10121899</pre><br />
| valign="top" | <pre>rog</pre><br />
| 69 nodes, 213 edges (same as the above query for Q7KSF4), but with one of the query nodes having i.order = 0 and i.query = 10121899 and the remaining 3 query nodes having i.order = 10<br />
| Pass<br />
|-<br />
| valign="top" | <pre>14605208</pre><br />
| valign="top" | <pre>PMID</pre><br />
| rowspan="3" | 929 nodes and 1605 edges returned all with PMID of 14605208<br />
|<br />
|-<br />
| valign="top" | <pre>14605208</pre><br />
| valign="top" | <pre>PMID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
|<br />
|-<br />
| valign="top" | <pre>14605208</pre><br />
| valign="top" | <pre>PMID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
|<br />
|-<br />
| valign="top" | <pre>47513</pre><br />
| valign="top" | <pre>src_intxn_id</pre><br />
| valign="top" rowspan="7" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
| 2 nodes and 1 edge returned (one query node, Q7KSF4_DROME)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>EBI-212627</pre><br />
| valign="top" | <pre>src_intxn_id</pre><br />
| 2 nodes and 5 edges returned (from bind, dip, intact, mint and BIND_Translation), with 2 query nodes (CRBN_DROME and Q9W279_DROME)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>147805</pre><br />
| valign="top" | <pre>src_intxn_id</pre><br />
| Returns 4 nodes and 4 interactions because the BIND/BIND_Translation and BioGRID interaction identifier spaces overlap (so 147805 refers to completely different interactions in different databases)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>227650</pre><br />
| valign="top" | <pre>omim</pre><br />
| 96 nodes (including 18 complex nodes) and 498 edges returned, with the query node having i.geneID = 2175 and i.digid = 460<br />
| Pass<br />
|-<br />
| valign="top" | <pre>449</pre><br />
| valign="top" | <pre>digid</pre><br />
| 321 nodes and 1010 edges returned, with the 3 query nodes having i.omim = 612219<br />
| Pass<br />
|-<br />
| valign="top" | <pre>460</pre><br />
| valign="top" | <pre>digid</pre><br />
| 668 nodes and 17554 edges returned, with the 16 query nodes having i.digid = 460<br />
| Pass<br />
|-<br />
| valign="top" | <pre>fanconi</pre><br />
| valign="top" | <pre>dig_title</pre><br />
| ''Query helper invoked, now the dig_title is a non-exact match''<br />
| Pass <br />
|}<br />
<br />
=== Invalid input tests ===<br />
<br />
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"<br />
! align="center" style="background:#f0f0f0;" | Query<br />
! align="center" style="background:#f0f0f0;" | Search Type<br />
! align="center" style="background:#f0f0f0;" | Options<br />
! align="center" style="background:#f0f0f0;" | Expected Result<br />
! align="center" style="background:#f0f0f0;" | Pass/Fail<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>RefSeq_Ac</pre><br />
|<br />
| No results are returned<br />
|Pass<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
|<br />
| No results are returned<br />
|Pass<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
|<br />
| No results are returned<br />
|Pass<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>geneID</pre><br />
|<br />
| No results are returned<br />
|Pass<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>mass</pre><br />
|<br />
| No results are returned<br />
|Pass<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>pmid</pre><br />
|<br />
| No results are returned<br />
|Pass<br />
|-<br />
| valign="top" | <pre>23</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
|<br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>-1</pre><br />
| valign="top" | <pre>mass</pre><br />
|<br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>-1</pre><br />
| valign="top" | <pre>pmid</pre><br />
|<br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>0000</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
|<br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>00001</pre><br />
| valign="top" | <pre>geneID</pre><br />
|<br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>12345</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
|<br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>abcd</pre><br />
| valign="top" | <pre>ipi</pre><br />
|<br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>abcde</pre><br />
| valign="top" | <pre>RefSeq_Ac</pre><br />
|<br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>abcde</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
|<br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>abcde</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
|<br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>abcde</pre><br />
| valign="top" | <pre>geneID</pre><br />
|<br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>abcdes</pre><br />
| valign="top" | <pre>geneID</pre><br />
|<br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>MW</pre><br />
| valign="top" | <pre>mass</pre><br />
|<br />
| No results are returned<br />
| Pass<br />
|-<br />
|}<br />
<br />
=== Not currently tested ===<br />
<br />
* src_intxn_id search 1<br />
* omim search 1<br />
* digid search 1<br />
* audit against external database - Intact<br />
* audit against external database - MINT<br />
* audit against external database - BioGRID<br />
* iterations 1<br />
* use canonical expansion 1<br />
<br />
=== User interface notes ===<br />
<br />
Many search types such as UniProt_ID now lead to exact-only searches. The production of results should not be allowed for imprecise protein names, for example, since the user might have entered gene names, selected UniProt_ID by mistake and would not be aware of their mistake because their search returned results. Also, since the first few characters of UniProt_ID search terms may be shared by multiple proteins from different organisms, an inexact match would need to trigger the query helper.<br />
<br />
Generally, searches should provide predictable outcomes without resorting to the attribute browsers to discover which search terms produced which results. For example, AH2_ARATH which returns no results from an exact match search, should not encourage similar terms to be used for searching. Previously AH2_ARATH returned CAH2_ARATH. Imagine if the user accidentally had such a query term embedded in a long list. They would never detect this search error!<br />
<br />
Where the taxonomy field is set to <tt>Any</tt>, a warning will be given. It is envisaged that the user will most frequently be working with a single organism's proteins or would at least tolerate being reminded that potentially irrelevant proteins might be searched for due to naming coincidences.<br />
<br />
The iterations setting resets to 1 after a query, even one which led to the query helper being shown, where the query will be completed by trying the search again.<br />
<br />
The i.query attribute on nodes will collect queries as they are performed. Thus, nodes will appear blue in a graph even if the current query had no direct relationship with the node.<br />
<br />
Exporting lists of attribute values should be as simple as selecting the values in the attribute browser and opening a context menu and copying the selection. However, it is also possible (when the context menus don't work) to use the "File" -> "Export" -> "Node Attributes" menu entry and to choose "i.geneID", then saving and processing the saved file to get a list. This seems to be rather unreliable, however.<br />
<br />
== Export cases ==<br />
<br />
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"<br />
! align="center" style="background:#f0f0f0;" | Query/Search Type/Options<br />
! align="center" style="background:#f0f0f0;" | Export Type<br />
! align="center" style="background:#f0f0f0;" | Expected Result<br />
! align="center" style="background:#f0f0f0;" | Pass/Fail<br />
|-<br />
| valign="top" rowspan="2" | <pre>CXCR4<br />
<br />
geneSymbol<br />
<br />
Taxon id: Any<br />
Iterations: 0<br />
Create new view: no<br />
Use canonical expansion: no</pre><br />
| valign="top" | <pre>i.UniProt_Ac_TOP</pre><br />
| 1 node showing P61073<br />
| Pass<br />
|-<br />
| valign="top" | <pre>i.canonical_rog_TOP</pre><br />
| 1 node showing 107322<br />
| Pass<br />
|}<br />
<br />
== Currently untested areas ==<br />
<br />
* Preferences<br />
* iRefScape menu<br />
* Right-click menu<br />
* Node attributes<br />
* Edge attributes<br />
* Wizard<br />
* Installation<br />
* Help system<br />
* Windows and sessions<br />
* Loading from file<br />
<br />
==To be corrected==<br />
*Remove the non-proprietary flag/check for current data<br />
*Handle the neighbourhood completion when expanding network (do not use all the nodes)<br />
*show_inxc dynamic index behaviour change not working<br />
*Scaling GUI at low resolution, maximise button may get hidden<br />
*Path finding cancelling time<br />
*focus progress when path finding<br />
*Ending with collapsed node error<br />
*unselect all nodes before edge filtering<br />
<br />
==List of GeneIDs to test the new canonical expansion==<br />
<br />
Available in data version 8.4:<br />
<br />
*945577 http://www.ncbi.nlm.nih.gov/gene/?term=945577<br />
*947704 http://www.ncbi.nlm.nih.gov/gene/?term=947704<br />
*2765365 http://www.ncbi.nlm.nih.gov/gene/?term=2765365<br />
*944797 http://www.ncbi.nlm.nih.gov/gene/?term=944797<br />
*29924 http://www.ncbi.nlm.nih.gov/gene/?term=29924 <br />
*948517 http://www.ncbi.nlm.nih.gov/gene/?term=948517<br />
*3673 http://www.ncbi.nlm.nih.gov/gene/?term=3673 <br />
*946848 http://www.ncbi.nlm.nih.gov/gene/?term=946848<br />
*653361 http://www.ncbi.nlm.nih.gov/gene/?term=653361<br />
*5657 http://www.ncbi.nlm.nih.gov/gene/?term=5657<br />
<br />
== All iRefIndex Pages ==<br />
<br />
[[Category:iRefIndex]]</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefScape_Test_Cases_1.0&diff=3516iRefScape Test Cases 1.02011-06-22T13:56:37Z<p>Sabry: /* Invalid input tests */</p>
<hr />
<div>Last edited: {{REVISIONYEAR}}-{{padleft:{{REVISIONMONTH}}|2}}-{{REVISIONDAY2}}<br />
<br />
All tests have been performed against iRefIndex 8.1 data.<br />
<br />
==Search cases==<br />
<br />
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"<br />
! align="center" style="background:#f0f0f0;" | Query<br />
! align="center" style="background:#f0f0f0;" | Search Type<br />
! align="center" style="background:#f0f0f0;" | Options<br />
! align="center" style="background:#f0f0f0;" | Expected Result<br />
! align="center" style="background:#f0f0f0;" | Pass/Fail<br />
|-<br />
| rowspan="10" valign="top" | <pre>Q39009<br />
Q9ZNV8</pre><br />
| rowspan="12" valign="top" | <pre>UniProt_Ac</pre><br />
| rowspan="9" valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: no<br />
Use canonical expansion: no<br />
Add edges between neighbours: no</pre><br />
| 33 nodes, 94 edges. 2 queried nodes are blue (DMC_ARATH and AHP2_ARATH)<br />
| Pass<br />
|-<br />
| Node AHP2_ARATH linkout from i.RefSeq_Ac_TOP attribute (NP_189581) to Entrez Protein gives http://www.ncbi.nlm.nih.gov/protein/NP_189581?report=GenPept<br />
| Pass<br />
|-<br />
| i.taxid is 3702 and i.geneID is 822593<br />
| Pass<br />
|-<br />
| Node AHP2_ARATH linkout from i.UniProt_Ac_TOP attribute (Q9ZNV8) to UniProt/KB beta gives http://www.uniprot.org/uniprot/Q9ZNV8<br />
| Pass<br />
|-<br />
| UniProt record agrees with iRefScape on iRefSeq_Ac_TOP (see "Sequence databases"), i.taxid, i.geneID (see "Genome annotation databases")<br />
| Pass<br />
|-<br />
| Two edges between query nodes are EBI-1555390, EBI-1555417<br />
| Pass<br />
|-<br />
| Linkouts for query node edges (i.src_intxn_id) to Intact ("Interaction databases") provide PubMed #17937504 which should match i.PMID, and an interaction detection method of "anti tag coip" which should match i.method_name<br />
| Pass<br />
|-<br />
| The molecule names are DMC1 and ATHP1 in IntAct and these names should be available under the i.interactor_alias node attribute<br />
| Pass<br />
|-<br />
| Both interactions should have http://wodaklab.org/iRefWeb/interaction/show/102203 as i.iRefWEB<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: no<br />
Use canonical expansion: no<br />
Add edges between neighbours: no</pre><br />
| 2 nodes, 3 edges; 2 queried nodes are blue (DMC_ARATH and AHP2_ARATH) and are connected by two edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Q39009-1<br />
Q9ZNV8-2</pre><br />
| rowspan="2" valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: no<br />
Use canonical expansion: no<br />
Add edges between neighbours: no</pre><br />
| Return the same results as for UniProtKB: the isoform information is ignored when searching<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Q39009.1<br />
Q9ZNV8.2</pre><br />
| Returns no results. Version information is not a valid annotation for UniProtKB.<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| rowspan="5" valign="top" | <pre>RefSeq_Ac</pre><br />
| rowspan="11" valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 11 nodes, 29 edges. i.RefSeq_Ac = NP_188928 was returned; edges returned include EBI-1555390, EBI-1555417 between DMC1_ARATH and AHP2_ARATH<br />
| Pass<br />
|-<br />
| <pre>NP_188928</pre><br />
| The same results are returned<br />
| Pass<br />
|-<br />
| <pre>NP_188928.567</pre><br />
| The same results are returned<br />
| Pass<br />
|-<br />
| <pre>188928</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| <pre>NP 188928</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>geneID</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>ipi</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>mass</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>rog</pre><br />
| No results are returned<br />
| Pass (''no error given, though'')<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH</pre><br />
| valign="top" rowspan="6" | <pre>UniProt_ID</pre><br />
| valign="top" rowspan="10" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 26 nodes, 67 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2 ARATH</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>ARATH</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AH2_ARATH</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH.2</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH</pre><br />
| valign="top" | <pre>geneID</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH</pre><br />
| valign="top" | <pre>ipi</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>821860<br />
822593</pre><br />
| valign="top" | <pre>geneID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 33 nodes and 94 edges. (Should return the same result as a UniProt_Ac query for Q39009 and Q9ZNV8.)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>821860</pre><br />
| valign="top" | <pre>geneID</pre><br />
| valign="top" rowspan="4"| <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 1 node<br />
| Pass<br />
|-<br />
| valign="top" | <pre>821860</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>821860</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>821860</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>1234</pre><br />
| valign="top" | <pre>geneID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 47 nodes and 158 edges<br />
| Pass<br />
|-<br />
| valign="top" | All geneIds from a search for <pre>1234</pre> (45 values producing 44 unique gene identifiers)<br />
| valign="top" | <pre>geneID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 80 nodes and 733 edges (upon last attempt)<br />
|<br />
|-<br />
| colspan="5" | '''Note:''' This test is made incredibly difficult by the apparently unreliability of the export function (what Paul is talking about here is the Cytoscape export,not the iRefScape export).<br />
|-<br />
| valign="top" | <pre>CXCR4</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 2 nodes<br />
| Pass<br />
|-<br />
| valign="top" | <pre>P61073-2</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| valign="top" rowspan="2" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 2 nodes (CXCR4 and CXCR4_HUMAN)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>P61073</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| 1 node (CXCR4_HUMAN)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>P61073-2</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| valign="top" rowspan="2" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
| 2 nodes (CXCR4 and CXCR4_HUMAN)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>P61073</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| 2 nodes (CXCR4 and CXCR4_HUMAN)<br />
| Pass<br />
|-<br />
| colspan="5" | '''Note:''' P61073-2 and P61073 are isoforms of CXCR4. Searching for P61073-2 actually results in the removal of the "-2" and a search for all isoforms, under the assumption that the user is unsure which isoform should be retrieved; as a result, all isoforms are returned, even though a specific isoform was requested. In contrast, the search without a "-" character results in just one protein with that exact name being returned.<br />
|-<br />
| valign="top" | <pre>CXCR</pre><br />
| valign="top" rowspan="4" | <pre>geneSymbol</pre><br />
| valign="top" rowspan="4" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>CXCR4</pre><br />
| rowspan="3"| 2 nodes with i.UniProt_Ac_TOP set to P61073 and P61073-2<br />
| Pass<br />
|-<br />
| valign="top" | <pre>cxcR4</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>CXC<br />
CXCR<br />
CXCR4</pre><br />
| Pass<br />
|-<br />
| colspan="5" | '''Note:''' no indication is given that CXC and CXCR failed to provide matches when the successfully used CXCR4 term is present. Maybe some feedback could be given about this.<br />
|-<br />
| valign="top" | <pre>CXCR5</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| valign="top" rowspan="3" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 3 nodes<br />
| Pass<br />
|-<br />
| valign="top" | <pre>CXCR5</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>PTK2</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| 6 nodes (involving 5 taxons)<br />
| Pass<br />
|-<br />
| valign="top" rowspan="3" | <pre>RPB1</pre><br />
| valign="top" rowspan="3" | <pre>geneSymbol</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 1 node (RPB1_SCHPO)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Taxon id: 4932<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| No results returned (even though an alias for yeast RPO21, gene identifier 851415, is RPB1, this search only searches on official gene symbols from Entrez<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Taxon id: 9606<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| No results returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>5366033</pre><br />
| valign="top" | <pre>rog</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: no<br />
Use canonical expansion: no</pre><br />
| 2 nodes (POL_HV1H2 and POL_HV1B1 interacting with it)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>IPI00543858<br />
IPI00517160</pre><br />
| valign="top" rowspan="4" | <pre>ipi</pre><br />
| valign="top" rowspan="4" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: no<br />
Use canonical expansion: no</pre><br />
| rowspan="3" | 33 nodes, 94 edges. 2 queried nodes are blue (DMC_ARATH and AHP2_ARATH)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>IPI00543858.1<br />
IPI00517160.1</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>00543858<br />
00517160</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>00543858<br />
0051716</pre><br />
| 33 nodes, 94 edges, but only after IPI00517160 has been chosen from the query helper<br />
| Pass<br />
|-<br />
| colspan="5" | '''Note:''' the transfer of the search term from the query helper and the augmentation of results from the term isn't particularly easy to accomplish, or it isn't obvious how to accomplish this successfully, because the iRefScape panel is hidden in the main window (a Cytoscape bug which appears to switch the visible panel all the time) and because a new search is required (without a new view being created, which is potentially how the original search might be set up).<br />
|-<br />
| valign="top" | <pre>IPI</pre><br />
| valign="top" rowspan="2" | <pre>ipi</pre><br />
| valign="top" rowspan="2" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: no<br />
Use canonical expansion: no</pre><br />
| Initiates query helper<br />
| Pass<br />
|-<br />
| valign="top" | <pre>IPI00543858</pre><br />
| 26 nodes, 67 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>72854<-->72866</pre><br />
| valign="top" | <pre>mass</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| The query helper is shown. Upon transferring the 4 suggestions into the query box and searching again, 5 nodes are retrieved.<br />
| Pass<br />
|-<br />
| colspan="5" | '''Note:''' the nodes are not laid out in a nice way, probably because no edges connect them.<br />
|-<br />
| valign="top" | <pre>72854 kda</pre><br />
| valign="top" | <pre>mass</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>72854<-->72856 kda</pre><br />
| valign="top" | <pre>mass</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| Query helper with 3 possible results<br />
| Pass<br />
|-<br />
| valign="top" | <pre>11401546</pre><br />
| valign="top" rowspan="12" | <pre>PMID</pre><br />
| valign="top" rowspan="12" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 4 nodes and 7 edges are returned. Three edges have PMID 11401546 and these involve the 4 nodes shown. All other edges (from different PMIDs) involve these proteins.<br />
|<br />
|-<br />
| valign="top" | <pre>11401546.1</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>1140154</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>SPTAN1</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>11401546<br />
SPTAN1</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10551855<br />
11401546</pre><br />
| 6 nodes and 27 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10551855|11401546</pre><br />
| 6 nodes and 27 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10551855| 11401546</pre><br />
| 6 nodes and 27 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10551855 | 11401546</pre><br />
| 6 nodes and 27 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10551855 [tab] 11401546</pre><br />
| 6 nodes and 27 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10551855, 11401546</pre><br />
| 6 nodes and 27 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10551855 11401546</pre><br />
| No results are returned (since space-delimited queries are not supported)<br />
| Pass<br />
|-<br />
| colspan="5" | The following example searches are listed in the [[README_Cytoscape_plugin_0.8x#Using_the_Search_Panel|Using the Search Panel]] documentation.<br />
|-<br />
| valign="top" | <pre>Q7KSF4</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
| 69 nodes, 213 edges, with the 4 query nodes having i.query = Q7KSF4, one of the query nodes having i.order = 0 (Q7KSF4_DROME) and the others having i.order = 10 (as canonical group members)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Q7KSF4</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 1 node (Q7KSF4_DROME) verifying the attributes in the previous search<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_996224</pre><br />
| valign="top" | <pre>RefSeq_Ac</pre><br />
| valign="top" rowspan="3" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
| rowspan="2" | 69 nodes, 213 edges (same as the above query for Q7KSF4)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Q7KSF4_DROME</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>42066</pre><br />
| valign="top" | <pre>geneID</pre><br />
| rowspan="3" | 69 nodes, 213 edges, with the 4 query nodes having i.order = 0 since all also have i.geneID = 42066<br />
| Pass<br />
|-<br />
| valign="top" | <pre>42066</pre><br />
| valign="top" | <pre>geneID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>cher</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| valign="top" rowspan="4" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>72854<-->72866</pre><br />
| valign="top" | <pre>mass</pre><br />
| 44 nodes, 140 edges, with 8 query nodes, 5 of which with i.mass in (72854, 72855, 72856, 72861) having i.order = 0 and the remaining 3 query nodes with i.mass outside the given range having i.order = 10<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10121899</pre><br />
| valign="top" | <pre>rog</pre><br />
| 69 nodes, 213 edges (same as the above query for Q7KSF4), but with one of the query nodes having i.order = 0 and i.query = 10121899 and the remaining 3 query nodes having i.order = 10<br />
| Pass<br />
|-<br />
| valign="top" | <pre>14605208</pre><br />
| valign="top" | <pre>PMID</pre><br />
| rowspan="3" | 929 nodes and 1605 edges returned all with PMID of 14605208<br />
|<br />
|-<br />
| valign="top" | <pre>14605208</pre><br />
| valign="top" | <pre>PMID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
|<br />
|-<br />
| valign="top" | <pre>14605208</pre><br />
| valign="top" | <pre>PMID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
|<br />
|-<br />
| valign="top" | <pre>47513</pre><br />
| valign="top" | <pre>src_intxn_id</pre><br />
| valign="top" rowspan="7" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
| 2 nodes and 1 edge returned (one query node, Q7KSF4_DROME)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>EBI-212627</pre><br />
| valign="top" | <pre>src_intxn_id</pre><br />
| 2 nodes and 5 edges returned (from bind, dip, intact, mint and BIND_Translation), with 2 query nodes (CRBN_DROME and Q9W279_DROME)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>147805</pre><br />
| valign="top" | <pre>src_intxn_id</pre><br />
| Returns 4 nodes and 4 interactions because the BIND/BIND_Translation and BioGRID interaction identifier spaces overlap (so 147805 refers to completely different interactions in different databases)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>227650</pre><br />
| valign="top" | <pre>omim</pre><br />
| 96 nodes (including 18 complex nodes) and 498 edges returned, with the query node having i.geneID = 2175 and i.digid = 460<br />
| Pass<br />
|-<br />
| valign="top" | <pre>449</pre><br />
| valign="top" | <pre>digid</pre><br />
| 321 nodes and 1010 edges returned, with the 3 query nodes having i.omim = 612219<br />
| Pass<br />
|-<br />
| valign="top" | <pre>460</pre><br />
| valign="top" | <pre>digid</pre><br />
| 668 nodes and 17554 edges returned, with the 16 query nodes having i.digid = 460<br />
| Pass<br />
|-<br />
| valign="top" | <pre>fanconi</pre><br />
| valign="top" | <pre>dig_title</pre><br />
| ''Query helper invoked, now the dig_title is a non-exact match''<br />
| Pass <br />
|}<br />
<br />
=== Invalid input tests ===<br />
<br />
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"<br />
! align="center" style="background:#f0f0f0;" | Query<br />
! align="center" style="background:#f0f0f0;" | Search Type<br />
! align="center" style="background:#f0f0f0;" | Options<br />
! align="center" style="background:#f0f0f0;" | Expected Result<br />
! align="center" style="background:#f0f0f0;" | Pass/Fail<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>RefSeq_Ac</pre><br />
|<br />
| No results are returned<br />
|Pass<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
|<br />
| No results are returned<br />
|Pass<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
|<br />
| No results are returned<br />
|Pass<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>geneID</pre><br />
|<br />
| No results are returned<br />
|Pass<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>mass</pre><br />
|<br />
| No results are returned<br />
|Pass<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>pmid</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>23</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
|<br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>-1</pre><br />
| valign="top" | <pre>mass</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>-1</pre><br />
| valign="top" | <pre>pmid</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>0000</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>00001</pre><br />
| valign="top" | <pre>geneID</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>12345</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>abcd</pre><br />
| valign="top" | <pre>ipi</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>abcde</pre><br />
| valign="top" | <pre>RefSeq_Ac</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>abcde</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>abcde</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>abcde</pre><br />
| valign="top" | <pre>geneID</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>abcdes</pre><br />
| valign="top" | <pre>geneID</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>MW</pre><br />
| valign="top" | <pre>mass</pre><br />
|<br />
| No results are returned<br />
|<br />
|}<br />
<br />
=== Not currently tested ===<br />
<br />
* src_intxn_id search 1<br />
* omim search 1<br />
* digid search 1<br />
* audit against external database - Intact<br />
* audit against external database - MINT<br />
* audit against external database - BioGRID<br />
* iterations 1<br />
* use canonical expansion 1<br />
<br />
=== User interface notes ===<br />
<br />
Many search types such as UniProt_ID now lead to exact-only searches. The production of results should not be allowed for imprecise protein names, for example, since the user might have entered gene names, selected UniProt_ID by mistake and would not be aware of their mistake because their search returned results. Also, since the first few characters of UniProt_ID search terms may be shared by multiple proteins from different organisms, an inexact match would need to trigger the query helper.<br />
<br />
Generally, searches should provide predictable outcomes without resorting to the attribute browsers to discover which search terms produced which results. For example, AH2_ARATH which returns no results from an exact match search, should not encourage similar terms to be used for searching. Previously AH2_ARATH returned CAH2_ARATH. Imagine if the user accidentally had such a query term embedded in a long list. They would never detect this search error!<br />
<br />
Where the taxonomy field is set to <tt>Any</tt>, a warning will be given. It is envisaged that the user will most frequently be working with a single organism's proteins or would at least tolerate being reminded that potentially irrelevant proteins might be searched for due to naming coincidences.<br />
<br />
The iterations setting resets to 1 after a query, even one which led to the query helper being shown, where the query will be completed by trying the search again.<br />
<br />
The i.query attribute on nodes will collect queries as they are performed. Thus, nodes will appear blue in a graph even if the current query had no direct relationship with the node.<br />
<br />
Exporting lists of attribute values should be as simple as selecting the values in the attribute browser and opening a context menu and copying the selection. However, it is also possible (when the context menus don't work) to use the "File" -> "Export" -> "Node Attributes" menu entry and to choose "i.geneID", then saving and processing the saved file to get a list. This seems to be rather unreliable, however.<br />
<br />
== Export cases ==<br />
<br />
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"<br />
! align="center" style="background:#f0f0f0;" | Query/Search Type/Options<br />
! align="center" style="background:#f0f0f0;" | Export Type<br />
! align="center" style="background:#f0f0f0;" | Expected Result<br />
! align="center" style="background:#f0f0f0;" | Pass/Fail<br />
|-<br />
| valign="top" rowspan="2" | <pre>CXCR4<br />
<br />
geneSymbol<br />
<br />
Taxon id: Any<br />
Iterations: 0<br />
Create new view: no<br />
Use canonical expansion: no</pre><br />
| valign="top" | <pre>i.UniProt_Ac_TOP</pre><br />
| 1 node showing P61073<br />
| Pass<br />
|-<br />
| valign="top" | <pre>i.canonical_rog_TOP</pre><br />
| 1 node showing 107322<br />
| Pass<br />
|}<br />
<br />
== Currently untested areas ==<br />
<br />
* Preferences<br />
* iRefScape menu<br />
* Right-click menu<br />
* Node attributes<br />
* Edge attributes<br />
* Wizard<br />
* Installation<br />
* Help system<br />
* Windows and sessions<br />
* Loading from file<br />
<br />
==To be corrected==<br />
*Remove the non-proprietary flag/check for current data<br />
*Handle the neighbourhood completion when expanding network (do not use all the nodes)<br />
*show_inxc dynamic index behaviour change not working<br />
*Scaling GUI at low resolution, maximise button may get hidden<br />
*Path finding cancelling time<br />
*focus progress when path finding<br />
*Ending with collapsed node error<br />
*unselect all nodes before edge filtering<br />
<br />
==List of GeneIDs to test the new canonical expansion==<br />
<br />
Available in data version 8.4:<br />
<br />
*945577 http://www.ncbi.nlm.nih.gov/gene/?term=945577<br />
*947704 http://www.ncbi.nlm.nih.gov/gene/?term=947704<br />
*2765365 http://www.ncbi.nlm.nih.gov/gene/?term=2765365<br />
*944797 http://www.ncbi.nlm.nih.gov/gene/?term=944797<br />
*29924 http://www.ncbi.nlm.nih.gov/gene/?term=29924 <br />
*948517 http://www.ncbi.nlm.nih.gov/gene/?term=948517<br />
*3673 http://www.ncbi.nlm.nih.gov/gene/?term=3673 <br />
*946848 http://www.ncbi.nlm.nih.gov/gene/?term=946848<br />
*653361 http://www.ncbi.nlm.nih.gov/gene/?term=653361<br />
*5657 http://www.ncbi.nlm.nih.gov/gene/?term=5657<br />
<br />
== All iRefIndex Pages ==<br />
<br />
[[Category:iRefIndex]]</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefScape_Test_Cases_1.0&diff=3515iRefScape Test Cases 1.02011-06-22T12:06:48Z<p>Sabry: /* Search cases */</p>
<hr />
<div>Last edited: {{REVISIONYEAR}}-{{padleft:{{REVISIONMONTH}}|2}}-{{REVISIONDAY2}}<br />
<br />
All tests have been performed against iRefIndex 8.1 data.<br />
<br />
==Search cases==<br />
<br />
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"<br />
! align="center" style="background:#f0f0f0;" | Query<br />
! align="center" style="background:#f0f0f0;" | Search Type<br />
! align="center" style="background:#f0f0f0;" | Options<br />
! align="center" style="background:#f0f0f0;" | Expected Result<br />
! align="center" style="background:#f0f0f0;" | Pass/Fail<br />
|-<br />
| rowspan="10" valign="top" | <pre>Q39009<br />
Q9ZNV8</pre><br />
| rowspan="12" valign="top" | <pre>UniProt_Ac</pre><br />
| rowspan="9" valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: no<br />
Use canonical expansion: no<br />
Add edges between neighbours: no</pre><br />
| 33 nodes, 94 edges. 2 queried nodes are blue (DMC_ARATH and AHP2_ARATH)<br />
| Pass<br />
|-<br />
| Node AHP2_ARATH linkout from i.RefSeq_Ac_TOP attribute (NP_189581) to Entrez Protein gives http://www.ncbi.nlm.nih.gov/protein/NP_189581?report=GenPept<br />
| Pass<br />
|-<br />
| i.taxid is 3702 and i.geneID is 822593<br />
| Pass<br />
|-<br />
| Node AHP2_ARATH linkout from i.UniProt_Ac_TOP attribute (Q9ZNV8) to UniProt/KB beta gives http://www.uniprot.org/uniprot/Q9ZNV8<br />
| Pass<br />
|-<br />
| UniProt record agrees with iRefScape on iRefSeq_Ac_TOP (see "Sequence databases"), i.taxid, i.geneID (see "Genome annotation databases")<br />
| Pass<br />
|-<br />
| Two edges between query nodes are EBI-1555390, EBI-1555417<br />
| Pass<br />
|-<br />
| Linkouts for query node edges (i.src_intxn_id) to Intact ("Interaction databases") provide PubMed #17937504 which should match i.PMID, and an interaction detection method of "anti tag coip" which should match i.method_name<br />
| Pass<br />
|-<br />
| The molecule names are DMC1 and ATHP1 in IntAct and these names should be available under the i.interactor_alias node attribute<br />
| Pass<br />
|-<br />
| Both interactions should have http://wodaklab.org/iRefWeb/interaction/show/102203 as i.iRefWEB<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: no<br />
Use canonical expansion: no<br />
Add edges between neighbours: no</pre><br />
| 2 nodes, 3 edges; 2 queried nodes are blue (DMC_ARATH and AHP2_ARATH) and are connected by two edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Q39009-1<br />
Q9ZNV8-2</pre><br />
| rowspan="2" valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: no<br />
Use canonical expansion: no<br />
Add edges between neighbours: no</pre><br />
| Return the same results as for UniProtKB: the isoform information is ignored when searching<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Q39009.1<br />
Q9ZNV8.2</pre><br />
| Returns no results. Version information is not a valid annotation for UniProtKB.<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| rowspan="5" valign="top" | <pre>RefSeq_Ac</pre><br />
| rowspan="11" valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 11 nodes, 29 edges. i.RefSeq_Ac = NP_188928 was returned; edges returned include EBI-1555390, EBI-1555417 between DMC1_ARATH and AHP2_ARATH<br />
| Pass<br />
|-<br />
| <pre>NP_188928</pre><br />
| The same results are returned<br />
| Pass<br />
|-<br />
| <pre>NP_188928.567</pre><br />
| The same results are returned<br />
| Pass<br />
|-<br />
| <pre>188928</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| <pre>NP 188928</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>geneID</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>ipi</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>mass</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>rog</pre><br />
| No results are returned<br />
| Pass (''no error given, though'')<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH</pre><br />
| valign="top" rowspan="6" | <pre>UniProt_ID</pre><br />
| valign="top" rowspan="10" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 26 nodes, 67 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2 ARATH</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>ARATH</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AH2_ARATH</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH.2</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH</pre><br />
| valign="top" | <pre>geneID</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH</pre><br />
| valign="top" | <pre>ipi</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>821860<br />
822593</pre><br />
| valign="top" | <pre>geneID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 33 nodes and 94 edges. (Should return the same result as a UniProt_Ac query for Q39009 and Q9ZNV8.)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>821860</pre><br />
| valign="top" | <pre>geneID</pre><br />
| valign="top" rowspan="4"| <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 1 node<br />
| Pass<br />
|-<br />
| valign="top" | <pre>821860</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>821860</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>821860</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>1234</pre><br />
| valign="top" | <pre>geneID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 47 nodes and 158 edges<br />
| Pass<br />
|-<br />
| valign="top" | All geneIds from a search for <pre>1234</pre> (45 values producing 44 unique gene identifiers)<br />
| valign="top" | <pre>geneID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 80 nodes and 733 edges (upon last attempt)<br />
|<br />
|-<br />
| colspan="5" | '''Note:''' This test is made incredibly difficult by the apparently unreliability of the export function (what Paul is talking about here is the Cytoscape export,not the iRefScape export).<br />
|-<br />
| valign="top" | <pre>CXCR4</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 2 nodes<br />
| Pass<br />
|-<br />
| valign="top" | <pre>P61073-2</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| valign="top" rowspan="2" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 2 nodes (CXCR4 and CXCR4_HUMAN)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>P61073</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| 1 node (CXCR4_HUMAN)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>P61073-2</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| valign="top" rowspan="2" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
| 2 nodes (CXCR4 and CXCR4_HUMAN)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>P61073</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| 2 nodes (CXCR4 and CXCR4_HUMAN)<br />
| Pass<br />
|-<br />
| colspan="5" | '''Note:''' P61073-2 and P61073 are isoforms of CXCR4. Searching for P61073-2 actually results in the removal of the "-2" and a search for all isoforms, under the assumption that the user is unsure which isoform should be retrieved; as a result, all isoforms are returned, even though a specific isoform was requested. In contrast, the search without a "-" character results in just one protein with that exact name being returned.<br />
|-<br />
| valign="top" | <pre>CXCR</pre><br />
| valign="top" rowspan="4" | <pre>geneSymbol</pre><br />
| valign="top" rowspan="4" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>CXCR4</pre><br />
| rowspan="3"| 2 nodes with i.UniProt_Ac_TOP set to P61073 and P61073-2<br />
| Pass<br />
|-<br />
| valign="top" | <pre>cxcR4</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>CXC<br />
CXCR<br />
CXCR4</pre><br />
| Pass<br />
|-<br />
| colspan="5" | '''Note:''' no indication is given that CXC and CXCR failed to provide matches when the successfully used CXCR4 term is present. Maybe some feedback could be given about this.<br />
|-<br />
| valign="top" | <pre>CXCR5</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| valign="top" rowspan="3" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 3 nodes<br />
| Pass<br />
|-<br />
| valign="top" | <pre>CXCR5</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>PTK2</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| 6 nodes (involving 5 taxons)<br />
| Pass<br />
|-<br />
| valign="top" rowspan="3" | <pre>RPB1</pre><br />
| valign="top" rowspan="3" | <pre>geneSymbol</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 1 node (RPB1_SCHPO)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Taxon id: 4932<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| No results returned (even though an alias for yeast RPO21, gene identifier 851415, is RPB1, this search only searches on official gene symbols from Entrez<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Taxon id: 9606<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| No results returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>5366033</pre><br />
| valign="top" | <pre>rog</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: no<br />
Use canonical expansion: no</pre><br />
| 2 nodes (POL_HV1H2 and POL_HV1B1 interacting with it)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>IPI00543858<br />
IPI00517160</pre><br />
| valign="top" rowspan="4" | <pre>ipi</pre><br />
| valign="top" rowspan="4" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: no<br />
Use canonical expansion: no</pre><br />
| rowspan="3" | 33 nodes, 94 edges. 2 queried nodes are blue (DMC_ARATH and AHP2_ARATH)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>IPI00543858.1<br />
IPI00517160.1</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>00543858<br />
00517160</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>00543858<br />
0051716</pre><br />
| 33 nodes, 94 edges, but only after IPI00517160 has been chosen from the query helper<br />
| Pass<br />
|-<br />
| colspan="5" | '''Note:''' the transfer of the search term from the query helper and the augmentation of results from the term isn't particularly easy to accomplish, or it isn't obvious how to accomplish this successfully, because the iRefScape panel is hidden in the main window (a Cytoscape bug which appears to switch the visible panel all the time) and because a new search is required (without a new view being created, which is potentially how the original search might be set up).<br />
|-<br />
| valign="top" | <pre>IPI</pre><br />
| valign="top" rowspan="2" | <pre>ipi</pre><br />
| valign="top" rowspan="2" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: no<br />
Use canonical expansion: no</pre><br />
| Initiates query helper<br />
| Pass<br />
|-<br />
| valign="top" | <pre>IPI00543858</pre><br />
| 26 nodes, 67 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>72854<-->72866</pre><br />
| valign="top" | <pre>mass</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| The query helper is shown. Upon transferring the 4 suggestions into the query box and searching again, 5 nodes are retrieved.<br />
| Pass<br />
|-<br />
| colspan="5" | '''Note:''' the nodes are not laid out in a nice way, probably because no edges connect them.<br />
|-<br />
| valign="top" | <pre>72854 kda</pre><br />
| valign="top" | <pre>mass</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>72854<-->72856 kda</pre><br />
| valign="top" | <pre>mass</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| Query helper with 3 possible results<br />
| Pass<br />
|-<br />
| valign="top" | <pre>11401546</pre><br />
| valign="top" rowspan="12" | <pre>PMID</pre><br />
| valign="top" rowspan="12" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 4 nodes and 7 edges are returned. Three edges have PMID 11401546 and these involve the 4 nodes shown. All other edges (from different PMIDs) involve these proteins.<br />
|<br />
|-<br />
| valign="top" | <pre>11401546.1</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>1140154</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>SPTAN1</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>11401546<br />
SPTAN1</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10551855<br />
11401546</pre><br />
| 6 nodes and 27 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10551855|11401546</pre><br />
| 6 nodes and 27 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10551855| 11401546</pre><br />
| 6 nodes and 27 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10551855 | 11401546</pre><br />
| 6 nodes and 27 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10551855 [tab] 11401546</pre><br />
| 6 nodes and 27 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10551855, 11401546</pre><br />
| 6 nodes and 27 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10551855 11401546</pre><br />
| No results are returned (since space-delimited queries are not supported)<br />
| Pass<br />
|-<br />
| colspan="5" | The following example searches are listed in the [[README_Cytoscape_plugin_0.8x#Using_the_Search_Panel|Using the Search Panel]] documentation.<br />
|-<br />
| valign="top" | <pre>Q7KSF4</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
| 69 nodes, 213 edges, with the 4 query nodes having i.query = Q7KSF4, one of the query nodes having i.order = 0 (Q7KSF4_DROME) and the others having i.order = 10 (as canonical group members)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Q7KSF4</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 1 node (Q7KSF4_DROME) verifying the attributes in the previous search<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_996224</pre><br />
| valign="top" | <pre>RefSeq_Ac</pre><br />
| valign="top" rowspan="3" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
| rowspan="2" | 69 nodes, 213 edges (same as the above query for Q7KSF4)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Q7KSF4_DROME</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>42066</pre><br />
| valign="top" | <pre>geneID</pre><br />
| rowspan="3" | 69 nodes, 213 edges, with the 4 query nodes having i.order = 0 since all also have i.geneID = 42066<br />
| Pass<br />
|-<br />
| valign="top" | <pre>42066</pre><br />
| valign="top" | <pre>geneID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>cher</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| valign="top" rowspan="4" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>72854<-->72866</pre><br />
| valign="top" | <pre>mass</pre><br />
| 44 nodes, 140 edges, with 8 query nodes, 5 of which with i.mass in (72854, 72855, 72856, 72861) having i.order = 0 and the remaining 3 query nodes with i.mass outside the given range having i.order = 10<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10121899</pre><br />
| valign="top" | <pre>rog</pre><br />
| 69 nodes, 213 edges (same as the above query for Q7KSF4), but with one of the query nodes having i.order = 0 and i.query = 10121899 and the remaining 3 query nodes having i.order = 10<br />
| Pass<br />
|-<br />
| valign="top" | <pre>14605208</pre><br />
| valign="top" | <pre>PMID</pre><br />
| rowspan="3" | 929 nodes and 1605 edges returned all with PMID of 14605208<br />
|<br />
|-<br />
| valign="top" | <pre>14605208</pre><br />
| valign="top" | <pre>PMID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
|<br />
|-<br />
| valign="top" | <pre>14605208</pre><br />
| valign="top" | <pre>PMID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
|<br />
|-<br />
| valign="top" | <pre>47513</pre><br />
| valign="top" | <pre>src_intxn_id</pre><br />
| valign="top" rowspan="7" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
| 2 nodes and 1 edge returned (one query node, Q7KSF4_DROME)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>EBI-212627</pre><br />
| valign="top" | <pre>src_intxn_id</pre><br />
| 2 nodes and 5 edges returned (from bind, dip, intact, mint and BIND_Translation), with 2 query nodes (CRBN_DROME and Q9W279_DROME)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>147805</pre><br />
| valign="top" | <pre>src_intxn_id</pre><br />
| Returns 4 nodes and 4 interactions because the BIND/BIND_Translation and BioGRID interaction identifier spaces overlap (so 147805 refers to completely different interactions in different databases)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>227650</pre><br />
| valign="top" | <pre>omim</pre><br />
| 96 nodes (including 18 complex nodes) and 498 edges returned, with the query node having i.geneID = 2175 and i.digid = 460<br />
| Pass<br />
|-<br />
| valign="top" | <pre>449</pre><br />
| valign="top" | <pre>digid</pre><br />
| 321 nodes and 1010 edges returned, with the 3 query nodes having i.omim = 612219<br />
| Pass<br />
|-<br />
| valign="top" | <pre>460</pre><br />
| valign="top" | <pre>digid</pre><br />
| 668 nodes and 17554 edges returned, with the 16 query nodes having i.digid = 460<br />
| Pass<br />
|-<br />
| valign="top" | <pre>fanconi</pre><br />
| valign="top" | <pre>dig_title</pre><br />
| ''Query helper invoked, now the dig_title is a non-exact match''<br />
| Pass <br />
|}<br />
<br />
=== Invalid input tests ===<br />
<br />
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"<br />
! align="center" style="background:#f0f0f0;" | Query<br />
! align="center" style="background:#f0f0f0;" | Search Type<br />
! align="center" style="background:#f0f0f0;" | Options<br />
! align="center" style="background:#f0f0f0;" | Expected Result<br />
! align="center" style="background:#f0f0f0;" | Pass/Fail<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>RefSeq_Ac</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>geneID</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>mass</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>pmid</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>23</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
|<br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>-1</pre><br />
| valign="top" | <pre>mass</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>-1</pre><br />
| valign="top" | <pre>pmid</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>0000</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>00001</pre><br />
| valign="top" | <pre>geneID</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>12345</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>abcd</pre><br />
| valign="top" | <pre>ipi</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>abcde</pre><br />
| valign="top" | <pre>RefSeq_Ac</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>abcde</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>abcde</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>abcde</pre><br />
| valign="top" | <pre>geneID</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>abcdes</pre><br />
| valign="top" | <pre>geneID</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>MW</pre><br />
| valign="top" | <pre>mass</pre><br />
|<br />
| No results are returned<br />
|<br />
|}<br />
<br />
=== Not currently tested ===<br />
<br />
* src_intxn_id search 1<br />
* omim search 1<br />
* digid search 1<br />
* audit against external database - Intact<br />
* audit against external database - MINT<br />
* audit against external database - BioGRID<br />
* iterations 1<br />
* use canonical expansion 1<br />
<br />
=== User interface notes ===<br />
<br />
Many search types such as UniProt_ID now lead to exact-only searches. The production of results should not be allowed for imprecise protein names, for example, since the user might have entered gene names, selected UniProt_ID by mistake and would not be aware of their mistake because their search returned results. Also, since the first few characters of UniProt_ID search terms may be shared by multiple proteins from different organisms, an inexact match would need to trigger the query helper.<br />
<br />
Generally, searches should provide predictable outcomes without resorting to the attribute browsers to discover which search terms produced which results. For example, AH2_ARATH which returns no results from an exact match search, should not encourage similar terms to be used for searching. Previously AH2_ARATH returned CAH2_ARATH. Imagine if the user accidentally had such a query term embedded in a long list. They would never detect this search error!<br />
<br />
Where the taxonomy field is set to <tt>Any</tt>, a warning will be given. It is envisaged that the user will most frequently be working with a single organism's proteins or would at least tolerate being reminded that potentially irrelevant proteins might be searched for due to naming coincidences.<br />
<br />
The iterations setting resets to 1 after a query, even one which led to the query helper being shown, where the query will be completed by trying the search again.<br />
<br />
The i.query attribute on nodes will collect queries as they are performed. Thus, nodes will appear blue in a graph even if the current query had no direct relationship with the node.<br />
<br />
Exporting lists of attribute values should be as simple as selecting the values in the attribute browser and opening a context menu and copying the selection. However, it is also possible (when the context menus don't work) to use the "File" -> "Export" -> "Node Attributes" menu entry and to choose "i.geneID", then saving and processing the saved file to get a list. This seems to be rather unreliable, however.<br />
<br />
== Export cases ==<br />
<br />
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"<br />
! align="center" style="background:#f0f0f0;" | Query/Search Type/Options<br />
! align="center" style="background:#f0f0f0;" | Export Type<br />
! align="center" style="background:#f0f0f0;" | Expected Result<br />
! align="center" style="background:#f0f0f0;" | Pass/Fail<br />
|-<br />
| valign="top" rowspan="2" | <pre>CXCR4<br />
<br />
geneSymbol<br />
<br />
Taxon id: Any<br />
Iterations: 0<br />
Create new view: no<br />
Use canonical expansion: no</pre><br />
| valign="top" | <pre>i.UniProt_Ac_TOP</pre><br />
| 1 node showing P61073<br />
| Pass<br />
|-<br />
| valign="top" | <pre>i.canonical_rog_TOP</pre><br />
| 1 node showing 107322<br />
| Pass<br />
|}<br />
<br />
== Currently untested areas ==<br />
<br />
* Preferences<br />
* iRefScape menu<br />
* Right-click menu<br />
* Node attributes<br />
* Edge attributes<br />
* Wizard<br />
* Installation<br />
* Help system<br />
* Windows and sessions<br />
* Loading from file<br />
<br />
==To be corrected==<br />
*Remove the non-proprietary flag/check for current data<br />
*Handle the neighbourhood completion when expanding network (do not use all the nodes)<br />
*show_inxc dynamic index behaviour change not working<br />
*Scaling GUI at low resolution, maximise button may get hidden<br />
*Path finding cancelling time<br />
*focus progress when path finding<br />
*Ending with collapsed node error<br />
*unselect all nodes before edge filtering<br />
<br />
==List of GeneIDs to test the new canonical expansion==<br />
<br />
Available in data version 8.4:<br />
<br />
*945577 http://www.ncbi.nlm.nih.gov/gene/?term=945577<br />
*947704 http://www.ncbi.nlm.nih.gov/gene/?term=947704<br />
*2765365 http://www.ncbi.nlm.nih.gov/gene/?term=2765365<br />
*944797 http://www.ncbi.nlm.nih.gov/gene/?term=944797<br />
*29924 http://www.ncbi.nlm.nih.gov/gene/?term=29924 <br />
*948517 http://www.ncbi.nlm.nih.gov/gene/?term=948517<br />
*3673 http://www.ncbi.nlm.nih.gov/gene/?term=3673 <br />
*946848 http://www.ncbi.nlm.nih.gov/gene/?term=946848<br />
*653361 http://www.ncbi.nlm.nih.gov/gene/?term=653361<br />
*5657 http://www.ncbi.nlm.nih.gov/gene/?term=5657<br />
<br />
== All iRefIndex Pages ==<br />
<br />
[[Category:iRefIndex]]</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefScape_Test_Cases_1.0&diff=3514iRefScape Test Cases 1.02011-06-22T12:02:01Z<p>Sabry: /* Search cases */</p>
<hr />
<div>Last edited: {{REVISIONYEAR}}-{{padleft:{{REVISIONMONTH}}|2}}-{{REVISIONDAY2}}<br />
<br />
All tests have been performed against iRefIndex 8.1 data.<br />
<br />
==Search cases==<br />
<br />
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"<br />
! align="center" style="background:#f0f0f0;" | Query<br />
! align="center" style="background:#f0f0f0;" | Search Type<br />
! align="center" style="background:#f0f0f0;" | Options<br />
! align="center" style="background:#f0f0f0;" | Expected Result<br />
! align="center" style="background:#f0f0f0;" | Pass/Fail<br />
|-<br />
| rowspan="10" valign="top" | <pre>Q39009<br />
Q9ZNV8</pre><br />
| rowspan="12" valign="top" | <pre>UniProt_Ac</pre><br />
| rowspan="9" valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: no<br />
Use canonical expansion: no<br />
Add edges between neighbours: no</pre><br />
| 33 nodes, 94 edges. 2 queried nodes are blue (DMC_ARATH and AHP2_ARATH)<br />
| Pass<br />
|-<br />
| Node AHP2_ARATH linkout from i.RefSeq_Ac_TOP attribute (NP_189581) to Entrez Protein gives http://www.ncbi.nlm.nih.gov/protein/NP_189581?report=GenPept<br />
| Pass<br />
|-<br />
| i.taxid is 3702 and i.geneID is 822593<br />
| Pass<br />
|-<br />
| Node AHP2_ARATH linkout from i.UniProt_Ac_TOP attribute (Q9ZNV8) to UniProt/KB beta gives http://www.uniprot.org/uniprot/Q9ZNV8<br />
| Pass<br />
|-<br />
| UniProt record agrees with iRefScape on iRefSeq_Ac_TOP (see "Sequence databases"), i.taxid, i.geneID (see "Genome annotation databases")<br />
| Pass<br />
|-<br />
| Two edges between query nodes are EBI-1555390, EBI-1555417<br />
| Pass<br />
|-<br />
| Linkouts for query node edges (i.src_intxn_id) to Intact ("Interaction databases") provide PubMed #17937504 which should match i.PMID, and an interaction detection method of "anti tag coip" which should match i.method_name<br />
| Pass<br />
|-<br />
| The molecule names are DMC1 and ATHP1 in IntAct and these names should be available under the i.interactor_alias node attribute<br />
| Pass<br />
|-<br />
| Both interactions should have http://wodaklab.org/iRefWeb/interaction/show/102203 as i.iRefWEB<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: no<br />
Use canonical expansion: no<br />
Add edges between neighbours: no</pre><br />
| 2 nodes, 3 edges; 2 queried nodes are blue (DMC_ARATH and AHP2_ARATH) and are connected by two edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Q39009-1<br />
Q9ZNV8-2</pre><br />
| rowspan="2" valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: no<br />
Use canonical expansion: no<br />
Add edges between neighbours: no</pre><br />
| Return the same results as for UniProtKB: the isoform information is ignored when searching<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Q39009.1<br />
Q9ZNV8.2</pre><br />
| Returns no results. Version information is not a valid annotation for UniProtKB.<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| rowspan="5" valign="top" | <pre>RefSeq_Ac</pre><br />
| rowspan="11" valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 11 nodes, 29 edges. i.RefSeq_Ac = NP_188928 was returned; edges returned include EBI-1555390, EBI-1555417 between DMC1_ARATH and AHP2_ARATH<br />
| Pass<br />
|-<br />
| <pre>NP_188928</pre><br />
| The same results are returned<br />
| Pass<br />
|-<br />
| <pre>NP_188928.567</pre><br />
| The same results are returned<br />
| Pass<br />
|-<br />
| <pre>188928</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| <pre>NP 188928</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>geneID</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>ipi</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>mass</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>rog</pre><br />
| No results are returned<br />
| Pass (''no error given, though'')<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH</pre><br />
| valign="top" rowspan="6" | <pre>UniProt_ID</pre><br />
| valign="top" rowspan="10" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 26 nodes, 67 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2 ARATH</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>ARATH</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AH2_ARATH</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH.2</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH</pre><br />
| valign="top" | <pre>geneID</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH</pre><br />
| valign="top" | <pre>ipi</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>821860<br />
822593</pre><br />
| valign="top" | <pre>geneID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 33 nodes and 94 edges. (Should return the same result as a UniProt_Ac query for Q39009 and Q9ZNV8.)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>821860</pre><br />
| valign="top" | <pre>geneID</pre><br />
| valign="top" rowspan="4"| <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 1 node<br />
| Pass<br />
|-<br />
| valign="top" | <pre>821860</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>821860</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>821860</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>1234</pre><br />
| valign="top" | <pre>geneID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 47 nodes and 158 edges<br />
| Pass<br />
|-<br />
| valign="top" | All geneIds from a search for <pre>1234</pre> (45 values producing 44 unique gene identifiers)<br />
| valign="top" | <pre>geneID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 80 nodes and 733 edges (upon last attempt)<br />
|<br />
|-<br />
| colspan="5" | '''Note:''' This test is made incredibly difficult by the apparently unreliability of the export function (what Paul is talking about here is the Cytoscape export,not the iRefScape export).<br />
|-<br />
| valign="top" | <pre>CXCR4</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 2 nodes<br />
| Pass<br />
|-<br />
| valign="top" | <pre>P61073-2</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| valign="top" rowspan="2" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 2 nodes (CXCR4 and CXCR4_HUMAN)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>P61073</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| 1 node (CXCR4_HUMAN)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>P61073-2</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| valign="top" rowspan="2" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
| 2 nodes (CXCR4 and CXCR4_HUMAN)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>P61073</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| 2 nodes (CXCR4 and CXCR4_HUMAN)<br />
| Pass<br />
|-<br />
| colspan="5" | '''Note:''' P61073-2 and P61073 are isoforms of CXCR4. Searching for P61073-2 actually results in the removal of the "-2" and a search for all isoforms, under the assumption that the user is unsure which isoform should be retrieved; as a result, all isoforms are returned, even though a specific isoform was requested. In contrast, the search without a "-" character results in just one protein with that exact name being returned.<br />
|-<br />
| valign="top" | <pre>CXCR</pre><br />
| valign="top" rowspan="4" | <pre>geneSymbol</pre><br />
| valign="top" rowspan="4" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>CXCR4</pre><br />
| rowspan="3"| 2 nodes with i.UniProt_Ac_TOP set to P61073 and P61073-2<br />
| Pass<br />
|-<br />
| valign="top" | <pre>cxcR4</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>CXC<br />
CXCR<br />
CXCR4</pre><br />
| Pass<br />
|-<br />
| colspan="5" | '''Note:''' no indication is given that CXC and CXCR failed to provide matches when the successfully used CXCR4 term is present. Maybe some feedback could be given about this.<br />
|-<br />
| valign="top" | <pre>CXCR5</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| valign="top" rowspan="3" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 3 nodes<br />
| Pass<br />
|-<br />
| valign="top" | <pre>CXCR5</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>PTK2</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| 6 nodes (involving 5 taxons)<br />
| Pass<br />
|-<br />
| valign="top" rowspan="3" | <pre>RPB1</pre><br />
| valign="top" rowspan="3" | <pre>geneSymbol</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 1 node (RPB1_SCHPO)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Taxon id: 4932<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| No results returned (even though an alias for yeast RPO21, gene identifier 851415, is RPB1, this search only searches on official gene symbols from Entrez<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Taxon id: 9606<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| No results returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>5366033</pre><br />
| valign="top" | <pre>rog</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: no<br />
Use canonical expansion: no</pre><br />
| 2 nodes (POL_HV1H2 and POL_HV1B1 interacting with it)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>IPI00543858<br />
IPI00517160</pre><br />
| valign="top" rowspan="4" | <pre>ipi</pre><br />
| valign="top" rowspan="4" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: no<br />
Use canonical expansion: no</pre><br />
| rowspan="3" | 33 nodes, 94 edges. 2 queried nodes are blue (DMC_ARATH and AHP2_ARATH)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>IPI00543858.1<br />
IPI00517160.1</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>00543858<br />
00517160</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>00543858<br />
0051716</pre><br />
| 33 nodes, 94 edges, but only after IPI00517160 has been chosen from the query helper<br />
| Pass<br />
|-<br />
| colspan="5" | '''Note:''' the transfer of the search term from the query helper and the augmentation of results from the term isn't particularly easy to accomplish, or it isn't obvious how to accomplish this successfully, because the iRefScape panel is hidden in the main window (a Cytoscape bug which appears to switch the visible panel all the time) and because a new search is required (without a new view being created, which is potentially how the original search might be set up).<br />
|-<br />
| valign="top" | <pre>IPI</pre><br />
| valign="top" rowspan="2" | <pre>ipi</pre><br />
| valign="top" rowspan="2" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: no<br />
Use canonical expansion: no</pre><br />
| Initiates query helper<br />
| Pass<br />
|-<br />
| valign="top" | <pre>IPI00543858</pre><br />
| 26 nodes, 67 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>72854<-->72866</pre><br />
| valign="top" | <pre>mass</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| The query helper is shown. Upon transferring the 4 suggestions into the query box and searching again, 5 nodes are retrieved.<br />
| Pass<br />
|-<br />
| colspan="5" | '''Note:''' the nodes are not laid out in a nice way, probably because no edges connect them.<br />
|-<br />
| valign="top" | <pre>72854 kda</pre><br />
| valign="top" | <pre>mass</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>72854<-->72856 kda</pre><br />
| valign="top" | <pre>mass</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| Query helper with 3 possible results<br />
| Pass<br />
|-<br />
| valign="top" | <pre>11401546</pre><br />
| valign="top" rowspan="12" | <pre>PMID</pre><br />
| valign="top" rowspan="12" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 4 nodes and 7 edges are returned. Three edges have PMID 11401546 and these involve the 4 nodes shown. All other edges (from different PMIDs) involve these proteins.<br />
|<br />
|-<br />
| valign="top" | <pre>11401546.1</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>1140154</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>SPTAN1</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>11401546<br />
SPTAN1</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10551855<br />
11401546</pre><br />
| 6 nodes and 27 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10551855|11401546</pre><br />
| 6 nodes and 27 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10551855| 11401546</pre><br />
| 6 nodes and 27 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10551855 | 11401546</pre><br />
| 6 nodes and 27 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10551855 [tab] 11401546</pre><br />
| 6 nodes and 27 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10551855, 11401546</pre><br />
| 6 nodes and 27 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10551855 11401546</pre><br />
| No results are returned (since space-delimited queries are not supported)<br />
| Pass<br />
|-<br />
| colspan="5" | The following example searches are listed in the [[README_Cytoscape_plugin_0.8x#Using_the_Search_Panel|Using the Search Panel]] documentation.<br />
|-<br />
| valign="top" | <pre>Q7KSF4</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
| 69 nodes, 213 edges, with the 4 query nodes having i.query = Q7KSF4, one of the query nodes having i.order = 0 (Q7KSF4_DROME) and the others having i.order = 10 (as canonical group members)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Q7KSF4</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 1 node (Q7KSF4_DROME) verifying the attributes in the previous search<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_996224</pre><br />
| valign="top" | <pre>RefSeq_Ac</pre><br />
| valign="top" rowspan="3" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
| rowspan="2" | 69 nodes, 213 edges (same as the above query for Q7KSF4)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Q7KSF4_DROME</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>42066</pre><br />
| valign="top" | <pre>geneID</pre><br />
| rowspan="3" | 69 nodes, 213 edges, with the 4 query nodes having i.order = 0 since all also have i.geneID = 42066<br />
| Pass<br />
|-<br />
| valign="top" | <pre>42066</pre><br />
| valign="top" | <pre>geneID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>cher</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| valign="top" rowspan="4" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>72854<-->72866</pre><br />
| valign="top" | <pre>mass</pre><br />
| 44 nodes, 140 edges, with 8 query nodes, 5 of which with i.mass in (72854, 72855, 72856, 72861) having i.order = 0 and the remaining 3 query nodes with i.mass outside the given range having i.order = 10<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10121899</pre><br />
| valign="top" | <pre>rog</pre><br />
| 69 nodes, 213 edges (same as the above query for Q7KSF4), but with one of the query nodes having i.order = 0 and i.query = 10121899 and the remaining 3 query nodes having i.order = 10<br />
| Pass<br />
|-<br />
| valign="top" | <pre>14605208</pre><br />
| valign="top" | <pre>PMID</pre><br />
| rowspan="3" | 929 nodes and 1605 edges returned all with PMID of 14605208<br />
|<br />
|-<br />
| valign="top" | <pre>14605208</pre><br />
| valign="top" | <pre>PMID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
|<br />
|-<br />
| valign="top" | <pre>14605208</pre><br />
| valign="top" | <pre>PMID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
|<br />
|-<br />
| valign="top" | <pre>47513</pre><br />
| valign="top" | <pre>src_intxn_id</pre><br />
| valign="top" rowspan="7" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
| 2 nodes and 1 edge returned (one query node, Q7KSF4_DROME)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>EBI-212627</pre><br />
| valign="top" | <pre>src_intxn_id</pre><br />
| 2 nodes and 5 edges returned (from bind, dip, intact, mint and BIND_Translation), with 2 query nodes (CRBN_DROME and Q9W279_DROME)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>147805</pre><br />
| valign="top" | <pre>src_intxn_id</pre><br />
| Returns 4 nodes and 4 interactions because the BIND/BIND_Translation and BioGRID interaction identifier spaces overlap (so 147805 refers to completely different interactions in different databases)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>227650</pre><br />
| valign="top" | <pre>omim</pre><br />
| 96 nodes (including 18 complex nodes) and 498 edges returned, with the query node having i.geneID = 2175 and i.digid = 460<br />
| Pass<br />
|-<br />
| valign="top" | <pre>449</pre><br />
| valign="top" | <pre>digid</pre><br />
| 321 nodes and 1010 edges returned, with the 3 query nodes having i.omim = 612219<br />
| Pass<br />
|-<br />
| valign="top" | <pre>460</pre><br />
| valign="top" | <pre>digid</pre><br />
| 668 nodes and 17554 edges returned, with the 16 query nodes having i.digid = 460<br />
| Pass<br />
|-<br />
| valign="top" | <pre>fanconi</pre><br />
| valign="top" | <pre>dig_title</pre><br />
| ''Presumably similar results to the previous query''<br />
| Fail (''iRefScape insists on an exact match and doesn't find anything'')<br />
|}<br />
<br />
=== Invalid input tests ===<br />
<br />
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"<br />
! align="center" style="background:#f0f0f0;" | Query<br />
! align="center" style="background:#f0f0f0;" | Search Type<br />
! align="center" style="background:#f0f0f0;" | Options<br />
! align="center" style="background:#f0f0f0;" | Expected Result<br />
! align="center" style="background:#f0f0f0;" | Pass/Fail<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>RefSeq_Ac</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>geneID</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>mass</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>pmid</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>23</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
|<br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>-1</pre><br />
| valign="top" | <pre>mass</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>-1</pre><br />
| valign="top" | <pre>pmid</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>0000</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>00001</pre><br />
| valign="top" | <pre>geneID</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>12345</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>abcd</pre><br />
| valign="top" | <pre>ipi</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>abcde</pre><br />
| valign="top" | <pre>RefSeq_Ac</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>abcde</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>abcde</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>abcde</pre><br />
| valign="top" | <pre>geneID</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>abcdes</pre><br />
| valign="top" | <pre>geneID</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>MW</pre><br />
| valign="top" | <pre>mass</pre><br />
|<br />
| No results are returned<br />
|<br />
|}<br />
<br />
=== Not currently tested ===<br />
<br />
* src_intxn_id search 1<br />
* omim search 1<br />
* digid search 1<br />
* audit against external database - Intact<br />
* audit against external database - MINT<br />
* audit against external database - BioGRID<br />
* iterations 1<br />
* use canonical expansion 1<br />
<br />
=== User interface notes ===<br />
<br />
Many search types such as UniProt_ID now lead to exact-only searches. The production of results should not be allowed for imprecise protein names, for example, since the user might have entered gene names, selected UniProt_ID by mistake and would not be aware of their mistake because their search returned results. Also, since the first few characters of UniProt_ID search terms may be shared by multiple proteins from different organisms, an inexact match would need to trigger the query helper.<br />
<br />
Generally, searches should provide predictable outcomes without resorting to the attribute browsers to discover which search terms produced which results. For example, AH2_ARATH which returns no results from an exact match search, should not encourage similar terms to be used for searching. Previously AH2_ARATH returned CAH2_ARATH. Imagine if the user accidentally had such a query term embedded in a long list. They would never detect this search error!<br />
<br />
Where the taxonomy field is set to <tt>Any</tt>, a warning will be given. It is envisaged that the user will most frequently be working with a single organism's proteins or would at least tolerate being reminded that potentially irrelevant proteins might be searched for due to naming coincidences.<br />
<br />
The iterations setting resets to 1 after a query, even one which led to the query helper being shown, where the query will be completed by trying the search again.<br />
<br />
The i.query attribute on nodes will collect queries as they are performed. Thus, nodes will appear blue in a graph even if the current query had no direct relationship with the node.<br />
<br />
Exporting lists of attribute values should be as simple as selecting the values in the attribute browser and opening a context menu and copying the selection. However, it is also possible (when the context menus don't work) to use the "File" -> "Export" -> "Node Attributes" menu entry and to choose "i.geneID", then saving and processing the saved file to get a list. This seems to be rather unreliable, however.<br />
<br />
== Export cases ==<br />
<br />
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"<br />
! align="center" style="background:#f0f0f0;" | Query/Search Type/Options<br />
! align="center" style="background:#f0f0f0;" | Export Type<br />
! align="center" style="background:#f0f0f0;" | Expected Result<br />
! align="center" style="background:#f0f0f0;" | Pass/Fail<br />
|-<br />
| valign="top" rowspan="2" | <pre>CXCR4<br />
<br />
geneSymbol<br />
<br />
Taxon id: Any<br />
Iterations: 0<br />
Create new view: no<br />
Use canonical expansion: no</pre><br />
| valign="top" | <pre>i.UniProt_Ac_TOP</pre><br />
| 1 node showing P61073<br />
| Pass<br />
|-<br />
| valign="top" | <pre>i.canonical_rog_TOP</pre><br />
| 1 node showing 107322<br />
| Pass<br />
|}<br />
<br />
== Currently untested areas ==<br />
<br />
* Preferences<br />
* iRefScape menu<br />
* Right-click menu<br />
* Node attributes<br />
* Edge attributes<br />
* Wizard<br />
* Installation<br />
* Help system<br />
* Windows and sessions<br />
* Loading from file<br />
<br />
==To be corrected==<br />
*Remove the non-proprietary flag/check for current data<br />
*Handle the neighbourhood completion when expanding network (do not use all the nodes)<br />
*show_inxc dynamic index behaviour change not working<br />
*Scaling GUI at low resolution, maximise button may get hidden<br />
*Path finding cancelling time<br />
*focus progress when path finding<br />
*Ending with collapsed node error<br />
*unselect all nodes before edge filtering<br />
<br />
==List of GeneIDs to test the new canonical expansion==<br />
<br />
Available in data version 8.4:<br />
<br />
*945577 http://www.ncbi.nlm.nih.gov/gene/?term=945577<br />
*947704 http://www.ncbi.nlm.nih.gov/gene/?term=947704<br />
*2765365 http://www.ncbi.nlm.nih.gov/gene/?term=2765365<br />
*944797 http://www.ncbi.nlm.nih.gov/gene/?term=944797<br />
*29924 http://www.ncbi.nlm.nih.gov/gene/?term=29924 <br />
*948517 http://www.ncbi.nlm.nih.gov/gene/?term=948517<br />
*3673 http://www.ncbi.nlm.nih.gov/gene/?term=3673 <br />
*946848 http://www.ncbi.nlm.nih.gov/gene/?term=946848<br />
*653361 http://www.ncbi.nlm.nih.gov/gene/?term=653361<br />
*5657 http://www.ncbi.nlm.nih.gov/gene/?term=5657<br />
<br />
== All iRefIndex Pages ==<br />
<br />
[[Category:iRefIndex]]</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefScape_Test_Cases_1.0&diff=3513iRefScape Test Cases 1.02011-06-22T12:00:56Z<p>Sabry: /* Search cases */</p>
<hr />
<div>Last edited: {{REVISIONYEAR}}-{{padleft:{{REVISIONMONTH}}|2}}-{{REVISIONDAY2}}<br />
<br />
All tests have been performed against iRefIndex 8.1 data.<br />
<br />
==Search cases==<br />
<br />
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"<br />
! align="center" style="background:#f0f0f0;" | Query<br />
! align="center" style="background:#f0f0f0;" | Search Type<br />
! align="center" style="background:#f0f0f0;" | Options<br />
! align="center" style="background:#f0f0f0;" | Expected Result<br />
! align="center" style="background:#f0f0f0;" | Pass/Fail<br />
|-<br />
| rowspan="10" valign="top" | <pre>Q39009<br />
Q9ZNV8</pre><br />
| rowspan="12" valign="top" | <pre>UniProt_Ac</pre><br />
| rowspan="9" valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: no<br />
Use canonical expansion: no<br />
Add edges between neighbours: no</pre><br />
| 33 nodes, 94 edges. 2 queried nodes are blue (DMC_ARATH and AHP2_ARATH)<br />
| Pass<br />
|-<br />
| Node AHP2_ARATH linkout from i.RefSeq_Ac_TOP attribute (NP_189581) to Entrez Protein gives http://www.ncbi.nlm.nih.gov/protein/NP_189581?report=GenPept<br />
| Pass<br />
|-<br />
| i.taxid is 3702 and i.geneID is 822593<br />
| Pass<br />
|-<br />
| Node AHP2_ARATH linkout from i.UniProt_Ac_TOP attribute (Q9ZNV8) to UniProt/KB beta gives http://www.uniprot.org/uniprot/Q9ZNV8<br />
| Pass<br />
|-<br />
| UniProt record agrees with iRefScape on iRefSeq_Ac_TOP (see "Sequence databases"), i.taxid, i.geneID (see "Genome annotation databases")<br />
| Pass<br />
|-<br />
| Two edges between query nodes are EBI-1555390, EBI-1555417<br />
| Pass<br />
|-<br />
| Linkouts for query node edges (i.src_intxn_id) to Intact ("Interaction databases") provide PubMed #17937504 which should match i.PMID, and an interaction detection method of "anti tag coip" which should match i.method_name<br />
| Pass<br />
|-<br />
| The molecule names are DMC1 and ATHP1 in IntAct and these names should be available under the i.interactor_alias node attribute<br />
| Pass<br />
|-<br />
| Both interactions should have http://wodaklab.org/iRefWeb/interaction/show/102203 as i.iRefWEB<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: no<br />
Use canonical expansion: no<br />
Add edges between neighbours: no</pre><br />
| 2 nodes, 3 edges; 2 queried nodes are blue (DMC_ARATH and AHP2_ARATH) and are connected by two edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Q39009-1<br />
Q9ZNV8-2</pre><br />
| rowspan="2" valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: no<br />
Use canonical expansion: no<br />
Add edges between neighbours: no</pre><br />
| Return the same results as for UniProtKB: the isoform information is ignored when searching<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Q39009.1<br />
Q9ZNV8.2</pre><br />
| Returns no results. Version information is not a valid annotation for UniProtKB.<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| rowspan="5" valign="top" | <pre>RefSeq_Ac</pre><br />
| rowspan="11" valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 11 nodes, 29 edges. i.RefSeq_Ac = NP_188928 was returned; edges returned include EBI-1555390, EBI-1555417 between DMC1_ARATH and AHP2_ARATH<br />
| Pass<br />
|-<br />
| <pre>NP_188928</pre><br />
| The same results are returned<br />
| Pass<br />
|-<br />
| <pre>NP_188928.567</pre><br />
| The same results are returned<br />
| Pass<br />
|-<br />
| <pre>188928</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| <pre>NP 188928</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>geneID</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>ipi</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>mass</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>rog</pre><br />
| No results are returned<br />
| Pass (''no error given, though'')<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH</pre><br />
| valign="top" rowspan="6" | <pre>UniProt_ID</pre><br />
| valign="top" rowspan="10" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 26 nodes, 67 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2 ARATH</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>ARATH</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AH2_ARATH</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH.2</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH</pre><br />
| valign="top" | <pre>geneID</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH</pre><br />
| valign="top" | <pre>ipi</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>821860<br />
822593</pre><br />
| valign="top" | <pre>geneID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 33 nodes and 94 edges. (Should return the same result as a UniProt_Ac query for Q39009 and Q9ZNV8.)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>821860</pre><br />
| valign="top" | <pre>geneID</pre><br />
| valign="top" rowspan="4"| <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 1 node<br />
| Pass<br />
|-<br />
| valign="top" | <pre>821860</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>821860</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>821860</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>1234</pre><br />
| valign="top" | <pre>geneID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 47 nodes and 158 edges<br />
| Pass<br />
|-<br />
| valign="top" | All geneIds from a search for <pre>1234</pre> (45 values producing 44 unique gene identifiers)<br />
| valign="top" | <pre>geneID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 80 nodes and 733 edges (upon last attempt)<br />
|<br />
|-<br />
| colspan="5" | '''Note:''' This test is made incredibly difficult by the apparently unreliability of the export function (what Paul is talking about here is the Cytoscape export,not the iRefScape export).<br />
|-<br />
| valign="top" | <pre>CXCR4</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 2 nodes<br />
| Pass<br />
|-<br />
| valign="top" | <pre>P61073-2</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| valign="top" rowspan="2" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 2 nodes (CXCR4 and CXCR4_HUMAN)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>P61073</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| 1 node (CXCR4_HUMAN)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>P61073-2</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| valign="top" rowspan="2" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
| 2 nodes (CXCR4 and CXCR4_HUMAN)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>P61073</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| 2 nodes (CXCR4 and CXCR4_HUMAN)<br />
| Pass<br />
|-<br />
| colspan="5" | '''Note:''' P61073-2 and P61073 are isoforms of CXCR4. Searching for P61073-2 actually results in the removal of the "-2" and a search for all isoforms, under the assumption that the user is unsure which isoform should be retrieved; as a result, all isoforms are returned, even though a specific isoform was requested. In contrast, the search without a "-" character results in just one protein with that exact name being returned.<br />
|-<br />
| valign="top" | <pre>CXCR</pre><br />
| valign="top" rowspan="4" | <pre>geneSymbol</pre><br />
| valign="top" rowspan="4" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>CXCR4</pre><br />
| rowspan="3"| 2 nodes with i.UniProt_Ac_TOP set to P61073 and P61073-2<br />
| Pass<br />
|-<br />
| valign="top" | <pre>cxcR4</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>CXC<br />
CXCR<br />
CXCR4</pre><br />
| Pass<br />
|-<br />
| colspan="5" | '''Note:''' no indication is given that CXC and CXCR failed to provide matches when the successfully used CXCR4 term is present. Maybe some feedback could be given about this.<br />
|-<br />
| valign="top" | <pre>CXCR5</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| valign="top" rowspan="3" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 3 nodes<br />
| Pass<br />
|-<br />
| valign="top" | <pre>CXCR5</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>PTK2</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| 6 nodes (involving 5 taxons)<br />
| Pass<br />
|-<br />
| valign="top" rowspan="3" | <pre>RPB1</pre><br />
| valign="top" rowspan="3" | <pre>geneSymbol</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 1 node (RPB1_SCHPO)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Taxon id: 4932<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| No results returned (even though an alias for yeast RPO21, gene identifier 851415, is RPB1, this search only searches on official gene symbols from Entrez<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Taxon id: 9606<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| No results returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>5366033</pre><br />
| valign="top" | <pre>rog</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: no<br />
Use canonical expansion: no</pre><br />
| 2 nodes (POL_HV1H2 and POL_HV1B1 interacting with it)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>IPI00543858<br />
IPI00517160</pre><br />
| valign="top" rowspan="4" | <pre>ipi</pre><br />
| valign="top" rowspan="4" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: no<br />
Use canonical expansion: no</pre><br />
| rowspan="3" | 33 nodes, 94 edges. 2 queried nodes are blue (DMC_ARATH and AHP2_ARATH)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>IPI00543858.1<br />
IPI00517160.1</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>00543858<br />
00517160</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>00543858<br />
0051716</pre><br />
| 33 nodes, 94 edges, but only after IPI00517160 has been chosen from the query helper<br />
| Pass<br />
|-<br />
| colspan="5" | '''Note:''' the transfer of the search term from the query helper and the augmentation of results from the term isn't particularly easy to accomplish, or it isn't obvious how to accomplish this successfully, because the iRefScape panel is hidden in the main window (a Cytoscape bug which appears to switch the visible panel all the time) and because a new search is required (without a new view being created, which is potentially how the original search might be set up).<br />
|-<br />
| valign="top" | <pre>IPI</pre><br />
| valign="top" rowspan="2" | <pre>ipi</pre><br />
| valign="top" rowspan="2" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: no<br />
Use canonical expansion: no</pre><br />
| Initiates query helper<br />
| Pass<br />
|-<br />
| valign="top" | <pre>IPI00543858</pre><br />
| 26 nodes, 67 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>72854<-->72866</pre><br />
| valign="top" | <pre>mass</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| The query helper is shown. Upon transferring the 4 suggestions into the query box and searching again, 5 nodes are retrieved.<br />
| Pass<br />
|-<br />
| colspan="5" | '''Note:''' the nodes are not laid out in a nice way, probably because no edges connect them.<br />
|-<br />
| valign="top" | <pre>72854 kda</pre><br />
| valign="top" | <pre>mass</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>72854<-->72856 kda</pre><br />
| valign="top" | <pre>mass</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| Query helper with 3 possible results<br />
| Pass<br />
|-<br />
| valign="top" | <pre>11401546</pre><br />
| valign="top" rowspan="12" | <pre>PMID</pre><br />
| valign="top" rowspan="12" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 4 nodes and 7 edges are returned. Three edges have PMID 11401546 and these involve the 4 nodes shown. All other edges (from different PMIDs) involve these proteins.<br />
|<br />
|-<br />
| valign="top" | <pre>11401546.1</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>1140154</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>SPTAN1</pre><br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>11401546<br />
SPTAN1</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10551855<br />
11401546</pre><br />
| 6 nodes and 27 edges<br />
|<br />
|-<br />
| valign="top" | <pre>10551855|11401546</pre><br />
| 6 nodes and 27 edges<br />
|<br />
|-<br />
| valign="top" | <pre>10551855| 11401546</pre><br />
| 6 nodes and 27 edges<br />
|<br />
|-<br />
| valign="top" | <pre>10551855 | 11401546</pre><br />
| 6 nodes and 27 edges<br />
|<br />
|-<br />
| valign="top" | <pre>10551855 [tab] 11401546</pre><br />
| 6 nodes and 27 edges<br />
|<br />
|-<br />
| valign="top" | <pre>10551855, 11401546</pre><br />
| 6 nodes and 27 edges<br />
|<br />
|-<br />
| valign="top" | <pre>10551855 11401546</pre><br />
| No results are returned (since space-delimited queries are not supported)<br />
|<br />
|-<br />
| colspan="5" | The following example searches are listed in the [[README_Cytoscape_plugin_0.8x#Using_the_Search_Panel|Using the Search Panel]] documentation.<br />
|-<br />
| valign="top" | <pre>Q7KSF4</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
| 69 nodes, 213 edges, with the 4 query nodes having i.query = Q7KSF4, one of the query nodes having i.order = 0 (Q7KSF4_DROME) and the others having i.order = 10 (as canonical group members)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Q7KSF4</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 1 node (Q7KSF4_DROME) verifying the attributes in the previous search<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_996224</pre><br />
| valign="top" | <pre>RefSeq_Ac</pre><br />
| valign="top" rowspan="3" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
| rowspan="2" | 69 nodes, 213 edges (same as the above query for Q7KSF4)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Q7KSF4_DROME</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>42066</pre><br />
| valign="top" | <pre>geneID</pre><br />
| rowspan="3" | 69 nodes, 213 edges, with the 4 query nodes having i.order = 0 since all also have i.geneID = 42066<br />
| Pass<br />
|-<br />
| valign="top" | <pre>42066</pre><br />
| valign="top" | <pre>geneID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>cher</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| valign="top" rowspan="4" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>72854<-->72866</pre><br />
| valign="top" | <pre>mass</pre><br />
| 44 nodes, 140 edges, with 8 query nodes, 5 of which with i.mass in (72854, 72855, 72856, 72861) having i.order = 0 and the remaining 3 query nodes with i.mass outside the given range having i.order = 10<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10121899</pre><br />
| valign="top" | <pre>rog</pre><br />
| 69 nodes, 213 edges (same as the above query for Q7KSF4), but with one of the query nodes having i.order = 0 and i.query = 10121899 and the remaining 3 query nodes having i.order = 10<br />
| Pass<br />
|-<br />
| valign="top" | <pre>14605208</pre><br />
| valign="top" | <pre>PMID</pre><br />
| rowspan="3" | 929 nodes and 1605 edges returned all with PMID of 14605208<br />
|<br />
|-<br />
| valign="top" | <pre>14605208</pre><br />
| valign="top" | <pre>PMID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
|<br />
|-<br />
| valign="top" | <pre>14605208</pre><br />
| valign="top" | <pre>PMID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
|<br />
|-<br />
| valign="top" | <pre>47513</pre><br />
| valign="top" | <pre>src_intxn_id</pre><br />
| valign="top" rowspan="7" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
| 2 nodes and 1 edge returned (one query node, Q7KSF4_DROME)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>EBI-212627</pre><br />
| valign="top" | <pre>src_intxn_id</pre><br />
| 2 nodes and 5 edges returned (from bind, dip, intact, mint and BIND_Translation), with 2 query nodes (CRBN_DROME and Q9W279_DROME)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>147805</pre><br />
| valign="top" | <pre>src_intxn_id</pre><br />
| Returns 4 nodes and 4 interactions because the BIND/BIND_Translation and BioGRID interaction identifier spaces overlap (so 147805 refers to completely different interactions in different databases)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>227650</pre><br />
| valign="top" | <pre>omim</pre><br />
| 96 nodes (including 18 complex nodes) and 498 edges returned, with the query node having i.geneID = 2175 and i.digid = 460<br />
| Pass<br />
|-<br />
| valign="top" | <pre>449</pre><br />
| valign="top" | <pre>digid</pre><br />
| 321 nodes and 1010 edges returned, with the 3 query nodes having i.omim = 612219<br />
| Pass<br />
|-<br />
| valign="top" | <pre>460</pre><br />
| valign="top" | <pre>digid</pre><br />
| 668 nodes and 17554 edges returned, with the 16 query nodes having i.digid = 460<br />
| Pass<br />
|-<br />
| valign="top" | <pre>fanconi</pre><br />
| valign="top" | <pre>dig_title</pre><br />
| ''Presumably similar results to the previous query''<br />
| Fail (''iRefScape insists on an exact match and doesn't find anything'')<br />
|}<br />
<br />
=== Invalid input tests ===<br />
<br />
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"<br />
! align="center" style="background:#f0f0f0;" | Query<br />
! align="center" style="background:#f0f0f0;" | Search Type<br />
! align="center" style="background:#f0f0f0;" | Options<br />
! align="center" style="background:#f0f0f0;" | Expected Result<br />
! align="center" style="background:#f0f0f0;" | Pass/Fail<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>RefSeq_Ac</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>geneID</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>mass</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>pmid</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>23</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
|<br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>-1</pre><br />
| valign="top" | <pre>mass</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>-1</pre><br />
| valign="top" | <pre>pmid</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>0000</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>00001</pre><br />
| valign="top" | <pre>geneID</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>12345</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>abcd</pre><br />
| valign="top" | <pre>ipi</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>abcde</pre><br />
| valign="top" | <pre>RefSeq_Ac</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>abcde</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>abcde</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>abcde</pre><br />
| valign="top" | <pre>geneID</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>abcdes</pre><br />
| valign="top" | <pre>geneID</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>MW</pre><br />
| valign="top" | <pre>mass</pre><br />
|<br />
| No results are returned<br />
|<br />
|}<br />
<br />
=== Not currently tested ===<br />
<br />
* src_intxn_id search 1<br />
* omim search 1<br />
* digid search 1<br />
* audit against external database - Intact<br />
* audit against external database - MINT<br />
* audit against external database - BioGRID<br />
* iterations 1<br />
* use canonical expansion 1<br />
<br />
=== User interface notes ===<br />
<br />
Many search types such as UniProt_ID now lead to exact-only searches. The production of results should not be allowed for imprecise protein names, for example, since the user might have entered gene names, selected UniProt_ID by mistake and would not be aware of their mistake because their search returned results. Also, since the first few characters of UniProt_ID search terms may be shared by multiple proteins from different organisms, an inexact match would need to trigger the query helper.<br />
<br />
Generally, searches should provide predictable outcomes without resorting to the attribute browsers to discover which search terms produced which results. For example, AH2_ARATH which returns no results from an exact match search, should not encourage similar terms to be used for searching. Previously AH2_ARATH returned CAH2_ARATH. Imagine if the user accidentally had such a query term embedded in a long list. They would never detect this search error!<br />
<br />
Where the taxonomy field is set to <tt>Any</tt>, a warning will be given. It is envisaged that the user will most frequently be working with a single organism's proteins or would at least tolerate being reminded that potentially irrelevant proteins might be searched for due to naming coincidences.<br />
<br />
The iterations setting resets to 1 after a query, even one which led to the query helper being shown, where the query will be completed by trying the search again.<br />
<br />
The i.query attribute on nodes will collect queries as they are performed. Thus, nodes will appear blue in a graph even if the current query had no direct relationship with the node.<br />
<br />
Exporting lists of attribute values should be as simple as selecting the values in the attribute browser and opening a context menu and copying the selection. However, it is also possible (when the context menus don't work) to use the "File" -> "Export" -> "Node Attributes" menu entry and to choose "i.geneID", then saving and processing the saved file to get a list. This seems to be rather unreliable, however.<br />
<br />
== Export cases ==<br />
<br />
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"<br />
! align="center" style="background:#f0f0f0;" | Query/Search Type/Options<br />
! align="center" style="background:#f0f0f0;" | Export Type<br />
! align="center" style="background:#f0f0f0;" | Expected Result<br />
! align="center" style="background:#f0f0f0;" | Pass/Fail<br />
|-<br />
| valign="top" rowspan="2" | <pre>CXCR4<br />
<br />
geneSymbol<br />
<br />
Taxon id: Any<br />
Iterations: 0<br />
Create new view: no<br />
Use canonical expansion: no</pre><br />
| valign="top" | <pre>i.UniProt_Ac_TOP</pre><br />
| 1 node showing P61073<br />
| Pass<br />
|-<br />
| valign="top" | <pre>i.canonical_rog_TOP</pre><br />
| 1 node showing 107322<br />
| Pass<br />
|}<br />
<br />
== Currently untested areas ==<br />
<br />
* Preferences<br />
* iRefScape menu<br />
* Right-click menu<br />
* Node attributes<br />
* Edge attributes<br />
* Wizard<br />
* Installation<br />
* Help system<br />
* Windows and sessions<br />
* Loading from file<br />
<br />
==To be corrected==<br />
*Remove the non-proprietary flag/check for current data<br />
*Handle the neighbourhood completion when expanding network (do not use all the nodes)<br />
*show_inxc dynamic index behaviour change not working<br />
*Scaling GUI at low resolution, maximise button may get hidden<br />
*Path finding cancelling time<br />
*focus progress when path finding<br />
*Ending with collapsed node error<br />
*unselect all nodes before edge filtering<br />
<br />
==List of GeneIDs to test the new canonical expansion==<br />
<br />
Available in data version 8.4:<br />
<br />
*945577 http://www.ncbi.nlm.nih.gov/gene/?term=945577<br />
*947704 http://www.ncbi.nlm.nih.gov/gene/?term=947704<br />
*2765365 http://www.ncbi.nlm.nih.gov/gene/?term=2765365<br />
*944797 http://www.ncbi.nlm.nih.gov/gene/?term=944797<br />
*29924 http://www.ncbi.nlm.nih.gov/gene/?term=29924 <br />
*948517 http://www.ncbi.nlm.nih.gov/gene/?term=948517<br />
*3673 http://www.ncbi.nlm.nih.gov/gene/?term=3673 <br />
*946848 http://www.ncbi.nlm.nih.gov/gene/?term=946848<br />
*653361 http://www.ncbi.nlm.nih.gov/gene/?term=653361<br />
*5657 http://www.ncbi.nlm.nih.gov/gene/?term=5657<br />
<br />
== All iRefIndex Pages ==<br />
<br />
[[Category:iRefIndex]]</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefScape_Test_Cases_1.0&diff=3512iRefScape Test Cases 1.02011-06-22T11:52:40Z<p>Sabry: /* Search cases */</p>
<hr />
<div>Last edited: {{REVISIONYEAR}}-{{padleft:{{REVISIONMONTH}}|2}}-{{REVISIONDAY2}}<br />
<br />
All tests have been performed against iRefIndex 8.1 data.<br />
<br />
==Search cases==<br />
<br />
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"<br />
! align="center" style="background:#f0f0f0;" | Query<br />
! align="center" style="background:#f0f0f0;" | Search Type<br />
! align="center" style="background:#f0f0f0;" | Options<br />
! align="center" style="background:#f0f0f0;" | Expected Result<br />
! align="center" style="background:#f0f0f0;" | Pass/Fail<br />
|-<br />
| rowspan="10" valign="top" | <pre>Q39009<br />
Q9ZNV8</pre><br />
| rowspan="12" valign="top" | <pre>UniProt_Ac</pre><br />
| rowspan="9" valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: no<br />
Use canonical expansion: no<br />
Add edges between neighbours: no</pre><br />
| 33 nodes, 94 edges. 2 queried nodes are blue (DMC_ARATH and AHP2_ARATH)<br />
| Pass<br />
|-<br />
| Node AHP2_ARATH linkout from i.RefSeq_Ac_TOP attribute (NP_189581) to Entrez Protein gives http://www.ncbi.nlm.nih.gov/protein/NP_189581?report=GenPept<br />
| Pass<br />
|-<br />
| i.taxid is 3702 and i.geneID is 822593<br />
| Pass<br />
|-<br />
| Node AHP2_ARATH linkout from i.UniProt_Ac_TOP attribute (Q9ZNV8) to UniProt/KB beta gives http://www.uniprot.org/uniprot/Q9ZNV8<br />
| Pass<br />
|-<br />
| UniProt record agrees with iRefScape on iRefSeq_Ac_TOP (see "Sequence databases"), i.taxid, i.geneID (see "Genome annotation databases")<br />
| Pass<br />
|-<br />
| Two edges between query nodes are EBI-1555390, EBI-1555417<br />
| Pass<br />
|-<br />
| Linkouts for query node edges (i.src_intxn_id) to Intact ("Interaction databases") provide PubMed #17937504 which should match i.PMID, and an interaction detection method of "anti tag coip" which should match i.method_name<br />
| Pass<br />
|-<br />
| The molecule names are DMC1 and ATHP1 in IntAct and these names should be available under the i.interactor_alias node attribute<br />
| Pass<br />
|-<br />
| Both interactions should have http://wodaklab.org/iRefWeb/interaction/show/102203 as i.iRefWEB<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: no<br />
Use canonical expansion: no<br />
Add edges between neighbours: no</pre><br />
| 2 nodes, 3 edges; 2 queried nodes are blue (DMC_ARATH and AHP2_ARATH) and are connected by two edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Q39009-1<br />
Q9ZNV8-2</pre><br />
| rowspan="2" valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: no<br />
Use canonical expansion: no<br />
Add edges between neighbours: no</pre><br />
| Return the same results as for UniProtKB: the isoform information is ignored when searching<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Q39009.1<br />
Q9ZNV8.2</pre><br />
| Returns no results. Version information is not a valid annotation for UniProtKB.<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| rowspan="5" valign="top" | <pre>RefSeq_Ac</pre><br />
| rowspan="11" valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 11 nodes, 29 edges. i.RefSeq_Ac = NP_188928 was returned; edges returned include EBI-1555390, EBI-1555417 between DMC1_ARATH and AHP2_ARATH<br />
| Pass<br />
|-<br />
| <pre>NP_188928</pre><br />
| The same results are returned<br />
| Pass<br />
|-<br />
| <pre>NP_188928.567</pre><br />
| The same results are returned<br />
| Pass<br />
|-<br />
| <pre>188928</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| <pre>NP 188928</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>geneID</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>ipi</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>mass</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_188928.2</pre><br />
| valign="top" | <pre>rog</pre><br />
| No results are returned<br />
| Pass (''no error given, though'')<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH</pre><br />
| valign="top" rowspan="6" | <pre>UniProt_ID</pre><br />
| valign="top" rowspan="10" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 26 nodes, 67 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2 ARATH</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>ARATH</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AH2_ARATH</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH.2</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH</pre><br />
| valign="top" | <pre>geneID</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>AHP2_ARATH</pre><br />
| valign="top" | <pre>ipi</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>821860<br />
822593</pre><br />
| valign="top" | <pre>geneID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 33 nodes and 94 edges. (Should return the same result as a UniProt_Ac query for Q39009 and Q9ZNV8.)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>821860</pre><br />
| valign="top" | <pre>geneID</pre><br />
| valign="top" rowspan="4"| <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 1 node<br />
| Pass<br />
|-<br />
| valign="top" | <pre>821860</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>821860</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>821860</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>1234</pre><br />
| valign="top" | <pre>geneID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 47 nodes and 158 edges<br />
| Pass<br />
|-<br />
| valign="top" | All geneIds from a search for <pre>1234</pre> (45 values producing 44 unique gene identifiers)<br />
| valign="top" | <pre>geneID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 80 nodes and 733 edges (upon last attempt)<br />
|<br />
|-<br />
| colspan="5" | '''Note:''' This test is made incredibly difficult by the apparently unreliability of the export function (what Paul is talking about here is the Cytoscape export,not the iRefScape export).<br />
|-<br />
| valign="top" | <pre>CXCR4</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 2 nodes<br />
| Pass<br />
|-<br />
| valign="top" | <pre>P61073-2</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| valign="top" rowspan="2" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 2 nodes (CXCR4 and CXCR4_HUMAN)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>P61073</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| 1 node (CXCR4_HUMAN)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>P61073-2</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| valign="top" rowspan="2" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
| 2 nodes (CXCR4 and CXCR4_HUMAN)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>P61073</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| 2 nodes (CXCR4 and CXCR4_HUMAN)<br />
| Pass<br />
|-<br />
| colspan="5" | '''Note:''' P61073-2 and P61073 are isoforms of CXCR4. Searching for P61073-2 actually results in the removal of the "-2" and a search for all isoforms, under the assumption that the user is unsure which isoform should be retrieved; as a result, all isoforms are returned, even though a specific isoform was requested. In contrast, the search without a "-" character results in just one protein with that exact name being returned.<br />
|-<br />
| valign="top" | <pre>CXCR</pre><br />
| valign="top" rowspan="4" | <pre>geneSymbol</pre><br />
| valign="top" rowspan="4" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>CXCR4</pre><br />
| rowspan="3"| 2 nodes with i.UniProt_Ac_TOP set to P61073 and P61073-2<br />
| Pass<br />
|-<br />
| valign="top" | <pre>cxcR4</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>CXC<br />
CXCR<br />
CXCR4</pre><br />
| Pass<br />
|-<br />
| colspan="5" | '''Note:''' no indication is given that CXC and CXCR failed to provide matches when the successfully used CXCR4 term is present. Maybe some feedback could be given about this.<br />
|-<br />
| valign="top" | <pre>CXCR5</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| valign="top" rowspan="3" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 3 nodes<br />
| Pass<br />
|-<br />
| valign="top" | <pre>CXCR5</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>PTK2</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| 6 nodes (involving 5 taxons)<br />
| Pass<br />
|-<br />
| valign="top" rowspan="3" | <pre>RPB1</pre><br />
| valign="top" rowspan="3" | <pre>geneSymbol</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 1 node (RPB1_SCHPO)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Taxon id: 4932<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| No results returned (even though an alias for yeast RPO21, gene identifier 851415, is RPB1, this search only searches on official gene symbols from Entrez<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Taxon id: 9606<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| No results returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>5366033</pre><br />
| valign="top" | <pre>rog</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: no<br />
Use canonical expansion: no</pre><br />
| 2 nodes (POL_HV1H2 and POL_HV1B1 interacting with it)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>IPI00543858<br />
IPI00517160</pre><br />
| valign="top" rowspan="4" | <pre>ipi</pre><br />
| valign="top" rowspan="4" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: no<br />
Use canonical expansion: no</pre><br />
| rowspan="3" | 33 nodes, 94 edges. 2 queried nodes are blue (DMC_ARATH and AHP2_ARATH)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>IPI00543858.1<br />
IPI00517160.1</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>00543858<br />
00517160</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>00543858<br />
0051716</pre><br />
| 33 nodes, 94 edges, but only after IPI00517160 has been chosen from the query helper<br />
| Pass<br />
|-<br />
| colspan="5" | '''Note:''' the transfer of the search term from the query helper and the augmentation of results from the term isn't particularly easy to accomplish, or it isn't obvious how to accomplish this successfully, because the iRefScape panel is hidden in the main window (a Cytoscape bug which appears to switch the visible panel all the time) and because a new search is required (without a new view being created, which is potentially how the original search might be set up).<br />
|-<br />
| valign="top" | <pre>IPI</pre><br />
| valign="top" rowspan="2" | <pre>ipi</pre><br />
| valign="top" rowspan="2" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: no<br />
Use canonical expansion: no</pre><br />
| Initiates query helper<br />
| Pass<br />
|-<br />
| valign="top" | <pre>IPI00543858</pre><br />
| 26 nodes, 67 edges<br />
| Pass<br />
|-<br />
| valign="top" | <pre>72854<-->72866</pre><br />
| valign="top" | <pre>mass</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| The query helper is shown. Upon transferring the 4 suggestions into the query box and searching again, 5 nodes are retrieved.<br />
| Pass<br />
|-<br />
| colspan="5" | '''Note:''' the nodes are not laid out in a nice way, probably because no edges connect them.<br />
|-<br />
| valign="top" | <pre>72854 kda</pre><br />
| valign="top" | <pre>mass</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>11401546</pre><br />
| valign="top" rowspan="12" | <pre>PMID</pre><br />
| valign="top" rowspan="12" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 4 nodes and 7 edges are returned. Three edges have PMID 11401546 and these involve the 4 nodes shown. All other edges (from different PMIDs) involve these proteins.<br />
|<br />
|-<br />
| valign="top" | <pre>11401546.1</pre><br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>1140154</pre><br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>SPTAN1</pre><br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>11401546<br />
SPTAN1</pre><br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>10551855<br />
11401546</pre><br />
| 6 nodes and 27 edges<br />
|<br />
|-<br />
| valign="top" | <pre>10551855|11401546</pre><br />
| 6 nodes and 27 edges<br />
|<br />
|-<br />
| valign="top" | <pre>10551855| 11401546</pre><br />
| 6 nodes and 27 edges<br />
|<br />
|-<br />
| valign="top" | <pre>10551855 | 11401546</pre><br />
| 6 nodes and 27 edges<br />
|<br />
|-<br />
| valign="top" | <pre>10551855 [tab] 11401546</pre><br />
| 6 nodes and 27 edges<br />
|<br />
|-<br />
| valign="top" | <pre>10551855, 11401546</pre><br />
| 6 nodes and 27 edges<br />
|<br />
|-<br />
| valign="top" | <pre>10551855 11401546</pre><br />
| No results are returned (since space-delimited queries are not supported)<br />
|<br />
|-<br />
| colspan="5" | The following example searches are listed in the [[README_Cytoscape_plugin_0.8x#Using_the_Search_Panel|Using the Search Panel]] documentation.<br />
|-<br />
| valign="top" | <pre>Q7KSF4</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
| 69 nodes, 213 edges, with the 4 query nodes having i.query = Q7KSF4, one of the query nodes having i.order = 0 (Q7KSF4_DROME) and the others having i.order = 10 (as canonical group members)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Q7KSF4</pre><br />
| valign="top" | <pre>UniProt_Ac</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| 1 node (Q7KSF4_DROME) verifying the attributes in the previous search<br />
| Pass<br />
|-<br />
| valign="top" | <pre>NP_996224</pre><br />
| valign="top" | <pre>RefSeq_Ac</pre><br />
| valign="top" rowspan="3" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
| rowspan="2" | 69 nodes, 213 edges (same as the above query for Q7KSF4)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>Q7KSF4_DROME</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>42066</pre><br />
| valign="top" | <pre>geneID</pre><br />
| rowspan="3" | 69 nodes, 213 edges, with the 4 query nodes having i.order = 0 since all also have i.geneID = 42066<br />
| Pass<br />
|-<br />
| valign="top" | <pre>42066</pre><br />
| valign="top" | <pre>geneID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>cher</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
| valign="top" rowspan="4" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
| Pass<br />
|-<br />
| valign="top" | <pre>72854<-->72866</pre><br />
| valign="top" | <pre>mass</pre><br />
| 44 nodes, 140 edges, with 8 query nodes, 5 of which with i.mass in (72854, 72855, 72856, 72861) having i.order = 0 and the remaining 3 query nodes with i.mass outside the given range having i.order = 10<br />
| Pass<br />
|-<br />
| valign="top" | <pre>10121899</pre><br />
| valign="top" | <pre>rog</pre><br />
| 69 nodes, 213 edges (same as the above query for Q7KSF4), but with one of the query nodes having i.order = 0 and i.query = 10121899 and the remaining 3 query nodes having i.order = 10<br />
| Pass<br />
|-<br />
| valign="top" | <pre>14605208</pre><br />
| valign="top" | <pre>PMID</pre><br />
| rowspan="3" | 929 nodes and 1605 edges returned all with PMID of 14605208<br />
|<br />
|-<br />
| valign="top" | <pre>14605208</pre><br />
| valign="top" | <pre>PMID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 0<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
|<br />
|-<br />
| valign="top" | <pre>14605208</pre><br />
| valign="top" | <pre>PMID</pre><br />
| valign="top" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: no</pre><br />
|<br />
|-<br />
| valign="top" | <pre>47513</pre><br />
| valign="top" | <pre>src_intxn_id</pre><br />
| valign="top" rowspan="7" | <pre>Taxon id: Any<br />
Iterations: 1<br />
Create new view: yes<br />
Use canonical expansion: yes</pre><br />
| 2 nodes and 1 edge returned (one query node, Q7KSF4_DROME)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>EBI-212627</pre><br />
| valign="top" | <pre>src_intxn_id</pre><br />
| 2 nodes and 5 edges returned (from bind, dip, intact, mint and BIND_Translation), with 2 query nodes (CRBN_DROME and Q9W279_DROME)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>147805</pre><br />
| valign="top" | <pre>src_intxn_id</pre><br />
| Returns 4 nodes and 4 interactions because the BIND/BIND_Translation and BioGRID interaction identifier spaces overlap (so 147805 refers to completely different interactions in different databases)<br />
| Pass<br />
|-<br />
| valign="top" | <pre>227650</pre><br />
| valign="top" | <pre>omim</pre><br />
| 96 nodes (including 18 complex nodes) and 498 edges returned, with the query node having i.geneID = 2175 and i.digid = 460<br />
| Pass<br />
|-<br />
| valign="top" | <pre>449</pre><br />
| valign="top" | <pre>digid</pre><br />
| 321 nodes and 1010 edges returned, with the 3 query nodes having i.omim = 612219<br />
| Pass<br />
|-<br />
| valign="top" | <pre>460</pre><br />
| valign="top" | <pre>digid</pre><br />
| 668 nodes and 17554 edges returned, with the 16 query nodes having i.digid = 460<br />
| Pass<br />
|-<br />
| valign="top" | <pre>fanconi</pre><br />
| valign="top" | <pre>dig_title</pre><br />
| ''Presumably similar results to the previous query''<br />
| Fail (''iRefScape insists on an exact match and doesn't find anything'')<br />
|}<br />
<br />
=== Invalid input tests ===<br />
<br />
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"<br />
! align="center" style="background:#f0f0f0;" | Query<br />
! align="center" style="background:#f0f0f0;" | Search Type<br />
! align="center" style="background:#f0f0f0;" | Options<br />
! align="center" style="background:#f0f0f0;" | Expected Result<br />
! align="center" style="background:#f0f0f0;" | Pass/Fail<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>RefSeq_Ac</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>geneID</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>mass</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>0</pre><br />
| valign="top" | <pre>pmid</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>23</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
|<br />
| No results are returned<br />
| Pass<br />
|-<br />
| valign="top" | <pre>-1</pre><br />
| valign="top" | <pre>mass</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>-1</pre><br />
| valign="top" | <pre>pmid</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>0000</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>00001</pre><br />
| valign="top" | <pre>geneID</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>12345</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>abcd</pre><br />
| valign="top" | <pre>ipi</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>abcde</pre><br />
| valign="top" | <pre>RefSeq_Ac</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>abcde</pre><br />
| valign="top" | <pre>UniProt_ID</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>abcde</pre><br />
| valign="top" | <pre>geneSymbol</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>abcde</pre><br />
| valign="top" | <pre>geneID</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>abcdes</pre><br />
| valign="top" | <pre>geneID</pre><br />
|<br />
| No results are returned<br />
|<br />
|-<br />
| valign="top" | <pre>MW</pre><br />
| valign="top" | <pre>mass</pre><br />
|<br />
| No results are returned<br />
|<br />
|}<br />
<br />
=== Not currently tested ===<br />
<br />
* src_intxn_id search 1<br />
* omim search 1<br />
* digid search 1<br />
* audit against external database - Intact<br />
* audit against external database - MINT<br />
* audit against external database - BioGRID<br />
* iterations 1<br />
* use canonical expansion 1<br />
<br />
=== User interface notes ===<br />
<br />
Many search types such as UniProt_ID now lead to exact-only searches. The production of results should not be allowed for imprecise protein names, for example, since the user might have entered gene names, selected UniProt_ID by mistake and would not be aware of their mistake because their search returned results. Also, since the first few characters of UniProt_ID search terms may be shared by multiple proteins from different organisms, an inexact match would need to trigger the query helper.<br />
<br />
Generally, searches should provide predictable outcomes without resorting to the attribute browsers to discover which search terms produced which results. For example, AH2_ARATH which returns no results from an exact match search, should not encourage similar terms to be used for searching. Previously AH2_ARATH returned CAH2_ARATH. Imagine if the user accidentally had such a query term embedded in a long list. They would never detect this search error!<br />
<br />
Where the taxonomy field is set to <tt>Any</tt>, a warning will be given. It is envisaged that the user will most frequently be working with a single organism's proteins or would at least tolerate being reminded that potentially irrelevant proteins might be searched for due to naming coincidences.<br />
<br />
The iterations setting resets to 1 after a query, even one which led to the query helper being shown, where the query will be completed by trying the search again.<br />
<br />
The i.query attribute on nodes will collect queries as they are performed. Thus, nodes will appear blue in a graph even if the current query had no direct relationship with the node.<br />
<br />
Exporting lists of attribute values should be as simple as selecting the values in the attribute browser and opening a context menu and copying the selection. However, it is also possible (when the context menus don't work) to use the "File" -> "Export" -> "Node Attributes" menu entry and to choose "i.geneID", then saving and processing the saved file to get a list. This seems to be rather unreliable, however.<br />
<br />
== Export cases ==<br />
<br />
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"<br />
! align="center" style="background:#f0f0f0;" | Query/Search Type/Options<br />
! align="center" style="background:#f0f0f0;" | Export Type<br />
! align="center" style="background:#f0f0f0;" | Expected Result<br />
! align="center" style="background:#f0f0f0;" | Pass/Fail<br />
|-<br />
| valign="top" rowspan="2" | <pre>CXCR4<br />
<br />
geneSymbol<br />
<br />
Taxon id: Any<br />
Iterations: 0<br />
Create new view: no<br />
Use canonical expansion: no</pre><br />
| valign="top" | <pre>i.UniProt_Ac_TOP</pre><br />
| 1 node showing P61073<br />
| Pass<br />
|-<br />
| valign="top" | <pre>i.canonical_rog_TOP</pre><br />
| 1 node showing 107322<br />
| Pass<br />
|}<br />
<br />
== Currently untested areas ==<br />
<br />
* Preferences<br />
* iRefScape menu<br />
* Right-click menu<br />
* Node attributes<br />
* Edge attributes<br />
* Wizard<br />
* Installation<br />
* Help system<br />
* Windows and sessions<br />
* Loading from file<br />
<br />
==To be corrected==<br />
*Remove the non-proprietary flag/check for current data<br />
*Handle the neighbourhood completion when expanding network (do not use all the nodes)<br />
*show_inxc dynamic index behaviour change not working<br />
*Scaling GUI at low resolution, maximise button may get hidden<br />
*Path finding cancelling time<br />
*focus progress when path finding<br />
*Ending with collapsed node error<br />
*unselect all nodes before edge filtering<br />
<br />
==List of GeneIDs to test the new canonical expansion==<br />
<br />
Available in data version 8.4:<br />
<br />
*945577 http://www.ncbi.nlm.nih.gov/gene/?term=945577<br />
*947704 http://www.ncbi.nlm.nih.gov/gene/?term=947704<br />
*2765365 http://www.ncbi.nlm.nih.gov/gene/?term=2765365<br />
*944797 http://www.ncbi.nlm.nih.gov/gene/?term=944797<br />
*29924 http://www.ncbi.nlm.nih.gov/gene/?term=29924 <br />
*948517 http://www.ncbi.nlm.nih.gov/gene/?term=948517<br />
*3673 http://www.ncbi.nlm.nih.gov/gene/?term=3673 <br />
*946848 http://www.ncbi.nlm.nih.gov/gene/?term=946848<br />
*653361 http://www.ncbi.nlm.nih.gov/gene/?term=653361<br />
*5657 http://www.ncbi.nlm.nih.gov/gene/?term=5657<br />
<br />
== All iRefIndex Pages ==<br />
<br />
[[Category:iRefIndex]]</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefIndex_Citations&diff=3507iRefIndex Citations2011-06-21T06:22:23Z<p>Sabry: /* 2011 */</p>
<hr />
<div>Some studies making use of iRefIndex<br />
<br />
==All citations==<br />
===2011===<br />
# Kritikos GD, Moschopoulos C, Vazirgiannis M, Kossida S. Noise reduction in protein-protein interaction graphs by the implementation of a novel weighting scheme.[http://www.ncbi.nlm.nih.gov/pubmed?term=21676899 '''PMID:21676899''']<br />
# Saliha Ece Acuner Ozbabacan,Hatice Billur Engin, Attila Gursoy1 and Ozlem Keskin1. Transient protein–protein interactions [http://www.ncbi.nlm.nih.gov/pubmed?term=21676899 '''PMID:21679454''']<br />
#Choi, H. et al. SAINT: probabilistic scoring of affinity purification-mass spectrometry data. Nat Methods 8, 70-73 (2011). [http://www.ncbi.nlm.nih.gov/pubmed?term=21131968 '''PMID:21131968''']. ([http://irefindex.uio.no/wiki/iRefIndex_Citations#Independent_research_projects_using_iRefIndex '''Read more'''])<br />
#Croft, D. et al. Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res 39, D691-697 (2011).[http://www.ncbi.nlm.nih.gov/pubmed?term=21067998 '''PMID: 21067998'''].([http://irefindex.uio.no/wiki/iRefIndex_Citations#Independent_research_projects_using_iRefIndex '''Read more'''])<br />
#Gillis, J. & Pavlidis, P. The role of indirect connections in gene networks in predicting function. Bioinformatics (2011). [http://www.ncbi.nlm.nih.gov/pubmed?term=21551147 '''PMID: 21551147''']. ([http://irefindex.uio.no/wiki/iRefIndex_Citations#Independent_research_projects_using_iRefIndex '''Read more'''])<br />
#Hao, Y. et al. OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms. Bioinformatics 27, 883-884 (2011). [http://www.ncbi.nlm.nih.gov/pubmed?term=21257609 '''PMID: 21257609'''] ([http://irefindex.uio.no/wiki/iRefIndex_Citations#Independent_research_projects_using_iRefIndex '''Read more'''])<br />
#Nolin, M.-A., Dumontier, M., Belleau, F. & Corbeil, J. Building an HIV data mashup using Bio2RDF. Briefings in Bioinformatics (2011).iRefindex was mentioned as a protein-protein interaction data provider and the contribution to Bio2RDF project. <br />
#Turinsky, A.L. et al. DAnCER: disease-annotated chromatin epigenetics resource. Nucleic Acids Res 39, D889-894 (2011). [http://www.ncbi.nlm.nih.gov/pubmed?term=20876685 '''PMID: 20876685''']. ([http://irefindex.uio.no/wiki/iRefIndex_Citations#Independent_research_projects_using_iRefIndex '''Read more'''])<br />
#Valsesia, A. et al. Network-guided analysis of genes with altered somatic copy number and gene expression reveals pathways commonly perturbed in metastatic melanoma. PLoS One 6, e18369 (2011). PMID: 21494657. ([http://irefindex.uio.no/wiki/iRefIndex_Citations#Independent_research_projects_using_iRefIndex '''Read more'''])<br />
#Vidal, M., Cusick, M.E. & Barabasi, A.L. Interactome networks and human disease. Cell 144, 986-998 (2011). PMID: 21414488. The literature curated data quality assessment project was mentioned. <br />
# Zhang, K.X. & Ouellette, B.F. CAERUS: predicting CAncER oUtcomeS using relationship between protein structural information, protein networks, gene expression data, and mutation data. PLoS Comput Biol 7, e1001114 (2011). PMID: 21483478.([http://irefindex.uio.no/wiki/iRefIndex_Citations#Independent_research_projects_using_iRefIndex '''Read more'''])<br />
<br />
===2010===<br />
#Ceol, A. et al. MINT, the molecular interaction database: 2009 update. Nucleic Acids Res 38, D532-539 (2010). PMID: 19897547. iRefIndex was mentioned as a consolidated data provider. <br />
#Garcia-Garcia, J., Guney, E., Aragues, R., Planas-Iglesias, J. & Oliva, B. Biana: a software framework for compiling biological interactions and analyzing networks. BMC Bioinformatics 11, 56 (2010). PMID: 20105306. iRefindex was compared to the system discussed in this paper. iRefIndex procedure was suggested as a Unification protocols to be used with the BIANA system.<br />
#Jain, S. & Bader, G.D. An improved method for scoring protein-protein interactions using semantic similarity within the gene ontology. BMC Bioinformatics 11, 562 (2010). PMID: 21078182.(see the section Independent research projects using iRefIndex)<br />
#Lopes, C.T. et al. Cytoscape Web: an interactive web-based network browser. Bioinformatics 26, 2347-2348 (2010). PMID: 20656902.iRefWeb was mentioned in this publication as a resource using Cytoscape web. <br />
#Nitsch, D., Goncalves, J.P., Ojeda, F., de Moor, B. & Moreau, Y. Candidate gene prioritization by network analysis of differential expression using machine learning approaches. BMC Bioinformatics 11, 460 (2010). PMID: 20840752. iRefIndex was mentioned as a consolidated data provider.<br />
#Pierri, C.L., Parisi, G. & Porcelli, V. Computational approaches for protein function prediction: A combined strategy from multiple sequence alignment to molecular docking-based virtual screening. Biochimica et Biophysica Acta (BBA) - Proteins & Proteomics 1804, 1695-1712 (2010). iRefIndex was mentioned as a protein-protein interaction data provider.<br />
<br />
===2009===<br />
#Blankenburg, H., Ramirez, F., Buch, J. & Albrecht, M. DASMIweb: online integration, analysis and assessment of distributed protein interaction data. Nucleic Acids Res 37, W122-128 (2009). PMID: 19502495. This project uses identifier cross referencing and grouping using Gene ID. These are practices iRefIndex trying to avoid. <br />
#Orchard, S. et al. Annual spring meeting of the Proteomics Standards Initiative. Proteomics 9, 4429-4432 (2009). PMID: 19670378. iRefIndex is mentioned in this publication because of the contribution to the PSICQUIC project. iRefIndex data is available via The psi common query interface because of this.<br />
#Terada, A. & Sese, J. Discovering large network motifs from a complex biological network. Journal of Physics: Conference Series 197, 012011 (2009).(see the section Independent research projects using iRefIndex)<br />
<br />
==Independent research projects using iRefIndex==<br />
Choi, H. et al. SAINT: probabilistic scoring of affinity purification-mass spectrometry data. Nat Methods 8, 70-73 (2011). PMID:18823568.<br />
*This publication discusses a computational tool (SAINT) to assign confidence scores to protein-protein interaction data generated using AP-MS. They have shown that SAINT is applicable to data of different scales and protein connectivity and allows transparent analysis of AP-MS data. This could also be used to filter AP-MS datasets containing non-specifically binding proteins. They have evaluated the performance of SAINT algorithm using iRefWeb and BioGRID. The iRefWeb search filters and parameters provide a nice way to construct custom data sets.<br />
Croft, D. et al. Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res 39, D691-697 (2011). PMID 21067998.<br />
*Curated bioinformatics database of human pathways and reactions. Uses PSIQUIC web services to overlay curated pathways with molecular interaction data from the Reactome Functional Interaction Network and external interaction databases such as IntAct, BioGRID, ChEMBL, iRefIndex, MINT and STRING. Expression Analysis tools enable ID mapping, pathway assignment and overrepresentation analysis of user-supplied data sets.<br />
Gillis, J. & Pavlidis, P. The role of indirect connections in gene networks in predicting function. Bioinformatics (2011). PMID 21551147.<br />
*Gene interactions can be used to infer functional relationships using a principle known as “guilt by association” (GBA).This research focuses on a extension of these methods, which is to incorporate the broader network structure (indirect connections among genes) into predictions. The iRefIndex data was used as a source when constructing the human PPI Network.<br />
Hao, Y. et al. OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms. Bioinformatics 27, 883-884 (2011). PMID: 21257609.<br />
*Cytoscape plugin that displays protein-protein interaction (PPI) networks from two organisms simultaneously, highlighting orthology relationships and aggregating several types of biomedical annotations. The iRefIndex data was used as PPI source.<br />
Jain, S. & Bader, G.D. An improved method for scoring protein-protein interactions using semantic similarity within the gene ontology. BMC Bioinformatics 11, 562 (2010). PMID 21078182.<br />
*More semantically similar the gene function annotations are among the interacting proteins, more likely the interaction is physiologically relevant. This method described in this paper uses this principle and will be useful as an evidence source in PPI prediction or in confidence assessment of PPI datasets. Compared to other such methods the algorithm described here considers unequal depth of biological knowledge representation in different branches of the GO graph. The iRefWeb was used to generate the data set.<br />
Terada, A. & Sese, J. Discovering large network motifs from a complex biological network. Journal of Physics: Conference Series 197, 012011 (2009).<br />
*Basic biological processes are highly related to each other. Network motif discovery detects frequently appearing network structures and also determines the role of vertices in a network. In this study, a novel algorithm called ARIANA was developed to find large network motifs even when the network has noise and uncertainty. By applying ARIANA to a real biological network, authors have found network motifs associated with regulation of cell. The iRefIndex was used construct a biological dataset to test this algorithm.<br />
Turinsky, A.L. et al. DAnCER: disease-annotated chromatin epigenetics resource. Nucleic Acids Res 39, D889-894 (2011). PMID 20876685.<br />
*Chromatin modification (CM) is a set of epigenetic processes that govern many aspects of DNA replication, transcription and repair. DAnCER resource integrates information on genes with CM function from five model organisms, including human. DAnCER integrates. disease information and functional annotations are mapped onto the protein interaction networks (constructed using iRefIndex), enabling the user to formulate new hypotheses on the function and disease associations of a given gene based on those of its interaction partners.<br />
Valsesia, A. et al. Network-guided analysis of genes with altered somatic copy number and gene expression reveals pathways commonly perturbed in metastatic melanoma. PLoS One 6, e18369 (2011). PMID 21494657.<br />
*Cancer genomes contain somatic copy number alterations (SCNA) that can significantly disturb the expression level of affected genes. This can disrupt pathways controlling normal growth. Using karyotyping, SNP and CGH arrays, and RNA-seq, they have identified SCNA affecting gene expression in human metastatic melanoma cell lines. They have showed that the combination of these techniques is useful to identify candidate genes potentially involved in tumorigenesis. A protein network-guided approach was used to determine whether any pathways were enriched in SCNA-genes in one or more samples.They have investigated whether the proteins encoded by the SCNA-genes were connected in known human protein interaction networks. In the protein network-guided analysis of SCNA, iRefIndex and Pathway Commons were used.<br />
Zhang, K.X. & Ouellette, B.F. CAERUS: predicting CAncER oUtcomeS using relationship between protein structural information, protein networks, gene expression data, and mutation data. PLoS Comput Biol 7, e1001114 (2011). PMID 21483478.<br />
*CAERUS: Predicting cancer outcomes Using Relationship between Protein Structural Information, Protein Networks, Gene Expression Data and Mutation Data. Carcinogenesis is a complex process with multiple genetic and environmental factors contributing to the development of one or more tumors. CAERUS can be used for identification of gene signatures to predict cancer outcomes based on the domain interaction network in human proteome. This work provides a prognostic tool to classify different cancer outcomes. When constructing the protein network iRefIndex was used.<br />
<br />
<br />
<br />
<br />
<br />
<br />
== All iRefIndex Pages ==<br />
<br />
Follow this link for a listing of all iRefIndex related pages (archived and current).<br />
[[Category:iRefIndex]]</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefIndex_Citations&diff=3504iRefIndex Citations2011-06-19T21:28:12Z<p>Sabry: /* 2011 */</p>
<hr />
<div>Some studies making use of iRefIndex<br />
<br />
==All citations==<br />
===2011===<br />
# Saliha Ece Acuner Ozbabacan,Hatice Billur Engin, Attila Gursoy1 and Ozlem Keskin1. Transient protein–protein interactions [http://www.ncbi.nlm.nih.gov/pubmed?term=21676899 '''PMID:21676899''']<br />
#Choi, H. et al. SAINT: probabilistic scoring of affinity purification-mass spectrometry data. Nat Methods 8, 70-73 (2011). [http://www.ncbi.nlm.nih.gov/pubmed?term=21131968 '''PMID:21131968''']. ([http://irefindex.uio.no/wiki/iRefIndex_Citations#Independent_research_projects_using_iRefIndex '''Read more'''])<br />
#Croft, D. et al. Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res 39, D691-697 (2011).[http://www.ncbi.nlm.nih.gov/pubmed?term=21067998 '''PMID: 21067998'''].([http://irefindex.uio.no/wiki/iRefIndex_Citations#Independent_research_projects_using_iRefIndex '''Read more'''])<br />
#Gillis, J. & Pavlidis, P. The role of indirect connections in gene networks in predicting function. Bioinformatics (2011). [http://www.ncbi.nlm.nih.gov/pubmed?term=21551147 '''PMID: 21551147''']. ([http://irefindex.uio.no/wiki/iRefIndex_Citations#Independent_research_projects_using_iRefIndex '''Read more'''])<br />
#Hao, Y. et al. OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms. Bioinformatics 27, 883-884 (2011). [http://www.ncbi.nlm.nih.gov/pubmed?term=21257609 '''PMID: 21257609'''] ([http://irefindex.uio.no/wiki/iRefIndex_Citations#Independent_research_projects_using_iRefIndex '''Read more'''])<br />
#Nolin, M.-A., Dumontier, M., Belleau, F. & Corbeil, J. Building an HIV data mashup using Bio2RDF. Briefings in Bioinformatics (2011).iRefindex was mentioned as a protein-protein interaction data provider and the contribution to Bio2RDF project. <br />
#Turinsky, A.L. et al. DAnCER: disease-annotated chromatin epigenetics resource. Nucleic Acids Res 39, D889-894 (2011). [http://www.ncbi.nlm.nih.gov/pubmed?term=20876685 '''PMID: 20876685''']. ([http://irefindex.uio.no/wiki/iRefIndex_Citations#Independent_research_projects_using_iRefIndex '''Read more'''])<br />
#Valsesia, A. et al. Network-guided analysis of genes with altered somatic copy number and gene expression reveals pathways commonly perturbed in metastatic melanoma. PLoS One 6, e18369 (2011). PMID: 21494657. ([http://irefindex.uio.no/wiki/iRefIndex_Citations#Independent_research_projects_using_iRefIndex '''Read more'''])<br />
#Vidal, M., Cusick, M.E. & Barabasi, A.L. Interactome networks and human disease. Cell 144, 986-998 (2011). PMID: 21414488. The literature curated data quality assessment project was mentioned. <br />
# Zhang, K.X. & Ouellette, B.F. CAERUS: predicting CAncER oUtcomeS using relationship between protein structural information, protein networks, gene expression data, and mutation data. PLoS Comput Biol 7, e1001114 (2011). PMID: 21483478.([http://irefindex.uio.no/wiki/iRefIndex_Citations#Independent_research_projects_using_iRefIndex '''Read more'''])<br />
<br />
===2010===<br />
#Ceol, A. et al. MINT, the molecular interaction database: 2009 update. Nucleic Acids Res 38, D532-539 (2010). PMID: 19897547. iRefIndex was mentioned as a consolidated data provider. <br />
#Garcia-Garcia, J., Guney, E., Aragues, R., Planas-Iglesias, J. & Oliva, B. Biana: a software framework for compiling biological interactions and analyzing networks. BMC Bioinformatics 11, 56 (2010). PMID: 20105306. iRefindex was compared to the system discussed in this paper. iRefIndex procedure was suggested as a Unification protocols to be used with the BIANA system.<br />
#Jain, S. & Bader, G.D. An improved method for scoring protein-protein interactions using semantic similarity within the gene ontology. BMC Bioinformatics 11, 562 (2010). PMID: 21078182.(see the section Independent research projects using iRefIndex)<br />
#Lopes, C.T. et al. Cytoscape Web: an interactive web-based network browser. Bioinformatics 26, 2347-2348 (2010). PMID: 20656902.iRefWeb was mentioned in this publication as a resource using Cytoscape web. <br />
#Nitsch, D., Goncalves, J.P., Ojeda, F., de Moor, B. & Moreau, Y. Candidate gene prioritization by network analysis of differential expression using machine learning approaches. BMC Bioinformatics 11, 460 (2010). PMID: 20840752. iRefIndex was mentioned as a consolidated data provider.<br />
#Pierri, C.L., Parisi, G. & Porcelli, V. Computational approaches for protein function prediction: A combined strategy from multiple sequence alignment to molecular docking-based virtual screening. Biochimica et Biophysica Acta (BBA) - Proteins & Proteomics 1804, 1695-1712 (2010). iRefIndex was mentioned as a protein-protein interaction data provider.<br />
<br />
===2009===<br />
#Blankenburg, H., Ramirez, F., Buch, J. & Albrecht, M. DASMIweb: online integration, analysis and assessment of distributed protein interaction data. Nucleic Acids Res 37, W122-128 (2009). PMID: 19502495. This project uses identifier cross referencing and grouping using Gene ID. These are practices iRefIndex trying to avoid. <br />
#Orchard, S. et al. Annual spring meeting of the Proteomics Standards Initiative. Proteomics 9, 4429-4432 (2009). PMID: 19670378. iRefIndex is mentioned in this publication because of the contribution to the PSICQUIC project. iRefIndex data is available via The psi common query interface because of this.<br />
#Terada, A. & Sese, J. Discovering large network motifs from a complex biological network. Journal of Physics: Conference Series 197, 012011 (2009).(see the section Independent research projects using iRefIndex)<br />
<br />
==Independent research projects using iRefIndex==<br />
Choi, H. et al. SAINT: probabilistic scoring of affinity purification-mass spectrometry data. Nat Methods 8, 70-73 (2011). PMID:18823568.<br />
*This publication discusses a computational tool (SAINT) to assign confidence scores to protein-protein interaction data generated using AP-MS. They have shown that SAINT is applicable to data of different scales and protein connectivity and allows transparent analysis of AP-MS data. This could also be used to filter AP-MS datasets containing non-specifically binding proteins. They have evaluated the performance of SAINT algorithm using iRefWeb and BioGRID. The iRefWeb search filters and parameters provide a nice way to construct custom data sets.<br />
Croft, D. et al. Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res 39, D691-697 (2011). PMID 21067998.<br />
*Curated bioinformatics database of human pathways and reactions. Uses PSIQUIC web services to overlay curated pathways with molecular interaction data from the Reactome Functional Interaction Network and external interaction databases such as IntAct, BioGRID, ChEMBL, iRefIndex, MINT and STRING. Expression Analysis tools enable ID mapping, pathway assignment and overrepresentation analysis of user-supplied data sets.<br />
Gillis, J. & Pavlidis, P. The role of indirect connections in gene networks in predicting function. Bioinformatics (2011). PMID 21551147.<br />
*Gene interactions can be used to infer functional relationships using a principle known as “guilt by association” (GBA).This research focuses on a extension of these methods, which is to incorporate the broader network structure (indirect connections among genes) into predictions. The iRefIndex data was used as a source when constructing the human PPI Network.<br />
Hao, Y. et al. OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms. Bioinformatics 27, 883-884 (2011). PMID: 21257609.<br />
*Cytoscape plugin that displays protein-protein interaction (PPI) networks from two organisms simultaneously, highlighting orthology relationships and aggregating several types of biomedical annotations. The iRefIndex data was used as PPI source.<br />
Jain, S. & Bader, G.D. An improved method for scoring protein-protein interactions using semantic similarity within the gene ontology. BMC Bioinformatics 11, 562 (2010). PMID 21078182.<br />
*More semantically similar the gene function annotations are among the interacting proteins, more likely the interaction is physiologically relevant. This method described in this paper uses this principle and will be useful as an evidence source in PPI prediction or in confidence assessment of PPI datasets. Compared to other such methods the algorithm described here considers unequal depth of biological knowledge representation in different branches of the GO graph. The iRefWeb was used to generate the data set.<br />
Terada, A. & Sese, J. Discovering large network motifs from a complex biological network. Journal of Physics: Conference Series 197, 012011 (2009).<br />
*Basic biological processes are highly related to each other. Network motif discovery detects frequently appearing network structures and also determines the role of vertices in a network. In this study, a novel algorithm called ARIANA was developed to find large network motifs even when the network has noise and uncertainty. By applying ARIANA to a real biological network, authors have found network motifs associated with regulation of cell. The iRefIndex was used construct a biological dataset to test this algorithm.<br />
Turinsky, A.L. et al. DAnCER: disease-annotated chromatin epigenetics resource. Nucleic Acids Res 39, D889-894 (2011). PMID 20876685.<br />
*Chromatin modification (CM) is a set of epigenetic processes that govern many aspects of DNA replication, transcription and repair. DAnCER resource integrates information on genes with CM function from five model organisms, including human. DAnCER integrates. disease information and functional annotations are mapped onto the protein interaction networks (constructed using iRefIndex), enabling the user to formulate new hypotheses on the function and disease associations of a given gene based on those of its interaction partners.<br />
Valsesia, A. et al. Network-guided analysis of genes with altered somatic copy number and gene expression reveals pathways commonly perturbed in metastatic melanoma. PLoS One 6, e18369 (2011). PMID 21494657.<br />
*Cancer genomes contain somatic copy number alterations (SCNA) that can significantly disturb the expression level of affected genes. This can disrupt pathways controlling normal growth. Using karyotyping, SNP and CGH arrays, and RNA-seq, they have identified SCNA affecting gene expression in human metastatic melanoma cell lines. They have showed that the combination of these techniques is useful to identify candidate genes potentially involved in tumorigenesis. A protein network-guided approach was used to determine whether any pathways were enriched in SCNA-genes in one or more samples.They have investigated whether the proteins encoded by the SCNA-genes were connected in known human protein interaction networks. In the protein network-guided analysis of SCNA, iRefIndex and Pathway Commons were used.<br />
Zhang, K.X. & Ouellette, B.F. CAERUS: predicting CAncER oUtcomeS using relationship between protein structural information, protein networks, gene expression data, and mutation data. PLoS Comput Biol 7, e1001114 (2011). PMID 21483478.<br />
*CAERUS: Predicting cancer outcomes Using Relationship between Protein Structural Information, Protein Networks, Gene Expression Data and Mutation Data. Carcinogenesis is a complex process with multiple genetic and environmental factors contributing to the development of one or more tumors. CAERUS can be used for identification of gene signatures to predict cancer outcomes based on the domain interaction network in human proteome. This work provides a prognostic tool to classify different cancer outcomes. When constructing the protein network iRefIndex was used.<br />
<br />
<br />
<br />
<br />
<br />
<br />
== All iRefIndex Pages ==<br />
<br />
Follow this link for a listing of all iRefIndex related pages (archived and current).<br />
[[Category:iRefIndex]]</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefIndex_Citations&diff=3503iRefIndex Citations2011-06-19T21:25:48Z<p>Sabry: /* 2011 */</p>
<hr />
<div>Some studies making use of iRefIndex<br />
<br />
==All citations==<br />
===2011===<br />
# Saliha Ece Acuner Ozbabacan,Hatice Billur Engin, Attila Gursoy1 and Ozlem Keskin1,Transient protein–protein interactions [http://www.ncbi.nlm.nih.gov/pubmed?term=21676899 '''PMID:21676899''']<br />
#Choi, H. et al. SAINT: probabilistic scoring of affinity purification-mass spectrometry data. Nat Methods 8, 70-73 (2011). [http://www.ncbi.nlm.nih.gov/pubmed?term=21131968 '''PMID:21131968''']. ([http://irefindex.uio.no/wiki/iRefIndex_Citations#Independent_research_projects_using_iRefIndex '''Read more'''])<br />
#Croft, D. et al. Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res 39, D691-697 (2011).[http://www.ncbi.nlm.nih.gov/pubmed?term=21067998 '''PMID: 21067998'''].([http://irefindex.uio.no/wiki/iRefIndex_Citations#Independent_research_projects_using_iRefIndex '''Read more'''])<br />
#Gillis, J. & Pavlidis, P. The role of indirect connections in gene networks in predicting function. Bioinformatics (2011). [http://www.ncbi.nlm.nih.gov/pubmed?term=21551147 '''PMID: 21551147''']. ([http://irefindex.uio.no/wiki/iRefIndex_Citations#Independent_research_projects_using_iRefIndex '''Read more'''])<br />
#Hao, Y. et al. OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms. Bioinformatics 27, 883-884 (2011). [http://www.ncbi.nlm.nih.gov/pubmed?term=21257609 '''PMID: 21257609'''] ([http://irefindex.uio.no/wiki/iRefIndex_Citations#Independent_research_projects_using_iRefIndex '''Read more'''])<br />
#Nolin, M.-A., Dumontier, M., Belleau, F. & Corbeil, J. Building an HIV data mashup using Bio2RDF. Briefings in Bioinformatics (2011).iRefindex was mentioned as a protein-protein interaction data provider and the contribution to Bio2RDF project. <br />
#Turinsky, A.L. et al. DAnCER: disease-annotated chromatin epigenetics resource. Nucleic Acids Res 39, D889-894 (2011). [http://www.ncbi.nlm.nih.gov/pubmed?term=20876685 '''PMID: 20876685''']. ([http://irefindex.uio.no/wiki/iRefIndex_Citations#Independent_research_projects_using_iRefIndex '''Read more'''])<br />
#Valsesia, A. et al. Network-guided analysis of genes with altered somatic copy number and gene expression reveals pathways commonly perturbed in metastatic melanoma. PLoS One 6, e18369 (2011). PMID: 21494657. ([http://irefindex.uio.no/wiki/iRefIndex_Citations#Independent_research_projects_using_iRefIndex '''Read more'''])<br />
#Vidal, M., Cusick, M.E. & Barabasi, A.L. Interactome networks and human disease. Cell 144, 986-998 (2011). PMID: 21414488. The literature curated data quality assessment project was mentioned. <br />
# Zhang, K.X. & Ouellette, B.F. CAERUS: predicting CAncER oUtcomeS using relationship between protein structural information, protein networks, gene expression data, and mutation data. PLoS Comput Biol 7, e1001114 (2011). PMID: 21483478.([http://irefindex.uio.no/wiki/iRefIndex_Citations#Independent_research_projects_using_iRefIndex '''Read more'''])<br />
<br />
===2010===<br />
#Ceol, A. et al. MINT, the molecular interaction database: 2009 update. Nucleic Acids Res 38, D532-539 (2010). PMID: 19897547. iRefIndex was mentioned as a consolidated data provider. <br />
#Garcia-Garcia, J., Guney, E., Aragues, R., Planas-Iglesias, J. & Oliva, B. Biana: a software framework for compiling biological interactions and analyzing networks. BMC Bioinformatics 11, 56 (2010). PMID: 20105306. iRefindex was compared to the system discussed in this paper. iRefIndex procedure was suggested as a Unification protocols to be used with the BIANA system.<br />
#Jain, S. & Bader, G.D. An improved method for scoring protein-protein interactions using semantic similarity within the gene ontology. BMC Bioinformatics 11, 562 (2010). PMID: 21078182.(see the section Independent research projects using iRefIndex)<br />
#Lopes, C.T. et al. Cytoscape Web: an interactive web-based network browser. Bioinformatics 26, 2347-2348 (2010). PMID: 20656902.iRefWeb was mentioned in this publication as a resource using Cytoscape web. <br />
#Nitsch, D., Goncalves, J.P., Ojeda, F., de Moor, B. & Moreau, Y. Candidate gene prioritization by network analysis of differential expression using machine learning approaches. BMC Bioinformatics 11, 460 (2010). PMID: 20840752. iRefIndex was mentioned as a consolidated data provider.<br />
#Pierri, C.L., Parisi, G. & Porcelli, V. Computational approaches for protein function prediction: A combined strategy from multiple sequence alignment to molecular docking-based virtual screening. Biochimica et Biophysica Acta (BBA) - Proteins & Proteomics 1804, 1695-1712 (2010). iRefIndex was mentioned as a protein-protein interaction data provider.<br />
<br />
===2009===<br />
#Blankenburg, H., Ramirez, F., Buch, J. & Albrecht, M. DASMIweb: online integration, analysis and assessment of distributed protein interaction data. Nucleic Acids Res 37, W122-128 (2009). PMID: 19502495. This project uses identifier cross referencing and grouping using Gene ID. These are practices iRefIndex trying to avoid. <br />
#Orchard, S. et al. Annual spring meeting of the Proteomics Standards Initiative. Proteomics 9, 4429-4432 (2009). PMID: 19670378. iRefIndex is mentioned in this publication because of the contribution to the PSICQUIC project. iRefIndex data is available via The psi common query interface because of this.<br />
#Terada, A. & Sese, J. Discovering large network motifs from a complex biological network. Journal of Physics: Conference Series 197, 012011 (2009).(see the section Independent research projects using iRefIndex)<br />
<br />
==Independent research projects using iRefIndex==<br />
Choi, H. et al. SAINT: probabilistic scoring of affinity purification-mass spectrometry data. Nat Methods 8, 70-73 (2011). PMID:18823568.<br />
*This publication discusses a computational tool (SAINT) to assign confidence scores to protein-protein interaction data generated using AP-MS. They have shown that SAINT is applicable to data of different scales and protein connectivity and allows transparent analysis of AP-MS data. This could also be used to filter AP-MS datasets containing non-specifically binding proteins. They have evaluated the performance of SAINT algorithm using iRefWeb and BioGRID. The iRefWeb search filters and parameters provide a nice way to construct custom data sets.<br />
Croft, D. et al. Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res 39, D691-697 (2011). PMID 21067998.<br />
*Curated bioinformatics database of human pathways and reactions. Uses PSIQUIC web services to overlay curated pathways with molecular interaction data from the Reactome Functional Interaction Network and external interaction databases such as IntAct, BioGRID, ChEMBL, iRefIndex, MINT and STRING. Expression Analysis tools enable ID mapping, pathway assignment and overrepresentation analysis of user-supplied data sets.<br />
Gillis, J. & Pavlidis, P. The role of indirect connections in gene networks in predicting function. Bioinformatics (2011). PMID 21551147.<br />
*Gene interactions can be used to infer functional relationships using a principle known as “guilt by association” (GBA).This research focuses on a extension of these methods, which is to incorporate the broader network structure (indirect connections among genes) into predictions. The iRefIndex data was used as a source when constructing the human PPI Network.<br />
Hao, Y. et al. OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms. Bioinformatics 27, 883-884 (2011). PMID: 21257609.<br />
*Cytoscape plugin that displays protein-protein interaction (PPI) networks from two organisms simultaneously, highlighting orthology relationships and aggregating several types of biomedical annotations. The iRefIndex data was used as PPI source.<br />
Jain, S. & Bader, G.D. An improved method for scoring protein-protein interactions using semantic similarity within the gene ontology. BMC Bioinformatics 11, 562 (2010). PMID 21078182.<br />
*More semantically similar the gene function annotations are among the interacting proteins, more likely the interaction is physiologically relevant. This method described in this paper uses this principle and will be useful as an evidence source in PPI prediction or in confidence assessment of PPI datasets. Compared to other such methods the algorithm described here considers unequal depth of biological knowledge representation in different branches of the GO graph. The iRefWeb was used to generate the data set.<br />
Terada, A. & Sese, J. Discovering large network motifs from a complex biological network. Journal of Physics: Conference Series 197, 012011 (2009).<br />
*Basic biological processes are highly related to each other. Network motif discovery detects frequently appearing network structures and also determines the role of vertices in a network. In this study, a novel algorithm called ARIANA was developed to find large network motifs even when the network has noise and uncertainty. By applying ARIANA to a real biological network, authors have found network motifs associated with regulation of cell. The iRefIndex was used construct a biological dataset to test this algorithm.<br />
Turinsky, A.L. et al. DAnCER: disease-annotated chromatin epigenetics resource. Nucleic Acids Res 39, D889-894 (2011). PMID 20876685.<br />
*Chromatin modification (CM) is a set of epigenetic processes that govern many aspects of DNA replication, transcription and repair. DAnCER resource integrates information on genes with CM function from five model organisms, including human. DAnCER integrates. disease information and functional annotations are mapped onto the protein interaction networks (constructed using iRefIndex), enabling the user to formulate new hypotheses on the function and disease associations of a given gene based on those of its interaction partners.<br />
Valsesia, A. et al. Network-guided analysis of genes with altered somatic copy number and gene expression reveals pathways commonly perturbed in metastatic melanoma. PLoS One 6, e18369 (2011). PMID 21494657.<br />
*Cancer genomes contain somatic copy number alterations (SCNA) that can significantly disturb the expression level of affected genes. This can disrupt pathways controlling normal growth. Using karyotyping, SNP and CGH arrays, and RNA-seq, they have identified SCNA affecting gene expression in human metastatic melanoma cell lines. They have showed that the combination of these techniques is useful to identify candidate genes potentially involved in tumorigenesis. A protein network-guided approach was used to determine whether any pathways were enriched in SCNA-genes in one or more samples.They have investigated whether the proteins encoded by the SCNA-genes were connected in known human protein interaction networks. In the protein network-guided analysis of SCNA, iRefIndex and Pathway Commons were used.<br />
Zhang, K.X. & Ouellette, B.F. CAERUS: predicting CAncER oUtcomeS using relationship between protein structural information, protein networks, gene expression data, and mutation data. PLoS Comput Biol 7, e1001114 (2011). PMID 21483478.<br />
*CAERUS: Predicting cancer outcomes Using Relationship between Protein Structural Information, Protein Networks, Gene Expression Data and Mutation Data. Carcinogenesis is a complex process with multiple genetic and environmental factors contributing to the development of one or more tumors. CAERUS can be used for identification of gene signatures to predict cancer outcomes based on the domain interaction network in human proteome. This work provides a prognostic tool to classify different cancer outcomes. When constructing the protein network iRefIndex was used.<br />
<br />
<br />
<br />
<br />
<br />
<br />
== All iRefIndex Pages ==<br />
<br />
Follow this link for a listing of all iRefIndex related pages (archived and current).<br />
[[Category:iRefIndex]]</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefIndex_Citations&diff=3502iRefIndex Citations2011-06-19T21:25:23Z<p>Sabry: /* 2011 */</p>
<hr />
<div>Some studies making use of iRefIndex<br />
<br />
==All citations==<br />
===2011===<br />
# Saliha Ece Acuner Ozbabacan,Hatice Billur Engin, Attila Gursoy1 and Ozlem Keskin1,Transient protein–protein interactions [http://www.ncbi.nlm.nih.gov/pubmed?term=21676899 '''PMID:21676899''']<br />
# [http://www.ncbi.nlm.nih.gov/pubmed?term=21676899 '''PMID:21676899''']<br />
#Choi, H. et al. SAINT: probabilistic scoring of affinity purification-mass spectrometry data. Nat Methods 8, 70-73 (2011). [http://www.ncbi.nlm.nih.gov/pubmed?term=21131968 '''PMID:21131968''']. ([http://irefindex.uio.no/wiki/iRefIndex_Citations#Independent_research_projects_using_iRefIndex '''Read more'''])<br />
#Croft, D. et al. Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res 39, D691-697 (2011).[http://www.ncbi.nlm.nih.gov/pubmed?term=21067998 '''PMID: 21067998'''].([http://irefindex.uio.no/wiki/iRefIndex_Citations#Independent_research_projects_using_iRefIndex '''Read more'''])<br />
#Gillis, J. & Pavlidis, P. The role of indirect connections in gene networks in predicting function. Bioinformatics (2011). [http://www.ncbi.nlm.nih.gov/pubmed?term=21551147 '''PMID: 21551147''']. ([http://irefindex.uio.no/wiki/iRefIndex_Citations#Independent_research_projects_using_iRefIndex '''Read more'''])<br />
#Hao, Y. et al. OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms. Bioinformatics 27, 883-884 (2011). [http://www.ncbi.nlm.nih.gov/pubmed?term=21257609 '''PMID: 21257609'''] ([http://irefindex.uio.no/wiki/iRefIndex_Citations#Independent_research_projects_using_iRefIndex '''Read more'''])<br />
#Nolin, M.-A., Dumontier, M., Belleau, F. & Corbeil, J. Building an HIV data mashup using Bio2RDF. Briefings in Bioinformatics (2011).iRefindex was mentioned as a protein-protein interaction data provider and the contribution to Bio2RDF project. <br />
#Turinsky, A.L. et al. DAnCER: disease-annotated chromatin epigenetics resource. Nucleic Acids Res 39, D889-894 (2011). [http://www.ncbi.nlm.nih.gov/pubmed?term=20876685 '''PMID: 20876685''']. ([http://irefindex.uio.no/wiki/iRefIndex_Citations#Independent_research_projects_using_iRefIndex '''Read more'''])<br />
#Valsesia, A. et al. Network-guided analysis of genes with altered somatic copy number and gene expression reveals pathways commonly perturbed in metastatic melanoma. PLoS One 6, e18369 (2011). PMID: 21494657. ([http://irefindex.uio.no/wiki/iRefIndex_Citations#Independent_research_projects_using_iRefIndex '''Read more'''])<br />
#Vidal, M., Cusick, M.E. & Barabasi, A.L. Interactome networks and human disease. Cell 144, 986-998 (2011). PMID: 21414488. The literature curated data quality assessment project was mentioned. <br />
# Zhang, K.X. & Ouellette, B.F. CAERUS: predicting CAncER oUtcomeS using relationship between protein structural information, protein networks, gene expression data, and mutation data. PLoS Comput Biol 7, e1001114 (2011). PMID: 21483478.([http://irefindex.uio.no/wiki/iRefIndex_Citations#Independent_research_projects_using_iRefIndex '''Read more'''])<br />
<br />
===2010===<br />
#Ceol, A. et al. MINT, the molecular interaction database: 2009 update. Nucleic Acids Res 38, D532-539 (2010). PMID: 19897547. iRefIndex was mentioned as a consolidated data provider. <br />
#Garcia-Garcia, J., Guney, E., Aragues, R., Planas-Iglesias, J. & Oliva, B. Biana: a software framework for compiling biological interactions and analyzing networks. BMC Bioinformatics 11, 56 (2010). PMID: 20105306. iRefindex was compared to the system discussed in this paper. iRefIndex procedure was suggested as a Unification protocols to be used with the BIANA system.<br />
#Jain, S. & Bader, G.D. An improved method for scoring protein-protein interactions using semantic similarity within the gene ontology. BMC Bioinformatics 11, 562 (2010). PMID: 21078182.(see the section Independent research projects using iRefIndex)<br />
#Lopes, C.T. et al. Cytoscape Web: an interactive web-based network browser. Bioinformatics 26, 2347-2348 (2010). PMID: 20656902.iRefWeb was mentioned in this publication as a resource using Cytoscape web. <br />
#Nitsch, D., Goncalves, J.P., Ojeda, F., de Moor, B. & Moreau, Y. Candidate gene prioritization by network analysis of differential expression using machine learning approaches. BMC Bioinformatics 11, 460 (2010). PMID: 20840752. iRefIndex was mentioned as a consolidated data provider.<br />
#Pierri, C.L., Parisi, G. & Porcelli, V. Computational approaches for protein function prediction: A combined strategy from multiple sequence alignment to molecular docking-based virtual screening. Biochimica et Biophysica Acta (BBA) - Proteins & Proteomics 1804, 1695-1712 (2010). iRefIndex was mentioned as a protein-protein interaction data provider.<br />
<br />
===2009===<br />
#Blankenburg, H., Ramirez, F., Buch, J. & Albrecht, M. DASMIweb: online integration, analysis and assessment of distributed protein interaction data. Nucleic Acids Res 37, W122-128 (2009). PMID: 19502495. This project uses identifier cross referencing and grouping using Gene ID. These are practices iRefIndex trying to avoid. <br />
#Orchard, S. et al. Annual spring meeting of the Proteomics Standards Initiative. Proteomics 9, 4429-4432 (2009). PMID: 19670378. iRefIndex is mentioned in this publication because of the contribution to the PSICQUIC project. iRefIndex data is available via The psi common query interface because of this.<br />
#Terada, A. & Sese, J. Discovering large network motifs from a complex biological network. Journal of Physics: Conference Series 197, 012011 (2009).(see the section Independent research projects using iRefIndex)<br />
<br />
==Independent research projects using iRefIndex==<br />
Choi, H. et al. SAINT: probabilistic scoring of affinity purification-mass spectrometry data. Nat Methods 8, 70-73 (2011). PMID:18823568.<br />
*This publication discusses a computational tool (SAINT) to assign confidence scores to protein-protein interaction data generated using AP-MS. They have shown that SAINT is applicable to data of different scales and protein connectivity and allows transparent analysis of AP-MS data. This could also be used to filter AP-MS datasets containing non-specifically binding proteins. They have evaluated the performance of SAINT algorithm using iRefWeb and BioGRID. The iRefWeb search filters and parameters provide a nice way to construct custom data sets.<br />
Croft, D. et al. Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res 39, D691-697 (2011). PMID 21067998.<br />
*Curated bioinformatics database of human pathways and reactions. Uses PSIQUIC web services to overlay curated pathways with molecular interaction data from the Reactome Functional Interaction Network and external interaction databases such as IntAct, BioGRID, ChEMBL, iRefIndex, MINT and STRING. Expression Analysis tools enable ID mapping, pathway assignment and overrepresentation analysis of user-supplied data sets.<br />
Gillis, J. & Pavlidis, P. The role of indirect connections in gene networks in predicting function. Bioinformatics (2011). PMID 21551147.<br />
*Gene interactions can be used to infer functional relationships using a principle known as “guilt by association” (GBA).This research focuses on a extension of these methods, which is to incorporate the broader network structure (indirect connections among genes) into predictions. The iRefIndex data was used as a source when constructing the human PPI Network.<br />
Hao, Y. et al. OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms. Bioinformatics 27, 883-884 (2011). PMID: 21257609.<br />
*Cytoscape plugin that displays protein-protein interaction (PPI) networks from two organisms simultaneously, highlighting orthology relationships and aggregating several types of biomedical annotations. The iRefIndex data was used as PPI source.<br />
Jain, S. & Bader, G.D. An improved method for scoring protein-protein interactions using semantic similarity within the gene ontology. BMC Bioinformatics 11, 562 (2010). PMID 21078182.<br />
*More semantically similar the gene function annotations are among the interacting proteins, more likely the interaction is physiologically relevant. This method described in this paper uses this principle and will be useful as an evidence source in PPI prediction or in confidence assessment of PPI datasets. Compared to other such methods the algorithm described here considers unequal depth of biological knowledge representation in different branches of the GO graph. The iRefWeb was used to generate the data set.<br />
Terada, A. & Sese, J. Discovering large network motifs from a complex biological network. Journal of Physics: Conference Series 197, 012011 (2009).<br />
*Basic biological processes are highly related to each other. Network motif discovery detects frequently appearing network structures and also determines the role of vertices in a network. In this study, a novel algorithm called ARIANA was developed to find large network motifs even when the network has noise and uncertainty. By applying ARIANA to a real biological network, authors have found network motifs associated with regulation of cell. The iRefIndex was used construct a biological dataset to test this algorithm.<br />
Turinsky, A.L. et al. DAnCER: disease-annotated chromatin epigenetics resource. Nucleic Acids Res 39, D889-894 (2011). PMID 20876685.<br />
*Chromatin modification (CM) is a set of epigenetic processes that govern many aspects of DNA replication, transcription and repair. DAnCER resource integrates information on genes with CM function from five model organisms, including human. DAnCER integrates. disease information and functional annotations are mapped onto the protein interaction networks (constructed using iRefIndex), enabling the user to formulate new hypotheses on the function and disease associations of a given gene based on those of its interaction partners.<br />
Valsesia, A. et al. Network-guided analysis of genes with altered somatic copy number and gene expression reveals pathways commonly perturbed in metastatic melanoma. PLoS One 6, e18369 (2011). PMID 21494657.<br />
*Cancer genomes contain somatic copy number alterations (SCNA) that can significantly disturb the expression level of affected genes. This can disrupt pathways controlling normal growth. Using karyotyping, SNP and CGH arrays, and RNA-seq, they have identified SCNA affecting gene expression in human metastatic melanoma cell lines. They have showed that the combination of these techniques is useful to identify candidate genes potentially involved in tumorigenesis. A protein network-guided approach was used to determine whether any pathways were enriched in SCNA-genes in one or more samples.They have investigated whether the proteins encoded by the SCNA-genes were connected in known human protein interaction networks. In the protein network-guided analysis of SCNA, iRefIndex and Pathway Commons were used.<br />
Zhang, K.X. & Ouellette, B.F. CAERUS: predicting CAncER oUtcomeS using relationship between protein structural information, protein networks, gene expression data, and mutation data. PLoS Comput Biol 7, e1001114 (2011). PMID 21483478.<br />
*CAERUS: Predicting cancer outcomes Using Relationship between Protein Structural Information, Protein Networks, Gene Expression Data and Mutation Data. Carcinogenesis is a complex process with multiple genetic and environmental factors contributing to the development of one or more tumors. CAERUS can be used for identification of gene signatures to predict cancer outcomes based on the domain interaction network in human proteome. This work provides a prognostic tool to classify different cancer outcomes. When constructing the protein network iRefIndex was used.<br />
<br />
<br />
<br />
<br />
<br />
<br />
== All iRefIndex Pages ==<br />
<br />
Follow this link for a listing of all iRefIndex related pages (archived and current).<br />
[[Category:iRefIndex]]</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefIndex_MITAB_Mapping&diff=3482iRefIndex MITAB Mapping2011-06-10T16:33:54Z<p>Sabry: /* Summary mapping created a summary table*/</p>
<hr />
<div>Unlike the parsing of PSI MI XML files, whose attributes correspond to certain tables and columns in the iRefIndex schema, the parsing and interpretation of MITAB files involves a separate mapping of MITAB format columns to such tables and columns in the schema.<br />
<br />
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"<br />
! MITAB columns<br />
! Data components<br />
! Entity<br />
! iRefIndex table and column assignments<br />
! iRefIndex category<br />
|-<br />
| uidA<br />
| rowspan="6" | <tt>''database'':''identifier''</tt><br />
| rowspan="6" | Interactor<br />
| rowspan="4" | <tt>int_xref.dbid = id(''database'')</tt><br><tt>int_xref.acc = ''identifier''</tt><br />
| rowspan="2" | object_primaryref<br />
|-<br />
| uidB<br />
|-<br />
| altA<br />
| rowspan="2" | object_secondaryref<br />
|-<br />
| altB<br />
|-<br />
| aliasA<br />
| rowspan="2" | <tt>int_name.name = ''identifier''</tt><br><tt>int_name.MI = 'MI:0000'</tt><br />
| rowspan="2" | object_alias<br />
|-<br />
| aliasB<br />
|-<br />
| rowspan="2" | method<br />
| rowspan="2" | <tt>''code''(''description'')</tt><br />
| rowspan="2" | Experiment<br />
| <tt>int_xref.dbid = id('psi-mi')</tt><br><tt>int_xref.acc = ''code''</tt><br />
| int_ditection_primaryref<br />
|-<br />
| <tt>int_name.MI = ''code''</tt><br><tt>int_name.name = ''description''</tt><br />
| int_ditection_shortlbl<br />
|-<br />
| authors<br />
| (free text)<br />
| rowspan="2" | Experiment<br />
|<br />
|<br />
|-<br />
| pmids<br />
| <tt>pubmed:''identifier''</tt><br />
| <tt>int_experiment.ex_bib_pri = ''identifier''</tt><br />
| (not applicable)<br />
|-<br />
| taxA<br />
| rowspan="2" | <tt>taxid:''identifier''</tt><br />
| rowspan="2" | Interactor<br />
| rowspan="2" | <tt>int_xref.taxid = ''identifier''</tt><br />
| rowspan="2" | (part of interactor entries labelled with object_primaryref and object_secondaryref only)<br />
|-<br />
| taxB<br />
|-<br />
| rowspan="2" | interactionType<br />
| rowspan="3" | <tt>''code''(''description'')</tt><br />
| rowspan="2" | Interaction<br />
| <tt>int_xref.dbid = id('psi-mi')</tt><br><tt>int_xref.acc = ''code''</tt><br />
| int_type_primaryref<br />
|-<br />
| <tt>int_name.MI = ''code''</tt><br><tt>int_name.name = ''description''</tt><br />
| int_type_sh<br />
|-<br />
| sourcedb<br />
| Interactor/interaction<br />
| <tt>int_source.source = id(''description'')</tt><br><tt>int_object.source = id(''description'')</tt><br><tt>int_source2object.source = id(''description'')</tt><br />
| (not applicable)<br />
|-<br />
| interactionIdentifiers<br />
| <tt>''database'':''identifier''</tt><br />
| Interaction<br />
| <tt>int_xref.dbid = ''database''</tt><br><tt>int_xref.acc = ''identifier''</tt><br />
| interaction_primaryref<br />
|-<br />
| confidence<br />
|<br />
|<br />
|<br />
|<br />
|}<br />
<br />
=== Summary mapping ===<br />
{|border="1" cellspacing="0" cellpadding="5" style="margin: 2em" {{table}}<br />
| align="center" style="background:#f0f0f0;"|'''Column_Number'''<br />
| align="center" style="background:#f0f0f0;"|'''Column_Name'''<br />
| align="center" style="background:#f0f0f0;"|'''UID_to _use'''<br />
| align="center" style="background:#f0f0f0;"|'''Table_to_use'''<br />
| align="center" style="background:#f0f0f0;"|'''Category_to_use'''<br />
| align="center" style="background:#f0f0f0;"|'''Category_ID'''<br />
|-<br />
| 1||uidA||Interactor_A||int_xref||object_primaryref||2<br />
|-<br />
| 2||uidB||Interactor_B||int_xref||object_primaryref||2<br />
|-<br />
| 3||altA||Interactor_A||int_xref||object_secondaryref||3<br />
|-<br />
| 4||altB||Interactor_B||int_xref||object_secondaryref||4<br />
|-<br />
| 5||aliasA (First )||Interactor_A||int_name||First entry object_shortlbl||10,11<br />
|-<br />
| 6||aliasB(First)||Interactor_B||int_name||First entry object_shortlbl||10,11<br />
|-<br />
| 5||aliasA(From second)||Interactor_A||int_name||object_alias||14<br />
|-<br />
| 6||aliasB(From second)||Interactor_B||int_name||object_alias||14<br />
|-<br />
| 7||Method (MI identfier)||Experiment||int_xref||int_detection_primaryref||6<br />
|-<br />
| 7||Method (name)||Experiment||int_name||int_detection_shortlbl||24<br />
|-<br />
| 8||author||Experiment||int_name||experim_shortlbl||18<br />
|-<br />
| 9||Pmids (frist one)||Experiment||int_xref||bib_primaryref ||4<br />
|-<br />
| 9||Pmids (Second one onwards)||Experiment||int_xref||bib_secondaryref ||5<br />
|-<br />
| 10||taxa||(used with uidA)||||||<br />
|-<br />
| 11||taxb||(used with uidB)||||||<br />
|-<br />
| 12||interactionType||Interaction||int_name||int_type_sh||27<br />
|-<br />
| 13||sourcedb||(used with interactionIdentifier)||||||<br />
|-<br />
| 14||interactionIdentifier||Interaction||int_xref||interaction_primaryref||0<br />
| <br />
|}</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefIndex_MITAB_Mapping&diff=3481iRefIndex MITAB Mapping2011-06-10T16:32:35Z<p>Sabry: </p>
<hr />
<div>Unlike the parsing of PSI MI XML files, whose attributes correspond to certain tables and columns in the iRefIndex schema, the parsing and interpretation of MITAB files involves a separate mapping of MITAB format columns to such tables and columns in the schema.<br />
<br />
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"<br />
! MITAB columns<br />
! Data components<br />
! Entity<br />
! iRefIndex table and column assignments<br />
! iRefIndex category<br />
|-<br />
| uidA<br />
| rowspan="6" | <tt>''database'':''identifier''</tt><br />
| rowspan="6" | Interactor<br />
| rowspan="4" | <tt>int_xref.dbid = id(''database'')</tt><br><tt>int_xref.acc = ''identifier''</tt><br />
| rowspan="2" | object_primaryref<br />
|-<br />
| uidB<br />
|-<br />
| altA<br />
| rowspan="2" | object_secondaryref<br />
|-<br />
| altB<br />
|-<br />
| aliasA<br />
| rowspan="2" | <tt>int_name.name = ''identifier''</tt><br><tt>int_name.MI = 'MI:0000'</tt><br />
| rowspan="2" | object_alias<br />
|-<br />
| aliasB<br />
|-<br />
| rowspan="2" | method<br />
| rowspan="2" | <tt>''code''(''description'')</tt><br />
| rowspan="2" | Experiment<br />
| <tt>int_xref.dbid = id('psi-mi')</tt><br><tt>int_xref.acc = ''code''</tt><br />
| int_ditection_primaryref<br />
|-<br />
| <tt>int_name.MI = ''code''</tt><br><tt>int_name.name = ''description''</tt><br />
| int_ditection_shortlbl<br />
|-<br />
| authors<br />
| (free text)<br />
| rowspan="2" | Experiment<br />
|<br />
|<br />
|-<br />
| pmids<br />
| <tt>pubmed:''identifier''</tt><br />
| <tt>int_experiment.ex_bib_pri = ''identifier''</tt><br />
| (not applicable)<br />
|-<br />
| taxA<br />
| rowspan="2" | <tt>taxid:''identifier''</tt><br />
| rowspan="2" | Interactor<br />
| rowspan="2" | <tt>int_xref.taxid = ''identifier''</tt><br />
| rowspan="2" | (part of interactor entries labelled with object_primaryref and object_secondaryref only)<br />
|-<br />
| taxB<br />
|-<br />
| rowspan="2" | interactionType<br />
| rowspan="3" | <tt>''code''(''description'')</tt><br />
| rowspan="2" | Interaction<br />
| <tt>int_xref.dbid = id('psi-mi')</tt><br><tt>int_xref.acc = ''code''</tt><br />
| int_type_primaryref<br />
|-<br />
| <tt>int_name.MI = ''code''</tt><br><tt>int_name.name = ''description''</tt><br />
| int_type_sh<br />
|-<br />
| sourcedb<br />
| Interactor/interaction<br />
| <tt>int_source.source = id(''description'')</tt><br><tt>int_object.source = id(''description'')</tt><br><tt>int_source2object.source = id(''description'')</tt><br />
| (not applicable)<br />
|-<br />
| interactionIdentifiers<br />
| <tt>''database'':''identifier''</tt><br />
| Interaction<br />
| <tt>int_xref.dbid = ''database''</tt><br><tt>int_xref.acc = ''identifier''</tt><br />
| interaction_primaryref<br />
|-<br />
| confidence<br />
|<br />
|<br />
|<br />
|<br />
|}<br />
<br />
=== Summary mapping ===<br />
{|border="1" cellspacing="0" cellpadding="5" style="margin: 2em" {{table}}<br />
| align="center" style="background:#f0f0f0;"|'''Column_Number'''<br />
| align="center" style="background:#f0f0f0;"|'''Column_Name'''<br />
| align="center" style="background:#f0f0f0;"|'''UID_to _use'''<br />
| align="center" style="background:#f0f0f0;"|'''Table_to_use'''<br />
| align="center" style="background:#f0f0f0;"|'''Category_to_use'''<br />
| align="center" style="background:#f0f0f0;"|'''Category_ID'''<br />
|-<br />
| 1||uidA||Interactor_A||int_xref||object_primaryref||2<br />
|-<br />
| 2||uidB||Interactor_B||int_xref||object_primaryref||2<br />
|-<br />
| 3||altA||Interactor_A||int_xref||object_secondaryref||3<br />
|-<br />
| 4||altB||Interactor_B||int_xref||object_secondaryref||4<br />
|-<br />
| 5||aliasA (First )||Interactor_A||int_name||First entry object_shortlbl||10,11<br />
|-<br />
| 6||aliasB(First)||Interactor_B||int_name||First entry object_shortlbl||10,11<br />
|-<br />
| 5||aliasA(From second)||Interactor_A||int_name||object_alias||<br />
|-<br />
| 6||aliasB(From second)||Interactor_B||int_name||object_alias||<br />
|-<br />
| 7||Method (MI identfier)||Experiment||int_xref||int_detection_primaryref||6<br />
|-<br />
| 7||Method (name)||Experiment||int_name||int_detection_shortlbl||24<br />
|-<br />
| 8||author||Experiment||int_name||experim_shortlbl||18<br />
|-<br />
| 9||Pmids (frist one)||Experiment||int_xref||bib_primaryref ||4<br />
|-<br />
| 9||Pmids (Second one onwards)||Experiment||int_xref||bib_secondaryref ||5<br />
|-<br />
| 10||taxa||(used with uidA)||||||<br />
|-<br />
| 11||taxb||(used with uidB)||||||<br />
|-<br />
| 12||interactionType||Interaction||int_name||int_type_sh||27<br />
|-<br />
| 13||sourcedb||(used with interactionIdentifier)||||||<br />
|-<br />
| 14||interactionIdentifier||Interaction||int_xref||interaction_primaryref||0<br />
| <br />
|}</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefIndex_MITAB_Mapping&diff=3480iRefIndex MITAB Mapping2011-06-10T16:09:52Z<p>Sabry: </p>
<hr />
<div>Unlike the parsing of PSI MI XML files, whose attributes correspond to certain tables and columns in the iRefIndex schema, the parsing and interpretation of MITAB files involves a separate mapping of MITAB format columns to such tables and columns in the schema.<br />
<br />
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"<br />
! MITAB columns<br />
! Data components<br />
! Entity<br />
! iRefIndex table and column assignments<br />
! iRefIndex category<br />
|-<br />
| uidA<br />
| rowspan="6" | <tt>''database'':''identifier''</tt><br />
| rowspan="6" | Interactor<br />
| rowspan="4" | <tt>int_xref.dbid = id(''database'')</tt><br><tt>int_xref.acc = ''identifier''</tt><br />
| rowspan="2" | object_primaryref<br />
|-<br />
| uidB<br />
|-<br />
| altA<br />
| rowspan="2" | object_secondaryref<br />
|-<br />
| altB<br />
|-<br />
| aliasA<br />
| rowspan="2" | <tt>int_name.name = ''identifier''</tt><br><tt>int_name.MI = 'MI:0000'</tt><br />
| rowspan="2" | object_alias<br />
|-<br />
| aliasB<br />
|-<br />
| rowspan="2" | method<br />
| rowspan="2" | <tt>''code''(''description'')</tt><br />
| rowspan="2" | Experiment<br />
| <tt>int_xref.dbid = id('psi-mi')</tt><br><tt>int_xref.acc = ''code''</tt><br />
| int_ditection_primaryref<br />
|-<br />
| <tt>int_name.MI = ''code''</tt><br><tt>int_name.name = ''description''</tt><br />
| int_ditection_shortlbl<br />
|-<br />
| authors<br />
| (free text)<br />
| rowspan="2" | Experiment<br />
|<br />
|<br />
|-<br />
| pmids<br />
| <tt>pubmed:''identifier''</tt><br />
| <tt>int_experiment.ex_bib_pri = ''identifier''</tt><br />
| (not applicable)<br />
|-<br />
| taxA<br />
| rowspan="2" | <tt>taxid:''identifier''</tt><br />
| rowspan="2" | Interactor<br />
| rowspan="2" | <tt>int_xref.taxid = ''identifier''</tt><br />
| rowspan="2" | (part of interactor entries labelled with object_primaryref and object_secondaryref only)<br />
|-<br />
| taxB<br />
|-<br />
| rowspan="2" | interactionType<br />
| rowspan="3" | <tt>''code''(''description'')</tt><br />
| rowspan="2" | Interaction<br />
| <tt>int_xref.dbid = id('psi-mi')</tt><br><tt>int_xref.acc = ''code''</tt><br />
| int_type_primaryref<br />
|-<br />
| <tt>int_name.MI = ''code''</tt><br><tt>int_name.name = ''description''</tt><br />
| int_type_sh<br />
|-<br />
| sourcedb<br />
| Interactor/interaction<br />
| <tt>int_source.source = id(''description'')</tt><br><tt>int_object.source = id(''description'')</tt><br><tt>int_source2object.source = id(''description'')</tt><br />
| (not applicable)<br />
|-<br />
| interactionIdentifiers<br />
| <tt>''database'':''identifier''</tt><br />
| Interaction<br />
| <tt>int_xref.dbid = ''database''</tt><br><tt>int_xref.acc = ''identifier''</tt><br />
| interaction_primaryref<br />
|-<br />
| confidence<br />
|<br />
|<br />
|<br />
|<br />
|}</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefIndex_MITAB_Mapping&diff=3479iRefIndex MITAB Mapping2011-06-10T16:09:21Z<p>Sabry: </p>
<hr />
<div>Unlike the parsing of PSI MI XML files, whose attributes correspond to certain tables and columns in the iRefIndex schema, the parsing and interpretation of MITAB files involves a separate mapping of MITAB format columns to such tables and columns in the schema.<br />
<br />
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"<br />
! MITAB columns<br />
! Data components<br />
! Entity<br />
! iRefIndex table and column assignments<br />
! iRefIndex category<br />
! UID to use<br />
|-<br />
| uidA<br />
| rowspan="6" | <tt>''database'':''identifier''</tt><br />
| rowspan="6" | Interactor<br />
| rowspan="4" | <tt>int_xref.dbid = id(''database'')</tt><br><tt>int_xref.acc = ''identifier''</tt><br />
| rowspan="2" | object_primaryref<br />
|-<br />
| uidB<br />
|-<br />
| altA<br />
| rowspan="2" | object_secondaryref<br />
|-<br />
| altB<br />
|-<br />
| aliasA<br />
| rowspan="2" | <tt>int_name.name = ''identifier''</tt><br><tt>int_name.MI = 'MI:0000'</tt><br />
| rowspan="2" | object_alias<br />
|-<br />
| aliasB<br />
|-<br />
| rowspan="2" | method<br />
| rowspan="2" | <tt>''code''(''description'')</tt><br />
| rowspan="2" | Experiment<br />
| <tt>int_xref.dbid = id('psi-mi')</tt><br><tt>int_xref.acc = ''code''</tt><br />
| int_ditection_primaryref<br />
|-<br />
| <tt>int_name.MI = ''code''</tt><br><tt>int_name.name = ''description''</tt><br />
| int_ditection_shortlbl<br />
|-<br />
| authors<br />
| (free text)<br />
| rowspan="2" | Experiment<br />
|<br />
|<br />
|-<br />
| pmids<br />
| <tt>pubmed:''identifier''</tt><br />
| <tt>int_experiment.ex_bib_pri = ''identifier''</tt><br />
| (not applicable)<br />
|-<br />
| taxA<br />
| rowspan="2" | <tt>taxid:''identifier''</tt><br />
| rowspan="2" | Interactor<br />
| rowspan="2" | <tt>int_xref.taxid = ''identifier''</tt><br />
| rowspan="2" | (part of interactor entries labelled with object_primaryref and object_secondaryref only)<br />
|-<br />
| taxB<br />
|-<br />
| rowspan="2" | interactionType<br />
| rowspan="3" | <tt>''code''(''description'')</tt><br />
| rowspan="2" | Interaction<br />
| <tt>int_xref.dbid = id('psi-mi')</tt><br><tt>int_xref.acc = ''code''</tt><br />
| int_type_primaryref<br />
|-<br />
| <tt>int_name.MI = ''code''</tt><br><tt>int_name.name = ''description''</tt><br />
| int_type_sh<br />
|-<br />
| sourcedb<br />
| Interactor/interaction<br />
| <tt>int_source.source = id(''description'')</tt><br><tt>int_object.source = id(''description'')</tt><br><tt>int_source2object.source = id(''description'')</tt><br />
| (not applicable)<br />
|-<br />
| interactionIdentifiers<br />
| <tt>''database'':''identifier''</tt><br />
| Interaction<br />
| <tt>int_xref.dbid = ''database''</tt><br><tt>int_xref.acc = ''identifier''</tt><br />
| interaction_primaryref<br />
|-<br />
| confidence<br />
|<br />
|<br />
|<br />
|<br />
|}</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefScape_1.0&diff=3475iRefScape 1.02011-06-09T10:58:26Z<p>Sabry: /* Tested systems */</p>
<hr />
<div>Last edited: {{REVISIONYEAR}}-{{padleft:{{REVISIONMONTH}}|2}}-{{REVISIONDAY2}}<br />
<br />
Release date: To be announced<br />
<br />
This page describes the iRefScape 1.0 plug-in for Cytoscape 2.8.1. See the following table for more detailed iRefScape compatibility information.<br />
<br />
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"<br />
! align="center" style="background:#f0f0f0;"|Cytoscape<br />
! align="center" style="background:#f0f0f0;"|iRefScape<br />
|-<br />
| 2.8.1<br />
| iRefScape 1.0 (described on this page)<br />
|-<br />
| 2.7.0<br />
| [[README_Cytoscape_plugin_0.9x|iRefScape 0.9]]<br />
|-<br />
| 2.6.3<br />
| [[README_Cytoscape_plugin_0.8x|iRefScape 0.8]]<br />
|}<br />
<br />
Join the [http://groups.google.com/group/irefindex?hl=en iRefIndex Google Group] to be informed of updates. See also the [[README_Cytoscape_plugin|latest release of iRefScape]] which may differ from the release described here.<br />
<br />
==Installation==<br />
<br />
The plugin can be installed using Cytoscape's plugin menu. Select "Manage plugins" and then "Available for Install" and then "Network and Attribute I/O" and finally the "iRefScape" entry (where the precise version will provide a specific version such as "iRefScape v.1.0").<br />
<br />
Follow the on-screen instructions.<br />
<br />
More detailed instructions, troubleshooting tips and alternative methods are available on the [[README_Cytoscape_plugin_1.0x_Installation|iRefIndex Cytoscape Plugin 1.0 installation page]] and this can be followed for subsequent releases of iRefScape as well, until replaced by a newer document.<br />
<br />
After, installation, select the "iRefScape" entry from Cytoscape's plugin menu.<br />
<br />
When the plugin is started for the first time, it will download the publicly available data set.<br />
<br />
<br />
=== Tested systems ===<br />
This version of the iRefScape plugin has been tested on the following operating systems.<br />
<br />
# Redhat Linux el5 (32 bit) (kernel 2.6.18) with JAVA 32 bit versions 1.6.0_01)<br />
# Windows 7 (64 bit) with JAVA 64 bit versions 1.6.0_25)<br />
# Ubuntu (32 bit)(version 8.04) with JAVA 32 bit versions 1.6.<br />
<br />
Please refer [http://irefindex.uio.no/wiki/README_Cytoscape_plugin_1.0x_Installation '''README_Cytoscape_plugin_1.0x_Installation'''] for more details on OS specific issues.<br />
<br />
== Using the Wizard - an example search ==<br />
<br />
Click the "Wizard" button - a pop-up window will appear. <br />
<br />
Follow these steps<br />
<br />
# Select "Search protein-protein interactions for a protein".<br />
# Select "UniProt identifier".<br />
# For "Taxonomy identifier", select "9606 (Human)" <br />
# Type <tt>QCR2_HUMAN</tt> in the provided space. Click "Next".<br />
# Click "Search & load".<br />
<br />
The images below show each of the steps in the wizard.<br />
<br />
<gallery perrow="5"><br />
Image:IRefIndex-Cytoscape-Wizard.png|The iRefIndex wizard<br />
Image:IRefIndex-Cytoscape-Wizard-step2.png|Choosing a result type<br />
Image:IRefIndex-Cytoscape-Wizard-step3.png|Choosing a taxonomy type<br />
Image:IRefIndex-Cytoscape-Wizard-step4.png|Specifying the search term<br />
Image:IRefIndex-Cytoscape-Wizard-step5.png|Additional options<br />
</gallery><br />
<br />
== Using the Search Panel ==<br />
<br />
To perform a search, the following steps are involved:<br />
<br />
# Enter query term(s)<br />
# Select a search type<br />
# Select taxonomy/organism<br />
# Adjust search options (iterations, new view, canonical expansion) - this is optional<br />
# Start the search<br />
<br />
=== Enter query term(s) ===<br />
<br />
Queries may be loaded from a file or by pasting the query into the text box (one query per line). Multiple queries can also be separated by pipe characters (<tt>|</tt>) or by tab characters. Queries with spaces in them should be enclosed in double quotes.<br />
<br />
=== Select a search type ===<br />
<br />
Example searches are listed below.<br />
<br />
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"<br />
! align="center" style="background:#f0f0f0;"|Search Type<br />
! align="center" style="background:#f0f0f0;"|Example<br />
! align="center" style="background:#f0f0f0;"|Notes<br />
|-<br />
| <tt>RefSeq_Ac</tt>||<tt>NP_996224</tt>||See http://www.ncbi.nlm.nih.gov/protein/221379660<br />
|-<br />
| <tt>UniProt_Ac</tt>||<tt>Q7KSF4</tt>||See http://www.uniprot.org/uniprot/Q7KSF4<br />
|-<br />
| <tt>UniProt_ID</tt>||<tt>Q7KSF4_DROME</tt>||See http://www.uniprot.org/uniprot/Q7KSF4<br />
|-<br />
| <tt>geneID</tt>||<tt>42066</tt>||See http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=42066<br />
|-<br />
| <tt>geneSymbol</tt>||<tt>cher</tt>||See http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=42066<br />
|-<br />
| <tt>mass</tt>||<tt>72854<-->72866</tt>||Search protein interactors for a range of molecular mass (in Da).<br />
|-<br />
| <tt>rog</tt>||<tt>10121899</tt>||Redundant object group: iRefIndex's internal identifier for a protein<br />
|-<br />
| <tt>PMID</tt>||<tt>14605208</tt>||PubMed Identifier where an interaction is described. See http://www.ncbi.nlm.nih.gov/pubmed. Iterations and "Use canonical expansion" have no effect on this search type. This search will return all protein interactors in the given PMID and will automatically draw all interactions known between these proteins (even if these interactions are supported by different PMIDs). Select edges in the resulting graph, and see the i.PMID attribute in the Edge Attribute Browser.<br />
|-<br />
| <tt>src_intxn_id</tt>||<tt>EBI-212627</tt>||Source interaction database identifier. Iterations and "Use canonical expansion" have no effect on this search type. Caution: multiple databases may have overlapping interaction record identifiers (e.g. <tt>147805</tt> returns records from both BIND and BioGrid) and there is no way to limit this search to a specific database at this time.<br />
Equivalent interactions from other databases will be automatically retrieved using this search type (see provided example).<br />
|-<br />
| <tt>omim</tt>||<tt>227650</tt>||OMIM identifier. See http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=227650<br />
|-<br />
| <tt>digid</tt>||<tt>449</tt>||Internal identifier for a group of phenotypically related diseases. See http://donaldson.uio.no/wiki/DiG:_Disease_groups. A digid can be found by first performing a search for some omim identifier - the digid will then appear as the i.digid node attribute.<br />
<!--<br />
|-<br />
| <tt>dig_title</tt>||<tt>fanconi</tt>||Text search for a group of phenotypically related diseases. See http://donaldson.uio.no/wiki/DiG:_Disease_groups<br />
|-<br />
--><br />
|}<br />
<br />
=== Select taxonomy/organism ===<br />
<br />
This will limit the search results to a particular organism. An organism can be selected from the list, or a taxonomy identifier can be entered into the field itself. See [http://www.ncbi.nlm.nih.gov/taxonomy Entrez Taxonomy] for more details on taxonomy identifiers. For most search types, it is acceptable to leave this field set to <tt>Any</tt>.<br />
<br />
=== Adjust search options ===<br />
<br />
The following optional adjustments can be made:<br />
<br />
==== Iterations ====<br />
<br />
A distance from the query list's members can be specified:<br />
<br />
* Selecting <tt>0</tt> will return only interactions between nodes found by the query list<br />
* Selecting <tt>1</tt> will return immediate neighbours of nodes in the query list<br />
<br />
==== Create new view ====<br />
<br />
A new view will be opened for the search results if this option is selected. Otherwise, the results will be added to the current view.<br />
<br />
==== Use canonical expansion ====<br />
<br />
Selecting this option will expand the search to include all proteins that are related to the query protein (for example, splice isoforms). See [[Canonicalization]] for technical details.<br />
<br />
=== Start the search ===<br />
<br />
Press the "Search and load" button to perform the search.<br />
<br />
== Viewing the Results ==<br />
<br />
=== Colours and Shapes ===<br />
<br />
* Blue nodes corresponds to proteins found by your query<br />
* Green nodes are interacting partners for your query protein<br />
* Purple hexagons are complex-nodes (also called pseudo-nodes); they keep partners of a complex together (i.e. QCR6_HUMAN is found in two complexes also involving "QCR2_HUMAN")<br />
* Orange-yellow edges indicate protein-protein interactions and pink edges represent membership of some protein in a complex<br />
<br />
=== Toggling Edges ===<br />
<br />
Multiple edges may appear between two nodes. These represent separate interaction records that support this link. Details on each original record can be viewed using the edge attribute viewer (below). You can toggle this multi-view on and off by selecting "Toggle selected multi-edges" in the iRefScape/View Tools menu. Only one of the edges will be shown in the collapsed view.<br />
<br />
<br />
=== iRefScape Menu ===<br />
<br />
The iRefScape menu in the CytoScape menu bar contains a number of other functions that may help with searching and viewing interaction data. These are described in more detail on a separate page [[README_Cytoscape_plugin_menu]].<br />
<br />
=== Expanding the Interaction Map ===<br />
<br />
You can search for additional interactions by right-clicking on a node and selecting "iRefIndex -- Retrieve interactions".<br />
<br />
Some example result displays are shown below.<br />
<br />
<gallery widths="500px" heights="300px"><br />
Image:QCR2_HUMAN_initial.png|Results<br />
Image:QCR2_HUMAN.png|Results (tidied)<br />
</gallery><br />
<br />
== Attributes ==<br />
<br />
[[Image:iRefIndex-0.83-node-attributes-close-up-closed.png|right|The node attributes menu]]<br />
<br />
There are two types of attributes available from iRefIndex: node attributes and edge attributes. These may be used to view information about selected nodes or edges (like <tt>i.taxid</tt>). Some features may allow the user to link out to additional data sources through the "right-click" menu (like <tt>i.geneID</tt>). Features may also be used to sort and select nodes and edges with specific attributes (like <tt>i.order</tt>). The <tt>i.query</tt> feature shows the user's query that is responsible for returning the node or edge.<br />
<br />
Brief descriptions and examples of each attribute are provided below. <br />
<br />
The user must first select the attributes that are to be displayed. This can be done by clicking on the "attribute" icon at the top of the node or edge attribute browser, as shown in the illustrative images.<br />
<br />
<div style="clear: right"></div><br />
=== Node Attributes ===<br />
<br />
[[Image:iRefIndex-0.83-node-attributes-close-up-open.png|right|The open node attributes menu]]<br />
<br />
Each node represents a distinct amino acid sequence (protein) from a distinct organism (taxonomy identifier). Each of the attributes below, provide additional information about the node. Although each node is distinct, a graph produced by iRefIndex may contain multiple nodes that are related proteins (such as splice isoform products from the same gene). These nodes will all have the same <tt>i.canonical_rog</tt> and <tt>i.canonical_rogid</tt> feature values. See the notes below.<br />
<br />
Node attributes that can be lists of items (like <tt>i.UniProt</tt>) will have a corresponding attribute called <tt>i.''attribute name''_TOP</tt> (for example, <tt>i.UniProt_TOP</tt>) which provides the first item of the associated list.<br />
<br />
<div style="clear: right"></div><br />
<br />
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"<br />
! align="center" style="background:#f0f0f0;"|Attribute name<br />
! align="center" style="background:#f0f0f0;"|Data type<br />
! align="center" style="background:#f0f0f0;"|Example value<br />
! align="center" style="background:#f0f0f0;"|Description<br />
|-<br />
| <tt>ID</tt>||Integer||<tt>10121899</tt>||This is a unique identifier for the node assigned by iRefIndex (no two nodes will have the same ID). Each node corresponds to a distinct amino acid sequence from a distinct taxonomy identifier. See also <tt>i.rog</tt> and <tt>i.rogid</tt>.<br />
|-<br />
| <tt>canonicalName</tt>||Integer||<tt>10121899</tt>||This is the same as <tt>ID</tt>. This attribute is set by Cytoscape and is unrelated to the <tt>i.canonical_rog</tt> or <tt>i.canonical_rogid</tt> used by iRefIndex<br />
|-<br />
| <tt>i.RefSeq_Ac</tt>||List||<tt>[NP_996224]</tt> ||All RefSeq accessions with an amino acid sequence and taxon identifier identical to the protein represented by this node. Right click on this entry and select "Search ''[RefSeq_Ac]'' on the web -- Entrez -- Protein" for more information. See also <tt>i.RefSeq_TOP</tt> for the first entry in this list of accessions.<br />
|-<br />
| <tt>i.UniProt_Ac</tt>||List||<tt>[Q7KSF4]</tt>||All UniProt accessions with an amino acid sequence and taxonomy identifier identical to the protein represented by this node. Right click on this entry and select "Search ''[UniProt_Ac]'' on the web -- UniProt -- KB Beta" for more information. See also <tt>i.UniProt_Ac_TOP</tt> for the first entry in this list of accessions.<br />
|-<br />
| <tt>i.UniProt_ID</tt>||List||<tt>[Q7KSF4_DROME]</tt> ||All UniProt identifers with an amino acid sequence and taxonomy identifier identical to the protein represented by this node. Right click on this entry and select "Search ''[UniProt_ID]'' on the web -- UniProt -- KB Beta" for more information. See also <tt>i.UniProt_ID_TOP</tt> for the first entry in this list of IDs.<br />
|-<br />
| <tt>i.canonical_rog</tt>||Integer||<tt>10121899</tt>||Related proteins (say splice isoforms from the same gene) will all belong to the same canonical group. One member of this group is assigned as the canonical representative of this group. The <tt>i.canonical_rog</tt> attribute lists the identifier of the protein's canonical group identifier. For example, all products of Entrez Gene 42066 have the same <tt>i.canonical_rog</tt> (<tt>10121899</tt>). Each of these gene products has its own identifier (because they each have a distinct amino acid sequence). One of the splice isoforms (<tt>NP_996224</tt>) was chosen as the canonical representative of this group. See the [http://irefindex.uio.no/wiki/Canonicalization canonicalization document] for more details on how canonical groups are constructed and how canonical representatives are chosen.<br />
|-<br />
| <tt>i.canonical_rogid</tt>||String||<tt>1ZFb1WlW0OgOlhiAPtkJTdb6oOg7227</tt>||This is a unique alphanumeric key for the canonical representative of the canonical group to which this node belongs. Briefly, an SHA-1 digest of the amino acid sequence is used to generate a unique 27 character key and this is prepended to the taxonomy identifier for the protein's source organism in order to make the rogid. See PMID 18823568 for details on how this key can be generated. This is a string equivalent of the <tt>i.canonical_rog</tt> attribute. All <tt>i.canonical_rog</tt> instances (each being an integer) have one corresponding <tt>i.canonical_rogid</tt>. See the [http://irefindex.uio.no/wiki/Canonicalization canonicalization document] for more details on how canonical groups are constructed and how canonical representatives are chosen. Note that the rogid for the protein represented by this specific node is listed under <tt>i.rogid</tt>.<br />
|-<br />
| <tt>i.dataset</tt>||Integer||<tt>0</tt>||In the batch query mode this can be used to locate the query batch (i.e. which group of queries were responsible for the node). In single query mode, when a sequence of queries are issued one after another this variable can be used to distinguish the results from each step. All nodes with a i.dataset value higher than 999 can be found using more than one batch of queries. <br />
|-<br />
| <tt>i.digid</tt>||List||<tt>449</tt>||This is an integer identifier that is shared by a group of disease entries in OMIM that are related by their titles. See the [http://donaldson.uio.no/wiki/DiG:_Disease_groups disease groups document] for more details. Also see <tt>i.omim</tt> and <tt>i.dig_title</tt>.<br />
|-<br />
<!--<br />
| <tt>i.dig_title</tt>||List||<tt>[Fanconi anemia, complementation group B, 300514 (3), VACTERL association with hydrocephalus, X-linked, 314390 (3)]</tt>||These are entries from OMIM's Morbid Map that are all part of the same disease group. See the [http://donaldson.uio.no/wiki/DiG:_Disease_groups disease groups document] for more details. Also see <tt>i.omim</tt> and <tt>i.digid</tt>.<br />
--><br />
|-<br />
| <tt>i.displayLabel</tt>||List||<tt>[Q7KSF4_DROME]</tt> ||This is a list of short labels chosen by iRefIndex to label the node using the VizMapper. The UniProt identifier is preferentially chosen (if one is available) followed by the Entrez Gene Symbol. See also <tt>i.displayLabel_TOP</tt> for the first entry in this list.<br />
|-<br />
| <tt>i.geneID</tt>||List||<tt>[42066]</tt>||All NCBI Entrez Gene identifiers that encode a protein sequence identical to that of this node. Right click on this entry and select "Search ''[geneID]'' on the web -- Entrez -- Gene" for more information. See also <tt>i.geneID_TOP</tt> for the first entry in this list.<br />
|-<br />
| <tt>i.geneSymbol</tt>||List||<tt>[CHER]</tt>||All NCBI Entrez Gene official symbols that encode a protein sequence identical to that of this node. Right click on this entry and select "Search ''[geneSymbol]'' on the web -- Entrez -- Gene" for more information. See also <tt>i.geneSymbol_TOP</tt> for the first entry in this list.<br />
|-<br />
| <tt>i.interactor_description</tt>||List||<tt>[Q7KSF4_DROME, CHER, DMEL_CG3937, SKO, DMEL CG3937, FLN, CG3937, CHER, DMEL\\CG3937, FLN, SKO, CHER, NAME=CHER, DMEL_CG3937]</tt>||A collection of all the names in their short form as given by the original interaction databases. See also <tt>i.interactor_description_TOP</tt> for the first entry in this list.<br />
|-<br />
| <tt>i.mass</tt>||Integer|| <tt>259142</tt> ||Mass associated with the protein sequence for this node. From UniProt, if available. You can search for nodes inside a mass range using the <tt>mass</tt> search type in the iRefIndex plugin.<br />
|-<br />
| <tt>i.omim</tt>||List||<tt>[608053]</tt>||List of OMIM disease identifiers associated with this protein. Right click on the entry and select "Search for ''[omim]'' on the web -- Entrez -- OMIM" for more information. <br />
|-<br />
| <tt>i.order</tt>||Integer|| <tt>0</tt> || The distance of this node from the query node (query node has distance <tt>0</tt>, nodes that are returned by a query because they are a part of the same canonical group have a value of <tt>10</tt>, direct neighbours have a value of<tt>1</tt>). Pseudonodes have negative values (<tt>-1</tt> is a complex holder, <tt>-2</tt> is a collapsed instance).<br />
|-<br />
| <tt>i.overall_degree_TOP</tt>||Integer|| <tt>42</tt> ||The total number of interactions described for this node in the iRefIndex database. Not all of these edges will be necessarily shown in the current view. This is the node degree in the full iRefIndex interactome. When calculating the value of this all proteins in iRefIndex (not only the ones currently loaded) will be used<br />
|-<br />
| <tt>i.popularity</tt>||List|| <tt>42</tt> || '''TO BE DESCRIBED'''<br />
|-<br />
| <tt>i.pseudonode</tt>||Boolean|| <tt>false</tt> || This is set to true is the node represents a "complex" or n-ary interaction record. Protein nodes with edges incident to a pseudonode are member interactors from the interaction record where specific interactions between pairs of interactors is unknown. Pseudonodes appear as hexagons when using the iRefIndex VizMapper style. <br />
|-<br />
| <tt>i.query</tt>||String||<tt>NP_996224</tt>||The user query used to retrieve this specific node. Neighbours of "query" nodes will not have an <tt>i.query</tt> value. Nodes returned by queries are coloured blue when using the iRefIndex VizMapper style.<br />
|-<br />
| <tt>i.rog</tt>||Integer||<tt>10121899</tt>||This is a unique identifier for the node assigned by iRefIndex (no two nodes will have the same ID). Each node corresponds to a distinct amino acid sequence associated with a distinct taxonomy identifier. <tt>i.rog</tt> also appears as the <tt>ID</tt> attribute. Each <tt>i.rog</tt> has a corresponding <tt>i.rogid</tt> - see below.<br />
|-<br />
| <tt>i.rogid</tt>||String||<tt>2mL9oLZ9g/SSPyK0nOz97RmOzPg3702</tt>||This is a unique alphanumeric key for the protein represented by this node. Briefly, an SHA-1 digest of the amino acid sequence is used to generate a unique 27 character key and this is prepended to the taxonomy identifier for the protein's source organism in order to make the rogid. See PMID 18823568 for details on how this key can be generated. This is a string equivalent of the <tt>i.rog</tt> attribute. All <tt>i.rog</tt> instances (each being an integer) have one corresponding <tt>i.rogid</tt>.<br />
|-<br />
| <tt>i.taxid</tt>||Integer||<tt>7227</tt>||The NCBI taxonomy identifier for this protein's source organism. See http://www.ncbi.nlm.nih.gov/taxonomy?term=7227 for more details of this example value for <tt>i.taxid</tt>.<br />
|-<br />
| <tt>i.xref</tt>||List||<tt>[AAF70826.1,Q9M6R5]</tt> ||All the accessions as given by the original interaction database records to describe this protein. See also <tt>i.xref_TOP</tt> for the first entry in this list.<br />
|-<br />
| <tt>i.alive</tt>||Boolean||<tt>true or false</tt> ||This is true for all nodes after a search operation. This variable is used by the iRefScape filter and after a filter is applied, all nodes matching the filter criteria will have a true value for this variable (all other nodes will have false).<br />
|-<br />
| <tt>i.alive_degree</tt>||Integer||<tt>0,1,2-...</tt> ||This is will give the node degree after a search. When an iRefScape filter is applied this will give the number of nodes with "i.alive=true" connected to a particular node(How many nodes matching the filter criteria has connections with a particular node). <br />
|-<br />
|}<br />
<br />
===Edge Attributes===<br />
<br />
Each edge represents a distinct primary database record that supports some relationship between the two incident nodes. So, if an interaction between two proteins has been annotated by two databases (or twice by the same database) then two edges will appear between those two protein nodes.<br />
<br />
<br />
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"<br />
! align="center" style="background:#f0f0f0;"|Attribute name<br />
! align="center" style="background:#f0f0f0;"|Data type<br />
! align="center" style="background:#f0f0f0;"|Example value<br />
! align="center" style="background:#f0f0f0;"|Description<br />
|-<br />
| <tt>ID</tt>||String||<tt>10121899 (2771704(40952)) 13911416</tt>||This is a unique identifier for the edge assigned by Cytoscape (no two edges will have same <tt>ID</tt>). See <tt>i.rig</tt> and <tt>i.rigid</tt> for unique identifiers for the edge assigned by iRefIndex.<br />
|-<br />
| <tt>i.PMID</tt>||Integer||<tt>14605208</tt>||Publication identifier of the publication where the interaction represented by the edge mentioned. Right click on this entry and select "Search ''[PMID]'' on the web -- Entrez -- Pubmed" for more details on the publication.<br />
|-<br />
| <tt>i.bait</tt>||Integer||<tt>13911416</tt>||Node ID for the protein that was used as a bait in this experiment. Only applicable where the experimental system (see <tt>i.method_name</tt>) used to support this relationship was a bait-prey system (for example, two hybrid).<br />
|-<br />
| <tt>i.canonical_rig</tt>||Integer||<tt>27799</tt>||See notes for the <tt>i.rig</tt> edge feature. This is the rig constructed for the interaction using its canonical rogs. Use a web browser to query http://wodaklab.org/iRefWeb/interaction/show/27799 (where <tt>27799</tt> is the <tt>i.canonical_rig</tt> value) to retrieve more information on this interaction and equivalent source interaction records.<br />
|-<br />
| <tt>i.experiment</tt>||String||<tt>Giot L [2003]</tt>||A short label for the experiment where this interaction was found (usually contains authors names).<br />
|-<br />
| <tt>i.flag</tt>||Integer||<tt>1</tt>||Used by iRefIndex plugin to control display of edges (<tt>0</tt> being the representative edge, used in edge toggle; <tt>1</tt> being an edge which will disappear during edge toggle; <tt>2</tt> being a complex holder edge; <tt>6</tt> being a path; <tt>7</tt> being an edge from or to a collapsed node).<br />
|-<br />
| <tt>i.host_taxid</tt>||Integer||<tt>7227</tt>||Indicates the organism taxonomy identifier where the interaction was experimentally demonstrated.<br />
|-<br />
| <tt>i.isLoop</tt>||Integer||<tt>1</tt>||Indicates whether the interaction is a self interaction (such as a dimer or possibly multimer of the same protein type). See the source interaction record for details.<br />
|-<br />
| <tt>i.method_cv</tt>||String||<tt>MI:0018</tt>||PSI-MI controlled vocabulary term identifier for the method used to provide evidence for this interaction. See http://www.ebi.ac.uk/ontology-lookup/ for more details. The name of the method is also given in the <tt>i.method_name</tt> feature.<br />
|-<br />
| <tt>i.method_name</tt>||String||<tt>two hybrid</tt>||PSI-MI controlled vocabulary term name for the method used to provide evidence for this interaction. See http://www.ebi.ac.uk/ontology-lookup/ for more details. The term identifer is also given in the <tt>i.method_cv</tt> feature.<br />
|-<br />
| <tt>i.participant_identification</tt>||String||<tt>predetermined participant</tt>||PSI-MI controlled vocabulary term for the participant identification method used to provide evidence for this interaction. See http://www.ebi.ac.uk/ontology-lookup/ for more details. The identifier for the term is also given in the <tt>i.participant_cv</tt> feature.<br />
|-<br />
| <tt>i.participant_cv</tt>||String||<tt>predetermined participant</tt>||PSI-MI controlled vocabulary term identifier for the participant identification method used to provide evidence for this interaction. See http://www.ebi.ac.uk/ontology-lookup/ for more details. The term itself is also given in the <tt>i.participant_identification</tt> feature.<br />
|-<br />
| <tt>i.query</tt>||String||<tt>NP_996224</tt>||The user's query that is responsible for returning this edge.<br />
|-<br />
| <tt>i.rig</tt>||Integer||<tt>27799</tt>||Redundant interaction group identifier for the interaction. <br />
This is an integer equivalent of <tt>i.rigid</tt>. Every rig has one corresponding rigid.<br />
|-<br />
| <tt>i.rigid</tt>||String||<tt>TAabV6yJ1XzUvEhYwZLpu5reBU0</tt>||Redundant interaction group identifier for the interaction. This is a universal key generated for the interaction by ordering according to ASCII value and concatentating the rogids participating in the interaction and then generating a Base-64 representation of an SHA-1 digest of the resulting string. See PMID 18823568 for details on how this key can be generated.<br />
|-<br />
| <tt>i.score_hpr</tt>||Integer||<tt>15</tt>||The hpr score (highest pmid re-use) is the highest number of interactions that any one PMID (supporting this interaction) is used to support. See PMID 18823568 for details. See also <tt>i.score_np</tt> and <tt>i.score_lpr</tt>.<br />
|-<br />
| <tt>i.score_lpr</tt>||Integer||<tt>11</tt>||The lpr score (lowest pmid re-use) is the lowest number of distinct interactions that any one PMID (supporting this interaction) is used to support. An lpr of greater than 20 is considered to be a high-throughput experiment. See PMID 18823568 for details. See also <tt>i.score_np</tt> and <tt>i.score_lpr</tt>.<br />
|-<br />
| <tt>i.score_np</tt>||Integer||<tt>2</tt>||Number of PubMed Identifiers (PMIDs) pointing to literature where this interaction is supported. See PMID 18823568 for details. See also <tt>i.score_lpr</tt>.<br />
|-<br />
| <tt>i.source_protein</tt>||Integer||<tt>-1</tt>||'''TO BE DESCRIBED'''<br />
|-<br />
| <tt>i.src_intxn_db</tt>||String||<tt>grid</tt>||Original interaction database where this interaction record was obtained.<br />
|-<br />
| <tt>i.src_intxn_id</tt>||String||<tt>38677</tt>||Original interaction database where this interaction record was obtained. <br />
In some case, it may be possible to right click and "Search ''[src_intxn_id]'' on the web -- Interaction databases -- the database" to see the original record.<br />
|-<br />
| <tt>i.type_cv</tt>||String||<tt>MI:0407</tt>||PSI-MI controlled vocabulary term identifier for the interaction type that occurs between the two proteins. See http://www.ebi.ac.uk/ontology-lookup/ for more details. The term itself is also given in the <tt>i.type_name</tt> feature.<br />
|-<br />
| <tt>i.type_name</tt>||String||<tt>direct interaction</tt>||PSI-MI controlled vocabulary term identifier for the interaction type that occurs between the two proteins. See http://www.ebi.ac.uk/ontology-lookup/ for more details. The term itself is also given in the <tt>i.type_name</tt> feature.<br />
|-<br />
| <tt>i.target_protein</tt>||Integer||<tt>-1</tt>||'''TO BE DESCRIBED'''<br />
|-<br />
|}<br />
<br />
=== User Attributes ===<br />
Importing - TBD<br />
<br />
Searching on - TBD<br />
<br />
== Obtaining CORUM, DIP and HPRD Data ==<br />
<br />
Due to licensing issues, we are unable to distribute these data with the plugin. CORUM data and free IMex data from DIP will be included in the next public release of iRefIndex.<br />
<br />
You can request these data under a collaborative agreement by emailing ian.donaldson@biotek.uio.no<br />
<br />
Under the agreement you agree to<br />
<br />
# Not redistribute the data outside your research group.<br />
# Provide us with feedback on your use of the data (problems and requests).<br />
<br />
We do not require authorship on any related publications.<br />
<br />
== Obtaining Updates to the Data ==<br />
<br />
You can check for and download updates to the dataset used by your plugin using the Wizard (see "Check for iRefIndex updates").<br />
<br />
iRefIndex updates are announced through the [http://groups.google.com/group/irefindex?hl=en iRefIndex Google Group]<br />
<br />
==Obtaining Updates to the Plugin==<br />
<br />
If you already have a plugin called iRefScape (a menu entry "iRefScape" under the plugin menu of Cytoscape) and you want to make sure you have the latest version, use "Update plugins" from the "Plugins" menu. However, if you want to reinstall the plugin, you should uninstall any previous version of the plugin first.<br />
<br />
Plugin updates are announced through the [http://groups.google.com/group/irefindex?hl=en iRefIndex Google Group]<br />
<br />
<!--<br />
<br />
== How to load batch query from file ==<br />
1. Create a text file with the following format:<br />
<p><type><NCBI_taxonomy_identifier></p><br />
<p>query_text_1</p><br />
<p>query_text_2</p><br />
<p>query_text_3</p><br />
<br />
<p>The first line of the file starts with a hash ("#") and then the type. The type could be</P><br />
*ACCESSION<br />
*NAME<br />
*GENID<br />
<br />
The query_text is your query (e.g.Q39009). Each query line has to be terminated by a new line character (press enter after each line) <br />
<p>[Sample batch file: [http://irefindex.uio.no/wikifiles//images/b/b1/Sample_batch_accessions.txt.zip]]</p><br />
<br />
==Integrating User Data into the Plugin==<br />
<br />
<br />
===How to create your own file to use as index===<br />
<br />
'''TO BE DESCRIBED'''<br />
<br />
===How to create node and edge attributes ===<br />
<br />
Example: Attaching [http://irefindex.uio.no/wiki/DiG:_Disease_groups disease group] identifiers to nodes<br />
<br />
==Updating==<br />
# From Cytoscape updater<br />
# Using plugins update feature<br />
<br />
== Log Files, Search Details and Errors ==<br />
# How to interpret log messages and save them for later reference. <br />
<br />
==Using the plugin as a search tool ==<br />
The plugin could also be used to search the current network. However, there is a better search option in Cytoscape with Google suggest which may be more convenient to use. The reason for including the search function was that the Cytoscape search filed remained inactive on some occasions for networks crated using the plugin. The reason for this is still unknown and deleting a node on the network seems to activate it, when this bug will be fixed the users are encouraged to use the Cytoscape search option.<br />
Currently, if a user performs a search with a term and if the corresponding protein is already loaded, the loaded protein (corresponding node) would be highlighted with Cytoscape default highlight colors. <br />
<br />
<br />
== Exit plugin and force terminate operations ==<br />
The exit button performs two functions. <br />
# First one is to exit iRefIndex plugin, where the outcome is to detach the plugin from Cytoscape. <br />
# The second function "FORCE STOP" (only available during a active task) is to terminate current operation. The "FORCE STOP" is useful when the search query or a subsequent operation takes too long to finish or none-responding. When a force stop is performed the out come is unpredictable and behavior was undefined, therefore results after such operation could not be trusted. <br />
<br />
--><br />
<br />
==Advanced search options==<br />
===Path-Finding===<br />
[[Image:iRefIndex-0.83-path-original.png|thumb|500px|The path in the results, highlighted in green. Solid green lines indicate presence of evidence for this step of the path in the direction specified by the query OR the presence of evidence that has no directionality. A dashed green line indicates there is evidence for this step of the path but only in the direction that is opposite to that specified in the query.]]<br />
<br />
iRefScape can be used to find interaction events connecting two proteins or a sequence of events involving several proteins. <br />
<br />
This process intakes two terminal nodes as input and returns all reasonable paths connecting these two. The results returned here are pathway independent. In other words, the sequences of interactions connecting the nodes are not constructed using currently published pathways. However, the paths returned may contain pathway centric information.<br />
<br />
The query format is as follows:<br />
<br />
NP_004976 <==> NP_002871<br />
<br />
Additional type and taxonomy parameters were also supplied as required:<br />
<br />
* '''Search type:''' <tt>RefSeq_Ac</tt><br />
* '''Taxonomy:''' <tt>9606 (Homo sapiens)</tt><br />
<br />
This query located all reasonable paths between <tt>NP_004976</tt> and <tt>NP_002871</tt> and the returned path also contains the shortest path between them. The results of the path finding was sorted in the ascending order of path length and the maximum path length was restricted to a default value of 6; this value can be modified by changing the value of "Maximum distance" from the "Path parameters" tab in the advanced options panel. The paths found in this way were "reasonable paths", this concept is different from finding the shortest path or finding all the paths. A "reasonable path" from A to B is a path extending from A to B where none of the intermediate points can be reached from A with fewer steps by a path that extends from A via B (in other words, when evaluating a path from A to B, nodes beyond B are not considered).<br />
<br />
<div style="clear: right"></div><br />
<br />
=== Reversing the Path ===<br />
<br />
[[Image:iRefIndex-0.83-path.png|thumb|500px|The path in the results, highlighted in green]]<br />
<br />
Due to the way the algorithm works, when the opposite search was performed...<br />
<br />
NP_002871 <==> NP_004976<br />
<br />
...it took 120 seconds and returned 3 paths. The reason for this is that <tt>NP_002871</tt> is directly connected to many hubs and therefore, the initial seed-list size was larger than when starting with <tt>NP_004976</tt>. The algorithm first tries the direction requested by the user and after that considers the opposite direction when creating the sub-network to look for the path. The time consuming step in the opposite search (<tt>NP_002871<==>NP_004976</tt>) is thus the initial evaluation step. When constructing the query for path-finding we used the attribute <tt>i.overall_degree_TOP</tt> and it provided the overall connectivity of the proteins within iRefIndex. The <tt>i.overall_degree_TOP</tt> value of <tt>RAF1</tt> was found to be 443 and for the <tt>KRAS</tt> isoform was found to be 2. Therefore, although not shown in the graph, <tt>RAF</tt> is connected to more than 400 other proteins than <tt>RAS1</tt>.<br />
<br />
In the image shown here, the green arrow shows the path.<br />
<br />
<div style="clear: right"></div><br />
=== Path Selection ===<br />
<br />
[[Image:iRefIndex-0.83-path-selector.png|thumb|500px|The path selector for the results]]<br />
<br />
After the path-finding is completed the "Path selection" panel can be used to selectively load the paths. In order to make the selection easier, the paths found can be described by a particular attribute type: by selecting a value from the list for "Convert pop-up type to" (such as <tt>RefSeq_Ac</tt>) and pressing the "Convert" button, a tooltip appearing over each path description will show the requested attribute values for each component of the path. Thus, a path description such as...<br />
<br />
321631 -> 2229473 -> 4410739 -> 4531114<br />
<br />
...will provide a tooltip showing the following identifiers:<br />
<br />
NP_002871 -> NP_001123914 -> NP_036979 -> NP_004976<br />
<br />
===List comparison===<br />
This feature is available with version 0.91 and later.<br />
<br />
This feature provides a way to compare two lists of proteins. When a <tt>COMPARE{<List1>,<List2>}</tt> format query is issued with default settings an interaction network is loaded with interactions involving only the proteins of the list and proteins which are not in the list but interacts with at least two proteins from each list (intermediate components). At the end of the operation, in addition to the Cytoscape network a adjacency cube (adjacency matrix with colours as the third dimension) is also created. This adjacency cube is synchronized with the network and can be used examine the results easily. A summary report function is provided to list the overall summary of each protein in the list sorted order so that the most connected protein appear first. The identifiers used to display the proteins in the adjacency cube are either iROGID or the ROGID of complexes. The user has the option to visualize these in popular identifier types using convert feature.<br />
<br />
Example query.<br />
<br />
COMPARE{P08588,P16671|P07550,P13945} (Example from PMID:20670417)<br />
<br />
This query compares two groups:<br />
<br />
# P08588,P16671<br />
# P07550,P13945<br />
<br />
Members within the group are separated with a comma (<tt>,</tt>); groups are separated by a pipe (<tt>|</tt>).<br />
<br />
====Questions and answers about list comparison====<br />
<br />
''What is the maximum number of members a group can have?''<br />
<br />
You could have any number of members, more members there are more time it will take for the operation and more memory it will need. For instance the above example search will complete comfortably in 1 minute with 256MB of allocated memory. If you have more than 100 members we recommend having at least 1GB dedicated memory for Cytoscape. <br />
<br />
''Can I compare more than two groups?''<br />
<br />
Yes, each group should be separated with a pipe character. The maximum number of recommended group count is 255.<br />
<br />
''What if a protein or protein resulting from query appears in more than one group?''<br />
<br />
All proteins found in more than one group is treated as a new group.<br />
<br />
''Can I compare members of already grouped identifiers?''<br />
<br />
Yes. As an example if you want to compare interactions among the disease group 141, the following query could be used:<br />
<br />
COMPARE{141}<br />
<br />
==Troubleshooting==<br />
<br />
* See http://cytoscape.org/ for a manual and a set of tutorials which describe the installation and use of Cytoscape.<br />
* For problems with Cytoscape installation or use, try the [http://groups-beta.google.com/group/cytoscape-helpdesk Cytoscape Help Desk].<br />
* If you have problems with installation or use, please share your experience with us through the [http://groups.google.com/group/irefindex?hl=en iRefIndex Google Group].<br />
* When updating data on Microsoft Windows XP and Vista, a "Failed to find resources message" may appear in the log message window. If this happens please run the update again and the plugin will check and correct the problem during the second attempt.<br />
* If you are working with large graphs, make sure Cytoscape has at least 128MB memory. See the [http://cytoscape.org/cgi-bin/moin.cgi/How_to_increase_memory_for_Cytoscape Cytoscape documentation] for more information on setting up memory allowances.<br />
<br />
== All iRefIndex Pages ==<br />
<br />
Follow this link for a listing of all iRefIndex related pages (archived and current).<br />
<br />
[[Category:iRefIndex]]</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefScape_1.0&diff=3474iRefScape 1.02011-06-09T10:57:58Z<p>Sabry: /* Installation */</p>
<hr />
<div>Last edited: {{REVISIONYEAR}}-{{padleft:{{REVISIONMONTH}}|2}}-{{REVISIONDAY2}}<br />
<br />
Release date: To be announced<br />
<br />
This page describes the iRefScape 1.0 plug-in for Cytoscape 2.8.1. See the following table for more detailed iRefScape compatibility information.<br />
<br />
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"<br />
! align="center" style="background:#f0f0f0;"|Cytoscape<br />
! align="center" style="background:#f0f0f0;"|iRefScape<br />
|-<br />
| 2.8.1<br />
| iRefScape 1.0 (described on this page)<br />
|-<br />
| 2.7.0<br />
| [[README_Cytoscape_plugin_0.9x|iRefScape 0.9]]<br />
|-<br />
| 2.6.3<br />
| [[README_Cytoscape_plugin_0.8x|iRefScape 0.8]]<br />
|}<br />
<br />
Join the [http://groups.google.com/group/irefindex?hl=en iRefIndex Google Group] to be informed of updates. See also the [[README_Cytoscape_plugin|latest release of iRefScape]] which may differ from the release described here.<br />
<br />
==Installation==<br />
<br />
The plugin can be installed using Cytoscape's plugin menu. Select "Manage plugins" and then "Available for Install" and then "Network and Attribute I/O" and finally the "iRefScape" entry (where the precise version will provide a specific version such as "iRefScape v.1.0").<br />
<br />
Follow the on-screen instructions.<br />
<br />
More detailed instructions, troubleshooting tips and alternative methods are available on the [[README_Cytoscape_plugin_1.0x_Installation|iRefIndex Cytoscape Plugin 1.0 installation page]] and this can be followed for subsequent releases of iRefScape as well, until replaced by a newer document.<br />
<br />
After, installation, select the "iRefScape" entry from Cytoscape's plugin menu.<br />
<br />
When the plugin is started for the first time, it will download the publicly available data set.<br />
<br />
<br />
=== Tested systems ===<br />
This version of the iRefScape plugin has been tested on the following operating systems.<br />
<br />
# Redhat Linux el5 (32 bit) (kernel 2.6.18) with JAVA 32 bit versions 1.6.0_01)<br />
# Windows 7 (64 bit) with JAVA 64 bit versions 1.6.0_25)<br />
# Ubuntu (32 bit)(version 8.04) with JAVA 32 bit versions 1.6.<br />
<br />
Please refer [http://irefindex.uio.no/wiki/README_Cytoscape_plugin_1.0x_Installation '''/README_Cytoscape_plugin_1.0x_Installation'''] for more details on OS specific issues.<br />
<br />
== Using the Wizard - an example search ==<br />
<br />
Click the "Wizard" button - a pop-up window will appear. <br />
<br />
Follow these steps<br />
<br />
# Select "Search protein-protein interactions for a protein".<br />
# Select "UniProt identifier".<br />
# For "Taxonomy identifier", select "9606 (Human)" <br />
# Type <tt>QCR2_HUMAN</tt> in the provided space. Click "Next".<br />
# Click "Search & load".<br />
<br />
The images below show each of the steps in the wizard.<br />
<br />
<gallery perrow="5"><br />
Image:IRefIndex-Cytoscape-Wizard.png|The iRefIndex wizard<br />
Image:IRefIndex-Cytoscape-Wizard-step2.png|Choosing a result type<br />
Image:IRefIndex-Cytoscape-Wizard-step3.png|Choosing a taxonomy type<br />
Image:IRefIndex-Cytoscape-Wizard-step4.png|Specifying the search term<br />
Image:IRefIndex-Cytoscape-Wizard-step5.png|Additional options<br />
</gallery><br />
<br />
== Using the Search Panel ==<br />
<br />
To perform a search, the following steps are involved:<br />
<br />
# Enter query term(s)<br />
# Select a search type<br />
# Select taxonomy/organism<br />
# Adjust search options (iterations, new view, canonical expansion) - this is optional<br />
# Start the search<br />
<br />
=== Enter query term(s) ===<br />
<br />
Queries may be loaded from a file or by pasting the query into the text box (one query per line). Multiple queries can also be separated by pipe characters (<tt>|</tt>) or by tab characters. Queries with spaces in them should be enclosed in double quotes.<br />
<br />
=== Select a search type ===<br />
<br />
Example searches are listed below.<br />
<br />
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"<br />
! align="center" style="background:#f0f0f0;"|Search Type<br />
! align="center" style="background:#f0f0f0;"|Example<br />
! align="center" style="background:#f0f0f0;"|Notes<br />
|-<br />
| <tt>RefSeq_Ac</tt>||<tt>NP_996224</tt>||See http://www.ncbi.nlm.nih.gov/protein/221379660<br />
|-<br />
| <tt>UniProt_Ac</tt>||<tt>Q7KSF4</tt>||See http://www.uniprot.org/uniprot/Q7KSF4<br />
|-<br />
| <tt>UniProt_ID</tt>||<tt>Q7KSF4_DROME</tt>||See http://www.uniprot.org/uniprot/Q7KSF4<br />
|-<br />
| <tt>geneID</tt>||<tt>42066</tt>||See http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=42066<br />
|-<br />
| <tt>geneSymbol</tt>||<tt>cher</tt>||See http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=42066<br />
|-<br />
| <tt>mass</tt>||<tt>72854<-->72866</tt>||Search protein interactors for a range of molecular mass (in Da).<br />
|-<br />
| <tt>rog</tt>||<tt>10121899</tt>||Redundant object group: iRefIndex's internal identifier for a protein<br />
|-<br />
| <tt>PMID</tt>||<tt>14605208</tt>||PubMed Identifier where an interaction is described. See http://www.ncbi.nlm.nih.gov/pubmed. Iterations and "Use canonical expansion" have no effect on this search type. This search will return all protein interactors in the given PMID and will automatically draw all interactions known between these proteins (even if these interactions are supported by different PMIDs). Select edges in the resulting graph, and see the i.PMID attribute in the Edge Attribute Browser.<br />
|-<br />
| <tt>src_intxn_id</tt>||<tt>EBI-212627</tt>||Source interaction database identifier. Iterations and "Use canonical expansion" have no effect on this search type. Caution: multiple databases may have overlapping interaction record identifiers (e.g. <tt>147805</tt> returns records from both BIND and BioGrid) and there is no way to limit this search to a specific database at this time.<br />
Equivalent interactions from other databases will be automatically retrieved using this search type (see provided example).<br />
|-<br />
| <tt>omim</tt>||<tt>227650</tt>||OMIM identifier. See http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=227650<br />
|-<br />
| <tt>digid</tt>||<tt>449</tt>||Internal identifier for a group of phenotypically related diseases. See http://donaldson.uio.no/wiki/DiG:_Disease_groups. A digid can be found by first performing a search for some omim identifier - the digid will then appear as the i.digid node attribute.<br />
<!--<br />
|-<br />
| <tt>dig_title</tt>||<tt>fanconi</tt>||Text search for a group of phenotypically related diseases. See http://donaldson.uio.no/wiki/DiG:_Disease_groups<br />
|-<br />
--><br />
|}<br />
<br />
=== Select taxonomy/organism ===<br />
<br />
This will limit the search results to a particular organism. An organism can be selected from the list, or a taxonomy identifier can be entered into the field itself. See [http://www.ncbi.nlm.nih.gov/taxonomy Entrez Taxonomy] for more details on taxonomy identifiers. For most search types, it is acceptable to leave this field set to <tt>Any</tt>.<br />
<br />
=== Adjust search options ===<br />
<br />
The following optional adjustments can be made:<br />
<br />
==== Iterations ====<br />
<br />
A distance from the query list's members can be specified:<br />
<br />
* Selecting <tt>0</tt> will return only interactions between nodes found by the query list<br />
* Selecting <tt>1</tt> will return immediate neighbours of nodes in the query list<br />
<br />
==== Create new view ====<br />
<br />
A new view will be opened for the search results if this option is selected. Otherwise, the results will be added to the current view.<br />
<br />
==== Use canonical expansion ====<br />
<br />
Selecting this option will expand the search to include all proteins that are related to the query protein (for example, splice isoforms). See [[Canonicalization]] for technical details.<br />
<br />
=== Start the search ===<br />
<br />
Press the "Search and load" button to perform the search.<br />
<br />
== Viewing the Results ==<br />
<br />
=== Colours and Shapes ===<br />
<br />
* Blue nodes corresponds to proteins found by your query<br />
* Green nodes are interacting partners for your query protein<br />
* Purple hexagons are complex-nodes (also called pseudo-nodes); they keep partners of a complex together (i.e. QCR6_HUMAN is found in two complexes also involving "QCR2_HUMAN")<br />
* Orange-yellow edges indicate protein-protein interactions and pink edges represent membership of some protein in a complex<br />
<br />
=== Toggling Edges ===<br />
<br />
Multiple edges may appear between two nodes. These represent separate interaction records that support this link. Details on each original record can be viewed using the edge attribute viewer (below). You can toggle this multi-view on and off by selecting "Toggle selected multi-edges" in the iRefScape/View Tools menu. Only one of the edges will be shown in the collapsed view.<br />
<br />
<br />
=== iRefScape Menu ===<br />
<br />
The iRefScape menu in the CytoScape menu bar contains a number of other functions that may help with searching and viewing interaction data. These are described in more detail on a separate page [[README_Cytoscape_plugin_menu]].<br />
<br />
=== Expanding the Interaction Map ===<br />
<br />
You can search for additional interactions by right-clicking on a node and selecting "iRefIndex -- Retrieve interactions".<br />
<br />
Some example result displays are shown below.<br />
<br />
<gallery widths="500px" heights="300px"><br />
Image:QCR2_HUMAN_initial.png|Results<br />
Image:QCR2_HUMAN.png|Results (tidied)<br />
</gallery><br />
<br />
== Attributes ==<br />
<br />
[[Image:iRefIndex-0.83-node-attributes-close-up-closed.png|right|The node attributes menu]]<br />
<br />
There are two types of attributes available from iRefIndex: node attributes and edge attributes. These may be used to view information about selected nodes or edges (like <tt>i.taxid</tt>). Some features may allow the user to link out to additional data sources through the "right-click" menu (like <tt>i.geneID</tt>). Features may also be used to sort and select nodes and edges with specific attributes (like <tt>i.order</tt>). The <tt>i.query</tt> feature shows the user's query that is responsible for returning the node or edge.<br />
<br />
Brief descriptions and examples of each attribute are provided below. <br />
<br />
The user must first select the attributes that are to be displayed. This can be done by clicking on the "attribute" icon at the top of the node or edge attribute browser, as shown in the illustrative images.<br />
<br />
<div style="clear: right"></div><br />
=== Node Attributes ===<br />
<br />
[[Image:iRefIndex-0.83-node-attributes-close-up-open.png|right|The open node attributes menu]]<br />
<br />
Each node represents a distinct amino acid sequence (protein) from a distinct organism (taxonomy identifier). Each of the attributes below, provide additional information about the node. Although each node is distinct, a graph produced by iRefIndex may contain multiple nodes that are related proteins (such as splice isoform products from the same gene). These nodes will all have the same <tt>i.canonical_rog</tt> and <tt>i.canonical_rogid</tt> feature values. See the notes below.<br />
<br />
Node attributes that can be lists of items (like <tt>i.UniProt</tt>) will have a corresponding attribute called <tt>i.''attribute name''_TOP</tt> (for example, <tt>i.UniProt_TOP</tt>) which provides the first item of the associated list.<br />
<br />
<div style="clear: right"></div><br />
<br />
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"<br />
! align="center" style="background:#f0f0f0;"|Attribute name<br />
! align="center" style="background:#f0f0f0;"|Data type<br />
! align="center" style="background:#f0f0f0;"|Example value<br />
! align="center" style="background:#f0f0f0;"|Description<br />
|-<br />
| <tt>ID</tt>||Integer||<tt>10121899</tt>||This is a unique identifier for the node assigned by iRefIndex (no two nodes will have the same ID). Each node corresponds to a distinct amino acid sequence from a distinct taxonomy identifier. See also <tt>i.rog</tt> and <tt>i.rogid</tt>.<br />
|-<br />
| <tt>canonicalName</tt>||Integer||<tt>10121899</tt>||This is the same as <tt>ID</tt>. This attribute is set by Cytoscape and is unrelated to the <tt>i.canonical_rog</tt> or <tt>i.canonical_rogid</tt> used by iRefIndex<br />
|-<br />
| <tt>i.RefSeq_Ac</tt>||List||<tt>[NP_996224]</tt> ||All RefSeq accessions with an amino acid sequence and taxon identifier identical to the protein represented by this node. Right click on this entry and select "Search ''[RefSeq_Ac]'' on the web -- Entrez -- Protein" for more information. See also <tt>i.RefSeq_TOP</tt> for the first entry in this list of accessions.<br />
|-<br />
| <tt>i.UniProt_Ac</tt>||List||<tt>[Q7KSF4]</tt>||All UniProt accessions with an amino acid sequence and taxonomy identifier identical to the protein represented by this node. Right click on this entry and select "Search ''[UniProt_Ac]'' on the web -- UniProt -- KB Beta" for more information. See also <tt>i.UniProt_Ac_TOP</tt> for the first entry in this list of accessions.<br />
|-<br />
| <tt>i.UniProt_ID</tt>||List||<tt>[Q7KSF4_DROME]</tt> ||All UniProt identifers with an amino acid sequence and taxonomy identifier identical to the protein represented by this node. Right click on this entry and select "Search ''[UniProt_ID]'' on the web -- UniProt -- KB Beta" for more information. See also <tt>i.UniProt_ID_TOP</tt> for the first entry in this list of IDs.<br />
|-<br />
| <tt>i.canonical_rog</tt>||Integer||<tt>10121899</tt>||Related proteins (say splice isoforms from the same gene) will all belong to the same canonical group. One member of this group is assigned as the canonical representative of this group. The <tt>i.canonical_rog</tt> attribute lists the identifier of the protein's canonical group identifier. For example, all products of Entrez Gene 42066 have the same <tt>i.canonical_rog</tt> (<tt>10121899</tt>). Each of these gene products has its own identifier (because they each have a distinct amino acid sequence). One of the splice isoforms (<tt>NP_996224</tt>) was chosen as the canonical representative of this group. See the [http://irefindex.uio.no/wiki/Canonicalization canonicalization document] for more details on how canonical groups are constructed and how canonical representatives are chosen.<br />
|-<br />
| <tt>i.canonical_rogid</tt>||String||<tt>1ZFb1WlW0OgOlhiAPtkJTdb6oOg7227</tt>||This is a unique alphanumeric key for the canonical representative of the canonical group to which this node belongs. Briefly, an SHA-1 digest of the amino acid sequence is used to generate a unique 27 character key and this is prepended to the taxonomy identifier for the protein's source organism in order to make the rogid. See PMID 18823568 for details on how this key can be generated. This is a string equivalent of the <tt>i.canonical_rog</tt> attribute. All <tt>i.canonical_rog</tt> instances (each being an integer) have one corresponding <tt>i.canonical_rogid</tt>. See the [http://irefindex.uio.no/wiki/Canonicalization canonicalization document] for more details on how canonical groups are constructed and how canonical representatives are chosen. Note that the rogid for the protein represented by this specific node is listed under <tt>i.rogid</tt>.<br />
|-<br />
| <tt>i.dataset</tt>||Integer||<tt>0</tt>||In the batch query mode this can be used to locate the query batch (i.e. which group of queries were responsible for the node). In single query mode, when a sequence of queries are issued one after another this variable can be used to distinguish the results from each step. All nodes with a i.dataset value higher than 999 can be found using more than one batch of queries. <br />
|-<br />
| <tt>i.digid</tt>||List||<tt>449</tt>||This is an integer identifier that is shared by a group of disease entries in OMIM that are related by their titles. See the [http://donaldson.uio.no/wiki/DiG:_Disease_groups disease groups document] for more details. Also see <tt>i.omim</tt> and <tt>i.dig_title</tt>.<br />
|-<br />
<!--<br />
| <tt>i.dig_title</tt>||List||<tt>[Fanconi anemia, complementation group B, 300514 (3), VACTERL association with hydrocephalus, X-linked, 314390 (3)]</tt>||These are entries from OMIM's Morbid Map that are all part of the same disease group. See the [http://donaldson.uio.no/wiki/DiG:_Disease_groups disease groups document] for more details. Also see <tt>i.omim</tt> and <tt>i.digid</tt>.<br />
--><br />
|-<br />
| <tt>i.displayLabel</tt>||List||<tt>[Q7KSF4_DROME]</tt> ||This is a list of short labels chosen by iRefIndex to label the node using the VizMapper. The UniProt identifier is preferentially chosen (if one is available) followed by the Entrez Gene Symbol. See also <tt>i.displayLabel_TOP</tt> for the first entry in this list.<br />
|-<br />
| <tt>i.geneID</tt>||List||<tt>[42066]</tt>||All NCBI Entrez Gene identifiers that encode a protein sequence identical to that of this node. Right click on this entry and select "Search ''[geneID]'' on the web -- Entrez -- Gene" for more information. See also <tt>i.geneID_TOP</tt> for the first entry in this list.<br />
|-<br />
| <tt>i.geneSymbol</tt>||List||<tt>[CHER]</tt>||All NCBI Entrez Gene official symbols that encode a protein sequence identical to that of this node. Right click on this entry and select "Search ''[geneSymbol]'' on the web -- Entrez -- Gene" for more information. See also <tt>i.geneSymbol_TOP</tt> for the first entry in this list.<br />
|-<br />
| <tt>i.interactor_description</tt>||List||<tt>[Q7KSF4_DROME, CHER, DMEL_CG3937, SKO, DMEL CG3937, FLN, CG3937, CHER, DMEL\\CG3937, FLN, SKO, CHER, NAME=CHER, DMEL_CG3937]</tt>||A collection of all the names in their short form as given by the original interaction databases. See also <tt>i.interactor_description_TOP</tt> for the first entry in this list.<br />
|-<br />
| <tt>i.mass</tt>||Integer|| <tt>259142</tt> ||Mass associated with the protein sequence for this node. From UniProt, if available. You can search for nodes inside a mass range using the <tt>mass</tt> search type in the iRefIndex plugin.<br />
|-<br />
| <tt>i.omim</tt>||List||<tt>[608053]</tt>||List of OMIM disease identifiers associated with this protein. Right click on the entry and select "Search for ''[omim]'' on the web -- Entrez -- OMIM" for more information. <br />
|-<br />
| <tt>i.order</tt>||Integer|| <tt>0</tt> || The distance of this node from the query node (query node has distance <tt>0</tt>, nodes that are returned by a query because they are a part of the same canonical group have a value of <tt>10</tt>, direct neighbours have a value of<tt>1</tt>). Pseudonodes have negative values (<tt>-1</tt> is a complex holder, <tt>-2</tt> is a collapsed instance).<br />
|-<br />
| <tt>i.overall_degree_TOP</tt>||Integer|| <tt>42</tt> ||The total number of interactions described for this node in the iRefIndex database. Not all of these edges will be necessarily shown in the current view. This is the node degree in the full iRefIndex interactome. When calculating the value of this all proteins in iRefIndex (not only the ones currently loaded) will be used<br />
|-<br />
| <tt>i.popularity</tt>||List|| <tt>42</tt> || '''TO BE DESCRIBED'''<br />
|-<br />
| <tt>i.pseudonode</tt>||Boolean|| <tt>false</tt> || This is set to true is the node represents a "complex" or n-ary interaction record. Protein nodes with edges incident to a pseudonode are member interactors from the interaction record where specific interactions between pairs of interactors is unknown. Pseudonodes appear as hexagons when using the iRefIndex VizMapper style. <br />
|-<br />
| <tt>i.query</tt>||String||<tt>NP_996224</tt>||The user query used to retrieve this specific node. Neighbours of "query" nodes will not have an <tt>i.query</tt> value. Nodes returned by queries are coloured blue when using the iRefIndex VizMapper style.<br />
|-<br />
| <tt>i.rog</tt>||Integer||<tt>10121899</tt>||This is a unique identifier for the node assigned by iRefIndex (no two nodes will have the same ID). Each node corresponds to a distinct amino acid sequence associated with a distinct taxonomy identifier. <tt>i.rog</tt> also appears as the <tt>ID</tt> attribute. Each <tt>i.rog</tt> has a corresponding <tt>i.rogid</tt> - see below.<br />
|-<br />
| <tt>i.rogid</tt>||String||<tt>2mL9oLZ9g/SSPyK0nOz97RmOzPg3702</tt>||This is a unique alphanumeric key for the protein represented by this node. Briefly, an SHA-1 digest of the amino acid sequence is used to generate a unique 27 character key and this is prepended to the taxonomy identifier for the protein's source organism in order to make the rogid. See PMID 18823568 for details on how this key can be generated. This is a string equivalent of the <tt>i.rog</tt> attribute. All <tt>i.rog</tt> instances (each being an integer) have one corresponding <tt>i.rogid</tt>.<br />
|-<br />
| <tt>i.taxid</tt>||Integer||<tt>7227</tt>||The NCBI taxonomy identifier for this protein's source organism. See http://www.ncbi.nlm.nih.gov/taxonomy?term=7227 for more details of this example value for <tt>i.taxid</tt>.<br />
|-<br />
| <tt>i.xref</tt>||List||<tt>[AAF70826.1,Q9M6R5]</tt> ||All the accessions as given by the original interaction database records to describe this protein. See also <tt>i.xref_TOP</tt> for the first entry in this list.<br />
|-<br />
| <tt>i.alive</tt>||Boolean||<tt>true or false</tt> ||This is true for all nodes after a search operation. This variable is used by the iRefScape filter and after a filter is applied, all nodes matching the filter criteria will have a true value for this variable (all other nodes will have false).<br />
|-<br />
| <tt>i.alive_degree</tt>||Integer||<tt>0,1,2-...</tt> ||This is will give the node degree after a search. When an iRefScape filter is applied this will give the number of nodes with "i.alive=true" connected to a particular node(How many nodes matching the filter criteria has connections with a particular node). <br />
|-<br />
|}<br />
<br />
===Edge Attributes===<br />
<br />
Each edge represents a distinct primary database record that supports some relationship between the two incident nodes. So, if an interaction between two proteins has been annotated by two databases (or twice by the same database) then two edges will appear between those two protein nodes.<br />
<br />
<br />
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"<br />
! align="center" style="background:#f0f0f0;"|Attribute name<br />
! align="center" style="background:#f0f0f0;"|Data type<br />
! align="center" style="background:#f0f0f0;"|Example value<br />
! align="center" style="background:#f0f0f0;"|Description<br />
|-<br />
| <tt>ID</tt>||String||<tt>10121899 (2771704(40952)) 13911416</tt>||This is a unique identifier for the edge assigned by Cytoscape (no two edges will have same <tt>ID</tt>). See <tt>i.rig</tt> and <tt>i.rigid</tt> for unique identifiers for the edge assigned by iRefIndex.<br />
|-<br />
| <tt>i.PMID</tt>||Integer||<tt>14605208</tt>||Publication identifier of the publication where the interaction represented by the edge mentioned. Right click on this entry and select "Search ''[PMID]'' on the web -- Entrez -- Pubmed" for more details on the publication.<br />
|-<br />
| <tt>i.bait</tt>||Integer||<tt>13911416</tt>||Node ID for the protein that was used as a bait in this experiment. Only applicable where the experimental system (see <tt>i.method_name</tt>) used to support this relationship was a bait-prey system (for example, two hybrid).<br />
|-<br />
| <tt>i.canonical_rig</tt>||Integer||<tt>27799</tt>||See notes for the <tt>i.rig</tt> edge feature. This is the rig constructed for the interaction using its canonical rogs. Use a web browser to query http://wodaklab.org/iRefWeb/interaction/show/27799 (where <tt>27799</tt> is the <tt>i.canonical_rig</tt> value) to retrieve more information on this interaction and equivalent source interaction records.<br />
|-<br />
| <tt>i.experiment</tt>||String||<tt>Giot L [2003]</tt>||A short label for the experiment where this interaction was found (usually contains authors names).<br />
|-<br />
| <tt>i.flag</tt>||Integer||<tt>1</tt>||Used by iRefIndex plugin to control display of edges (<tt>0</tt> being the representative edge, used in edge toggle; <tt>1</tt> being an edge which will disappear during edge toggle; <tt>2</tt> being a complex holder edge; <tt>6</tt> being a path; <tt>7</tt> being an edge from or to a collapsed node).<br />
|-<br />
| <tt>i.host_taxid</tt>||Integer||<tt>7227</tt>||Indicates the organism taxonomy identifier where the interaction was experimentally demonstrated.<br />
|-<br />
| <tt>i.isLoop</tt>||Integer||<tt>1</tt>||Indicates whether the interaction is a self interaction (such as a dimer or possibly multimer of the same protein type). See the source interaction record for details.<br />
|-<br />
| <tt>i.method_cv</tt>||String||<tt>MI:0018</tt>||PSI-MI controlled vocabulary term identifier for the method used to provide evidence for this interaction. See http://www.ebi.ac.uk/ontology-lookup/ for more details. The name of the method is also given in the <tt>i.method_name</tt> feature.<br />
|-<br />
| <tt>i.method_name</tt>||String||<tt>two hybrid</tt>||PSI-MI controlled vocabulary term name for the method used to provide evidence for this interaction. See http://www.ebi.ac.uk/ontology-lookup/ for more details. The term identifer is also given in the <tt>i.method_cv</tt> feature.<br />
|-<br />
| <tt>i.participant_identification</tt>||String||<tt>predetermined participant</tt>||PSI-MI controlled vocabulary term for the participant identification method used to provide evidence for this interaction. See http://www.ebi.ac.uk/ontology-lookup/ for more details. The identifier for the term is also given in the <tt>i.participant_cv</tt> feature.<br />
|-<br />
| <tt>i.participant_cv</tt>||String||<tt>predetermined participant</tt>||PSI-MI controlled vocabulary term identifier for the participant identification method used to provide evidence for this interaction. See http://www.ebi.ac.uk/ontology-lookup/ for more details. The term itself is also given in the <tt>i.participant_identification</tt> feature.<br />
|-<br />
| <tt>i.query</tt>||String||<tt>NP_996224</tt>||The user's query that is responsible for returning this edge.<br />
|-<br />
| <tt>i.rig</tt>||Integer||<tt>27799</tt>||Redundant interaction group identifier for the interaction. <br />
This is an integer equivalent of <tt>i.rigid</tt>. Every rig has one corresponding rigid.<br />
|-<br />
| <tt>i.rigid</tt>||String||<tt>TAabV6yJ1XzUvEhYwZLpu5reBU0</tt>||Redundant interaction group identifier for the interaction. This is a universal key generated for the interaction by ordering according to ASCII value and concatentating the rogids participating in the interaction and then generating a Base-64 representation of an SHA-1 digest of the resulting string. See PMID 18823568 for details on how this key can be generated.<br />
|-<br />
| <tt>i.score_hpr</tt>||Integer||<tt>15</tt>||The hpr score (highest pmid re-use) is the highest number of interactions that any one PMID (supporting this interaction) is used to support. See PMID 18823568 for details. See also <tt>i.score_np</tt> and <tt>i.score_lpr</tt>.<br />
|-<br />
| <tt>i.score_lpr</tt>||Integer||<tt>11</tt>||The lpr score (lowest pmid re-use) is the lowest number of distinct interactions that any one PMID (supporting this interaction) is used to support. An lpr of greater than 20 is considered to be a high-throughput experiment. See PMID 18823568 for details. See also <tt>i.score_np</tt> and <tt>i.score_lpr</tt>.<br />
|-<br />
| <tt>i.score_np</tt>||Integer||<tt>2</tt>||Number of PubMed Identifiers (PMIDs) pointing to literature where this interaction is supported. See PMID 18823568 for details. See also <tt>i.score_lpr</tt>.<br />
|-<br />
| <tt>i.source_protein</tt>||Integer||<tt>-1</tt>||'''TO BE DESCRIBED'''<br />
|-<br />
| <tt>i.src_intxn_db</tt>||String||<tt>grid</tt>||Original interaction database where this interaction record was obtained.<br />
|-<br />
| <tt>i.src_intxn_id</tt>||String||<tt>38677</tt>||Original interaction database where this interaction record was obtained. <br />
In some case, it may be possible to right click and "Search ''[src_intxn_id]'' on the web -- Interaction databases -- the database" to see the original record.<br />
|-<br />
| <tt>i.type_cv</tt>||String||<tt>MI:0407</tt>||PSI-MI controlled vocabulary term identifier for the interaction type that occurs between the two proteins. See http://www.ebi.ac.uk/ontology-lookup/ for more details. The term itself is also given in the <tt>i.type_name</tt> feature.<br />
|-<br />
| <tt>i.type_name</tt>||String||<tt>direct interaction</tt>||PSI-MI controlled vocabulary term identifier for the interaction type that occurs between the two proteins. See http://www.ebi.ac.uk/ontology-lookup/ for more details. The term itself is also given in the <tt>i.type_name</tt> feature.<br />
|-<br />
| <tt>i.target_protein</tt>||Integer||<tt>-1</tt>||'''TO BE DESCRIBED'''<br />
|-<br />
|}<br />
<br />
=== User Attributes ===<br />
Importing - TBD<br />
<br />
Searching on - TBD<br />
<br />
== Obtaining CORUM, DIP and HPRD Data ==<br />
<br />
Due to licensing issues, we are unable to distribute these data with the plugin. CORUM data and free IMex data from DIP will be included in the next public release of iRefIndex.<br />
<br />
You can request these data under a collaborative agreement by emailing ian.donaldson@biotek.uio.no<br />
<br />
Under the agreement you agree to<br />
<br />
# Not redistribute the data outside your research group.<br />
# Provide us with feedback on your use of the data (problems and requests).<br />
<br />
We do not require authorship on any related publications.<br />
<br />
== Obtaining Updates to the Data ==<br />
<br />
You can check for and download updates to the dataset used by your plugin using the Wizard (see "Check for iRefIndex updates").<br />
<br />
iRefIndex updates are announced through the [http://groups.google.com/group/irefindex?hl=en iRefIndex Google Group]<br />
<br />
==Obtaining Updates to the Plugin==<br />
<br />
If you already have a plugin called iRefScape (a menu entry "iRefScape" under the plugin menu of Cytoscape) and you want to make sure you have the latest version, use "Update plugins" from the "Plugins" menu. However, if you want to reinstall the plugin, you should uninstall any previous version of the plugin first.<br />
<br />
Plugin updates are announced through the [http://groups.google.com/group/irefindex?hl=en iRefIndex Google Group]<br />
<br />
<!--<br />
<br />
== How to load batch query from file ==<br />
1. Create a text file with the following format:<br />
<p><type><NCBI_taxonomy_identifier></p><br />
<p>query_text_1</p><br />
<p>query_text_2</p><br />
<p>query_text_3</p><br />
<br />
<p>The first line of the file starts with a hash ("#") and then the type. The type could be</P><br />
*ACCESSION<br />
*NAME<br />
*GENID<br />
<br />
The query_text is your query (e.g.Q39009). Each query line has to be terminated by a new line character (press enter after each line) <br />
<p>[Sample batch file: [http://irefindex.uio.no/wikifiles//images/b/b1/Sample_batch_accessions.txt.zip]]</p><br />
<br />
==Integrating User Data into the Plugin==<br />
<br />
<br />
===How to create your own file to use as index===<br />
<br />
'''TO BE DESCRIBED'''<br />
<br />
===How to create node and edge attributes ===<br />
<br />
Example: Attaching [http://irefindex.uio.no/wiki/DiG:_Disease_groups disease group] identifiers to nodes<br />
<br />
==Updating==<br />
# From Cytoscape updater<br />
# Using plugins update feature<br />
<br />
== Log Files, Search Details and Errors ==<br />
# How to interpret log messages and save them for later reference. <br />
<br />
==Using the plugin as a search tool ==<br />
The plugin could also be used to search the current network. However, there is a better search option in Cytoscape with Google suggest which may be more convenient to use. The reason for including the search function was that the Cytoscape search filed remained inactive on some occasions for networks crated using the plugin. The reason for this is still unknown and deleting a node on the network seems to activate it, when this bug will be fixed the users are encouraged to use the Cytoscape search option.<br />
Currently, if a user performs a search with a term and if the corresponding protein is already loaded, the loaded protein (corresponding node) would be highlighted with Cytoscape default highlight colors. <br />
<br />
<br />
== Exit plugin and force terminate operations ==<br />
The exit button performs two functions. <br />
# First one is to exit iRefIndex plugin, where the outcome is to detach the plugin from Cytoscape. <br />
# The second function "FORCE STOP" (only available during a active task) is to terminate current operation. The "FORCE STOP" is useful when the search query or a subsequent operation takes too long to finish or none-responding. When a force stop is performed the out come is unpredictable and behavior was undefined, therefore results after such operation could not be trusted. <br />
<br />
--><br />
<br />
==Advanced search options==<br />
===Path-Finding===<br />
[[Image:iRefIndex-0.83-path-original.png|thumb|500px|The path in the results, highlighted in green. Solid green lines indicate presence of evidence for this step of the path in the direction specified by the query OR the presence of evidence that has no directionality. A dashed green line indicates there is evidence for this step of the path but only in the direction that is opposite to that specified in the query.]]<br />
<br />
iRefScape can be used to find interaction events connecting two proteins or a sequence of events involving several proteins. <br />
<br />
This process intakes two terminal nodes as input and returns all reasonable paths connecting these two. The results returned here are pathway independent. In other words, the sequences of interactions connecting the nodes are not constructed using currently published pathways. However, the paths returned may contain pathway centric information.<br />
<br />
The query format is as follows:<br />
<br />
NP_004976 <==> NP_002871<br />
<br />
Additional type and taxonomy parameters were also supplied as required:<br />
<br />
* '''Search type:''' <tt>RefSeq_Ac</tt><br />
* '''Taxonomy:''' <tt>9606 (Homo sapiens)</tt><br />
<br />
This query located all reasonable paths between <tt>NP_004976</tt> and <tt>NP_002871</tt> and the returned path also contains the shortest path between them. The results of the path finding was sorted in the ascending order of path length and the maximum path length was restricted to a default value of 6; this value can be modified by changing the value of "Maximum distance" from the "Path parameters" tab in the advanced options panel. The paths found in this way were "reasonable paths", this concept is different from finding the shortest path or finding all the paths. A "reasonable path" from A to B is a path extending from A to B where none of the intermediate points can be reached from A with fewer steps by a path that extends from A via B (in other words, when evaluating a path from A to B, nodes beyond B are not considered).<br />
<br />
<div style="clear: right"></div><br />
<br />
=== Reversing the Path ===<br />
<br />
[[Image:iRefIndex-0.83-path.png|thumb|500px|The path in the results, highlighted in green]]<br />
<br />
Due to the way the algorithm works, when the opposite search was performed...<br />
<br />
NP_002871 <==> NP_004976<br />
<br />
...it took 120 seconds and returned 3 paths. The reason for this is that <tt>NP_002871</tt> is directly connected to many hubs and therefore, the initial seed-list size was larger than when starting with <tt>NP_004976</tt>. The algorithm first tries the direction requested by the user and after that considers the opposite direction when creating the sub-network to look for the path. The time consuming step in the opposite search (<tt>NP_002871<==>NP_004976</tt>) is thus the initial evaluation step. When constructing the query for path-finding we used the attribute <tt>i.overall_degree_TOP</tt> and it provided the overall connectivity of the proteins within iRefIndex. The <tt>i.overall_degree_TOP</tt> value of <tt>RAF1</tt> was found to be 443 and for the <tt>KRAS</tt> isoform was found to be 2. Therefore, although not shown in the graph, <tt>RAF</tt> is connected to more than 400 other proteins than <tt>RAS1</tt>.<br />
<br />
In the image shown here, the green arrow shows the path.<br />
<br />
<div style="clear: right"></div><br />
=== Path Selection ===<br />
<br />
[[Image:iRefIndex-0.83-path-selector.png|thumb|500px|The path selector for the results]]<br />
<br />
After the path-finding is completed the "Path selection" panel can be used to selectively load the paths. In order to make the selection easier, the paths found can be described by a particular attribute type: by selecting a value from the list for "Convert pop-up type to" (such as <tt>RefSeq_Ac</tt>) and pressing the "Convert" button, a tooltip appearing over each path description will show the requested attribute values for each component of the path. Thus, a path description such as...<br />
<br />
321631 -> 2229473 -> 4410739 -> 4531114<br />
<br />
...will provide a tooltip showing the following identifiers:<br />
<br />
NP_002871 -> NP_001123914 -> NP_036979 -> NP_004976<br />
<br />
===List comparison===<br />
This feature is available with version 0.91 and later.<br />
<br />
This feature provides a way to compare two lists of proteins. When a <tt>COMPARE{<List1>,<List2>}</tt> format query is issued with default settings an interaction network is loaded with interactions involving only the proteins of the list and proteins which are not in the list but interacts with at least two proteins from each list (intermediate components). At the end of the operation, in addition to the Cytoscape network a adjacency cube (adjacency matrix with colours as the third dimension) is also created. This adjacency cube is synchronized with the network and can be used examine the results easily. A summary report function is provided to list the overall summary of each protein in the list sorted order so that the most connected protein appear first. The identifiers used to display the proteins in the adjacency cube are either iROGID or the ROGID of complexes. The user has the option to visualize these in popular identifier types using convert feature.<br />
<br />
Example query.<br />
<br />
COMPARE{P08588,P16671|P07550,P13945} (Example from PMID:20670417)<br />
<br />
This query compares two groups:<br />
<br />
# P08588,P16671<br />
# P07550,P13945<br />
<br />
Members within the group are separated with a comma (<tt>,</tt>); groups are separated by a pipe (<tt>|</tt>).<br />
<br />
====Questions and answers about list comparison====<br />
<br />
''What is the maximum number of members a group can have?''<br />
<br />
You could have any number of members, more members there are more time it will take for the operation and more memory it will need. For instance the above example search will complete comfortably in 1 minute with 256MB of allocated memory. If you have more than 100 members we recommend having at least 1GB dedicated memory for Cytoscape. <br />
<br />
''Can I compare more than two groups?''<br />
<br />
Yes, each group should be separated with a pipe character. The maximum number of recommended group count is 255.<br />
<br />
''What if a protein or protein resulting from query appears in more than one group?''<br />
<br />
All proteins found in more than one group is treated as a new group.<br />
<br />
''Can I compare members of already grouped identifiers?''<br />
<br />
Yes. As an example if you want to compare interactions among the disease group 141, the following query could be used:<br />
<br />
COMPARE{141}<br />
<br />
==Troubleshooting==<br />
<br />
* See http://cytoscape.org/ for a manual and a set of tutorials which describe the installation and use of Cytoscape.<br />
* For problems with Cytoscape installation or use, try the [http://groups-beta.google.com/group/cytoscape-helpdesk Cytoscape Help Desk].<br />
* If you have problems with installation or use, please share your experience with us through the [http://groups.google.com/group/irefindex?hl=en iRefIndex Google Group].<br />
* When updating data on Microsoft Windows XP and Vista, a "Failed to find resources message" may appear in the log message window. If this happens please run the update again and the plugin will check and correct the problem during the second attempt.<br />
* If you are working with large graphs, make sure Cytoscape has at least 128MB memory. See the [http://cytoscape.org/cgi-bin/moin.cgi/How_to_increase_memory_for_Cytoscape Cytoscape documentation] for more information on setting up memory allowances.<br />
<br />
== All iRefIndex Pages ==<br />
<br />
Follow this link for a listing of all iRefIndex related pages (archived and current).<br />
<br />
[[Category:iRefIndex]]</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefScape_plugin_menu&diff=3473iRefScape plugin menu2011-06-09T10:31:26Z<p>Sabry: /* Simple batch file */</p>
<hr />
<div>==Search tools==<br />
<br />
===Retrieve interactions for the selected nodes===<br />
To load all protein-protein interactions and complexes involving one or more '''selected nodes'''. This action is the same as performing a iteration=1 search using iRefScape for the selected nodes.<br />
<br />
===Expand one level===<br />
To load all protein-protein interactions and complexes involving at least one of the nodes in the current network. The behaviour is same as performing iteration=1 search using iRefScape for all the nodes. <br />
<br />
===Load interactions between neighbours===<br />
To complete the interactions between the currently loaded nodes. When a search & load operation is performed in iRefScape, the network returned contains all the proteins interacting with the query and the corresponding interactions. This does not return interactions between the neighbours of the query. This operation is the same as performing an iteration=0 search using iRefScape for all the nodes.<br />
This action has no effect for networks for which this operation has already been performed using the option presented at the end of the search.<br />
<br />
===Clear load history (Reload everything next time)===<br />
This will clear the iRefScape cache memory containing currently loaded nodes and edges. IRefScape keeps track of what is loaded to avoid reloading and thus increase efficiency. Therefore, if a search is performed twice,the network will not be re-loaded unless the user has requested that results be shown in a new view or they have selected this menu option. If the user wishes to reload the network then this option has to be used. When using other methods of expanding the network like “Expand one level” iRefScape handles the cache clearing automatically.<br />
<br />
===Reset node degree===<br />
This option resets the i.alive_degree of nodes. i.alive_degree provides how many nodes with a certain attribute type is connected to each node (set using filters). <br />
<br />
==Loading user variables (this section is being edited)==<br />
User variables can be attached to nodes and be browsed using the attribute browser. This file can not be used as a searchable index (can not be used as a search type). please see section [http://irefindex.uio.no/wiki/README_Cytoscape_plugin_menu#iRefScape_user_searchable_index'''iRefScape_user_searchable_index'''] for details on searchable indices. <br />
<br />
There are three ways to load own variables for the user. <br />
#Use the Cytoscape attribute loading feature ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual'''])<br />
#Use a use attribute file with iRefScape (described in this section)<br />
#Include the attribute with the batch search file.(Described in section [http://irefindex.uio.no/wiki/README_Cytoscape_plugin_menu#Attribute_batch_file '''Attribute_batch_file''']).<br />
<br />
The iRefScape user attribute loader is provided as a complementing feature to the Cytoscape node attribute loading ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual''']). For most of the attribute loading operations the Cytoscape node attribute loader is sufficient and easier to use. However, when the iRefScape node attribute file is used, this can be used by using the menu entry iRefScape-> Search tools > Load user variables. In addition the file will be available for subsequent operations.<br />
<br />
===iRefScape user variable file format===<br />
The first line of the file provides instructions and this line is compulsory.<br />
Example. <br />
#i.rog New_attribute<br />
<br />
<br />
The first line always starts with a hash ("#") and immediately followed by the iReFscape variable name. This iRefScape variable name is used to locate the nodes via the new attribute will be attached. Then a tab is used as a column separator, followed by the name of the user attribute name.This user attribute name should be unique( not already used). In the above example the user attribute to use is the i.rog and the user attribute name is "New_attribute".<br />
<br />
From the second line onwards, the attributes with the mapping attribute are provided.<br />
Example <br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
<br />
The first column provides the iRefScape attribute to use and the second column provides the user attribute. Multiple attributes should be separated with a pipe ("|"). The example line shown would locate the node with i.rog=4399398 and attach the "TENC1|UniProtKB:Q63HR2|" value to it with the attribute name "New_attribute"<br />
<br />
*Each column is separated by a TAB.<br />
*Each line ends with a new line character ("\n")<br />
*The file should be constructed using a plain text editor (e.g. Kate, notepad) and word processing software like Microsoft word should not be used to construct this file.<br />
* The file extension is ".txt"<br />
* Sample file "ONE__EXT__ROG_#Name_5_.iruv" can be found in the iRefScape installation directory (iRefIndex directory)<br />
*The file name should have the format _rog_'''USER_VARIABLE_NAME'''.iruv (The text in bold is supplied by the user. e.g., _rog_myAttribute.iruv ).<br />
<br />
Sample file<br />
#i.rog New_name<br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
452957 GFI1B|UniProtKB:Q5VTD9|<br />
561552 TENC1|UniProtKB:Q63HR2-4|<br />
534065 GFI1B_MOUSE|UniProtKB:O70237|<br />
<br />
==iRefScape search with batch file==<br />
When there are many search queries, it is convenient to construct a batch file and load this to iRefScape. There are 3 type of batch files;<br />
#Simple batch file (recommended for users just wanting to search for a list of things)<br />
#Attribute batch file (Attach additional attributes) <br />
#User index batch file (Explained in section [http://irefindex.uio.no/wiki/README_Cytoscape_plugin_menu#iRefScape_user_searchable_index '''iRefScape_user_searchable_index'''])<br />
<br />
=== Simple batch file ===<br />
<br />
Example file content:<br />
#geneID:3702<br />
814707<br />
814714<br />
814714<br />
817659<br />
818662<br />
<br />
*The first line starts with a hash ("#") and this line is compulsory.<br />
*Immediately after the hash (no space in between) the iRefScape attribute name should be provided. Please see below for accepted list of identifier with the corresponding label.<br />
<br />
{| {{table}}<br />
| align="center" style="background:#f0f0f0;"|'''Label to use in the batch file'''<br />
| align="center" style="background:#f0f0f0;"|'''Description'''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
|-<br />
| rog||iROGID, the integer reference redundant object group identifier([http://irefindex.uio.no/wiki/Protein_identifier_mapping '''details of mapper files to locate the iRGOID can be found here)''']||||||<br />
|-<br />
| geneID||NCBI Gene ID, this is always an integer||||||<br />
|-<br />
| UniProt_Ac||UniProt/KB accession||||||<br />
|-<br />
| RefSeq_Ac||RefSeq Accession||||||<br />
|-<br />
| UniProt_ID||UniProt identifier||||||<br />
|-<br />
| geneSymbol||NCBI Gene symbol||||||<br />
|-<br />
| PMID||PubMed identifier ||||||<br />
|-<br />
| src_intxn_id||Interaction identifiers used by source databases||||||<br />
|-<br />
| omim||OMIM identifier ([http://www.ncbi.nlm.nih.gov/omim '''OMIM home page'''])||||||<br />
|-<br />
| digid||diseases group identifier ([http://irefindex.uio.no/wiki/DiG:_Disease_groups '''DiG home page'''])||||||<br />
|-<br />
| <br />
|}<br />
<br />
<!--<br />
==Only variables==<br />
Users can load there own variables for proteins which are mapped to a ROGID. The file should follow the format given below;<br />
#Should be a plain text file with exactly two columns and each line ending with a new line character (pressing enter).<br />
#First column should contain the ROGID<br />
#Second column should contain the user attribute/variable. <br />
#The file name should have the format _rog_'''USER_VARIABLE_NAME'''.iruv (The text in bold is supplied by the user. e.g., _rog_myAttribute.iruv ).<br />
<br />
<pre><br />
e.g<br />
#rog USER_VARIABLE<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
q6/pRFyay7gQ6bb2rzvKYgfkeaE9606 2<br />
8sODZSppCsuEgRmhSHp3UjwOf2M9606 3<br />
obze7v7i2yTIIcJjd7laIriNFg89606 4<br />
Ty0OLkmhoUPjUuLQQv5ykN057oM9606 5<br />
4bhW4sEt1YhYwHnHCyDNV3vvThs9606 6<br />
Al8M+JdB4H+QnwITh8KcicdI2x49606 6<br />
rkL/SGL1Enj6KoFkPbbcoJ5vKJE9606 6<br />
<br />
</pre><br />
--><br />
<br />
== Attribute batch file ==<br />
Users can attach additional attributes when performing batch queries (instead of loading the attributes after the search).<br />
<br />
The example shown below attaches an additional index "NOONAN_SYNDROME_TYPE" to the matching nodes.<br />
Example indexable batch file<br />
#geneSymbol:9606:NOONAN_SYNDROME_TYPE<br />
PTPN11 NS1<br />
SHOC2 NS2<br />
KRAS NS3<br />
SOS1 NS4<br />
RAF1 NS5<br />
NRAS NS6<br />
NF1 NFNS<br />
<br />
#The first line is compulsory and contains controlling information. the fist value after the hash ('#') is the iRefindex attribute type to be used(please see [http://irefindex.uio.no/wiki/README_Cytoscape_plugin_menu#Simple_batch_file '''Simple_batch_file'''] for attribute types). The second value is the NCBI taxonomy identifier ([http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ '''NCBI taxonomy browser''']). The third value is the name of the user attribute. All three values are seperated by a colon ":". It is possible to include multiple attributes in the same file. To do this first the attribute name should be defined in the first line and additional columns should be used to include the values. (Please not that if the batch file is also used as the template to construct user searchable index, only one user attribute is allowed in the file)<br />
<br />
== iRefScape user searchable index ==<br />
Users can construct their own indices to be used as search type. The easiest way to include a index is to use the advanced batch file mode. This process will;<br />
#Find the iROGID for the user variable<br />
#Construct searchable index.<br />
<br />
The example shown below constructs an index, where the user can perfume search using the Noonan syndrom type. <br />
Example indexable batch file<br />
#geneSymbol:9606:NOONAN_SYNDROME_TYPE<br />
PTPN11 NS1<br />
SHOC2 NS2<br />
KRAS NS3<br />
SOS1 NS4<br />
RAF1 NS5<br />
NRAS NS6<br />
NF1 NFNS<br />
<br />
#The first line is compulsory and contains controlling information. the fist value after the hash ('#') is the iRefindex attribute type to be used(please see [http://irefindex.uio.no/wiki/README_Cytoscape_plugin_menu#Simple_batch_file '''Simple_batch_file'''] for attribute types). The second value is the NCBI taxonomy identifier ([http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ '''NCBI taxonomy browser''']). The third value is the name of the user attribute. All three values are seperated by a colon ":".<br />
<br />
The data rows should always be two columns, where the columns are separated by a tab. The first value in a data row is the search string (what should be used to search iRefIndex). The values in the first column will appear in the search box at the end of the operation. The second column contains the user attribute. <br />
<br />
*the file name of the batch file should contain the prefix "INDEX_THIS_" to be considered for the indexing.<br />
<br />
Example file name<br />
INDEX_THIS_Sample_batch4.txt<br />
<br />
*The attribute do not appear as a separate attribute, but should instead look in the i.query field.<br />
<br />
==View tools==<br />
<br />
===Toggle selected multi-edges===<br />
iRefScape creates multiple edges between nodes to represent multiple evidences. If an interaction between two proteins has evidence from both MINT and IntAct, there will be 2 edges; one for MINT and one for IntAct. Although this provides more information for the user, sometime the user may prefer to collapse these edges to a single edge to facilitate viewing. When this action is performed on a network, all but a randomly selected edge between each node is hidden. The edges which are hidden has the i.flag=1 and the one remaining has i.flag=0. Therefore, while this process is random by default, the user can control which edges to keep and which to hide by editing the i.flag edge attribute before using the '''toggle multi-edge''' option.<br />
<br />
===Zoom to selected===<br />
This action brings the '''selected node(s)''' to the centre of the screen and makes the nodes as large as possible given that all selected nodes are visible. This action can also be performed manually using Cytoscape's zoom tool.<br />
<br />
===Select last iRefScape selection===<br />
This action shows the last selection '''performed by an iRefScape operation'''. This features does not record user selections or selections made by using Cytoscape tools (e.g filters).<br />
<br />
===Select nodes with different taxid than query node===<br />
Some interactions may involve proteins from multiple species. An interaction may truly occur between proteins from two species (e.g. an interaction between a Human protein and a virus protein). In other cases, this may be an artefact of how data was entered by the source database.<br />
<br />
===Select between nodes===<br />
This option highlights (selects) nodes interacting with at least two nodes that have been pre-selected by the user. The node attribute '''i.alive_degree''' will be recalculated to reflect the degree of each node with respect to this pre-selection.<br />
<br />
===Show spoke-represented complexes===<br />
Some complexes are represented as a set of binary interactions by some sources. This action attempts to highlight such complexes as a single unit by attaching them all to a single pseudonode. <br />
<br />
<br />
==Hide/Un-hide==<br />
<br />
===Hide selected nodes===<br />
This action hides the selected nodes. This operation is performed in a independent thread and more efficient than hiding using Cytoscape's 'hide node' utility for large networks.<br />
<br />
===Hide nodes (except pseudonodes)===<br />
This action hides all select nodes which represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Hide nodes not selected===<br />
Hides all nodes which are not currently selected<br />
<br />
===Hide nodes not selected (except pseudonodes)===<br />
Hides all nodes which are not currently selected and that represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Un-hide all===<br />
Un-hides all nodes which are hidden by the user.<br />
<br />
==Safe mode==<br />
This option is only available when using JAVA 1.5 and will not appear for Java 1.6 or newer. Selecting this will un-dock the iRefScape window and handles errors and exceptions thrown due to bugs in JAVA 1.5. When this mode is activated not all graphic features will be available.<br />
<br />
<br />
<br />
<br />
<br />
== All iRefIndex Pages ==<br />
<br />
Follow this link for a listing of all iRefIndex related pages (archived and current).<br />
[[Category:iRefIndex]]</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefScape_plugin_menu&diff=3472iRefScape plugin menu2011-06-09T10:30:35Z<p>Sabry: /* Simple batch file */</p>
<hr />
<div>==Search tools==<br />
<br />
===Retrieve interactions for the selected nodes===<br />
To load all protein-protein interactions and complexes involving one or more '''selected nodes'''. This action is the same as performing a iteration=1 search using iRefScape for the selected nodes.<br />
<br />
===Expand one level===<br />
To load all protein-protein interactions and complexes involving at least one of the nodes in the current network. The behaviour is same as performing iteration=1 search using iRefScape for all the nodes. <br />
<br />
===Load interactions between neighbours===<br />
To complete the interactions between the currently loaded nodes. When a search & load operation is performed in iRefScape, the network returned contains all the proteins interacting with the query and the corresponding interactions. This does not return interactions between the neighbours of the query. This operation is the same as performing an iteration=0 search using iRefScape for all the nodes.<br />
This action has no effect for networks for which this operation has already been performed using the option presented at the end of the search.<br />
<br />
===Clear load history (Reload everything next time)===<br />
This will clear the iRefScape cache memory containing currently loaded nodes and edges. IRefScape keeps track of what is loaded to avoid reloading and thus increase efficiency. Therefore, if a search is performed twice,the network will not be re-loaded unless the user has requested that results be shown in a new view or they have selected this menu option. If the user wishes to reload the network then this option has to be used. When using other methods of expanding the network like “Expand one level” iRefScape handles the cache clearing automatically.<br />
<br />
===Reset node degree===<br />
This option resets the i.alive_degree of nodes. i.alive_degree provides how many nodes with a certain attribute type is connected to each node (set using filters). <br />
<br />
==Loading user variables (this section is being edited)==<br />
User variables can be attached to nodes and be browsed using the attribute browser. This file can not be used as a searchable index (can not be used as a search type). please see section [http://irefindex.uio.no/wiki/README_Cytoscape_plugin_menu#iRefScape_user_searchable_index'''iRefScape_user_searchable_index'''] for details on searchable indices. <br />
<br />
There are three ways to load own variables for the user. <br />
#Use the Cytoscape attribute loading feature ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual'''])<br />
#Use a use attribute file with iRefScape (described in this section)<br />
#Include the attribute with the batch search file.(Described in section [http://irefindex.uio.no/wiki/README_Cytoscape_plugin_menu#Attribute_batch_file '''Attribute_batch_file''']).<br />
<br />
The iRefScape user attribute loader is provided as a complementing feature to the Cytoscape node attribute loading ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual''']). For most of the attribute loading operations the Cytoscape node attribute loader is sufficient and easier to use. However, when the iRefScape node attribute file is used, this can be used by using the menu entry iRefScape-> Search tools > Load user variables. In addition the file will be available for subsequent operations.<br />
<br />
===iRefScape user variable file format===<br />
The first line of the file provides instructions and this line is compulsory.<br />
Example. <br />
#i.rog New_attribute<br />
<br />
<br />
The first line always starts with a hash ("#") and immediately followed by the iReFscape variable name. This iRefScape variable name is used to locate the nodes via the new attribute will be attached. Then a tab is used as a column separator, followed by the name of the user attribute name.This user attribute name should be unique( not already used). In the above example the user attribute to use is the i.rog and the user attribute name is "New_attribute".<br />
<br />
From the second line onwards, the attributes with the mapping attribute are provided.<br />
Example <br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
<br />
The first column provides the iRefScape attribute to use and the second column provides the user attribute. Multiple attributes should be separated with a pipe ("|"). The example line shown would locate the node with i.rog=4399398 and attach the "TENC1|UniProtKB:Q63HR2|" value to it with the attribute name "New_attribute"<br />
<br />
*Each column is separated by a TAB.<br />
*Each line ends with a new line character ("\n")<br />
*The file should be constructed using a plain text editor (e.g. Kate, notepad) and word processing software like Microsoft word should not be used to construct this file.<br />
* The file extension is ".txt"<br />
* Sample file "ONE__EXT__ROG_#Name_5_.iruv" can be found in the iRefScape installation directory (iRefIndex directory)<br />
*The file name should have the format _rog_'''USER_VARIABLE_NAME'''.iruv (The text in bold is supplied by the user. e.g., _rog_myAttribute.iruv ).<br />
<br />
Sample file<br />
#i.rog New_name<br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
452957 GFI1B|UniProtKB:Q5VTD9|<br />
561552 TENC1|UniProtKB:Q63HR2-4|<br />
534065 GFI1B_MOUSE|UniProtKB:O70237|<br />
<br />
==iRefScape search with batch file==<br />
When there are many search queries, it is convenient to construct a batch file and load this to iRefScape. There are 3 type of batch files;<br />
#Simple batch file (recommended for users just wanting to search for a list of things)<br />
#Attribute batch file (Attach additional attributes) <br />
#User index batch file (Explained in section [http://irefindex.uio.no/wiki/README_Cytoscape_plugin_menu#iRefScape_user_searchable_index '''iRefScape_user_searchable_index'''])<br />
<br />
=== Simple batch file ===<br />
<br />
Example file content:<br />
#geneID:3702<br />
814707<br />
814714<br />
814714<br />
817659<br />
818662<br />
<br />
*The first line starts with a hash ("#") and this line is compulsory.<br />
*Immediately after the hash (no space in between) the iRefScape attribute name should be provided. Please see below for accepted list of identifier with the corresponding label.<br />
<br />
{| {{table}}<br />
| align="center" style="background:#f0f0f0;"|'''Label to use in the batch file'''<br />
| align="center" style="background:#f0f0f0;"|'''Description'''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
|-<br />
| rog||iROGID, the integer reference redundant object group identifier([http://irefindex.uio.no/wiki/Protein_identifier_mapping \'\'\'details of mapper files to locate the iRGOID can be found here)\'\'\']||||||<br />
|-<br />
| geneID||NCBI Gene ID, this is always an integer||||||<br />
|-<br />
| UniProt_Ac||UniProt/KB accession||||||<br />
|-<br />
| RefSeq_Ac||RefSeq Accession||||||<br />
|-<br />
| UniProt_ID||UniProt identifier||||||<br />
|-<br />
| geneSymbol||NCBI Gene symbol||||||<br />
|-<br />
| PMID||PubMed identifier ||||||<br />
|-<br />
| src_intxn_id||Interaction identifiers used by source databases||||||<br />
|-<br />
| omim||OMIM identifier ([http://www.ncbi.nlm.nih.gov/omim '''OMIM home page'''])||||||<br />
|-<br />
| digid||diseases group identifier ([http://irefindex.uio.no/wiki/DiG:_Disease_groups \'\'\'DiG home page\'\'\'])||||||<br />
|-<br />
| <br />
|}<br />
<br />
<!--<br />
==Only variables==<br />
Users can load there own variables for proteins which are mapped to a ROGID. The file should follow the format given below;<br />
#Should be a plain text file with exactly two columns and each line ending with a new line character (pressing enter).<br />
#First column should contain the ROGID<br />
#Second column should contain the user attribute/variable. <br />
#The file name should have the format _rog_'''USER_VARIABLE_NAME'''.iruv (The text in bold is supplied by the user. e.g., _rog_myAttribute.iruv ).<br />
<br />
<pre><br />
e.g<br />
#rog USER_VARIABLE<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
q6/pRFyay7gQ6bb2rzvKYgfkeaE9606 2<br />
8sODZSppCsuEgRmhSHp3UjwOf2M9606 3<br />
obze7v7i2yTIIcJjd7laIriNFg89606 4<br />
Ty0OLkmhoUPjUuLQQv5ykN057oM9606 5<br />
4bhW4sEt1YhYwHnHCyDNV3vvThs9606 6<br />
Al8M+JdB4H+QnwITh8KcicdI2x49606 6<br />
rkL/SGL1Enj6KoFkPbbcoJ5vKJE9606 6<br />
<br />
</pre><br />
--><br />
<br />
== Attribute batch file ==<br />
Users can attach additional attributes when performing batch queries (instead of loading the attributes after the search).<br />
<br />
The example shown below attaches an additional index "NOONAN_SYNDROME_TYPE" to the matching nodes.<br />
Example indexable batch file<br />
#geneSymbol:9606:NOONAN_SYNDROME_TYPE<br />
PTPN11 NS1<br />
SHOC2 NS2<br />
KRAS NS3<br />
SOS1 NS4<br />
RAF1 NS5<br />
NRAS NS6<br />
NF1 NFNS<br />
<br />
#The first line is compulsory and contains controlling information. the fist value after the hash ('#') is the iRefindex attribute type to be used(please see [http://irefindex.uio.no/wiki/README_Cytoscape_plugin_menu#Simple_batch_file '''Simple_batch_file'''] for attribute types). The second value is the NCBI taxonomy identifier ([http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ '''NCBI taxonomy browser''']). The third value is the name of the user attribute. All three values are seperated by a colon ":". It is possible to include multiple attributes in the same file. To do this first the attribute name should be defined in the first line and additional columns should be used to include the values. (Please not that if the batch file is also used as the template to construct user searchable index, only one user attribute is allowed in the file)<br />
<br />
== iRefScape user searchable index ==<br />
Users can construct their own indices to be used as search type. The easiest way to include a index is to use the advanced batch file mode. This process will;<br />
#Find the iROGID for the user variable<br />
#Construct searchable index.<br />
<br />
The example shown below constructs an index, where the user can perfume search using the Noonan syndrom type. <br />
Example indexable batch file<br />
#geneSymbol:9606:NOONAN_SYNDROME_TYPE<br />
PTPN11 NS1<br />
SHOC2 NS2<br />
KRAS NS3<br />
SOS1 NS4<br />
RAF1 NS5<br />
NRAS NS6<br />
NF1 NFNS<br />
<br />
#The first line is compulsory and contains controlling information. the fist value after the hash ('#') is the iRefindex attribute type to be used(please see [http://irefindex.uio.no/wiki/README_Cytoscape_plugin_menu#Simple_batch_file '''Simple_batch_file'''] for attribute types). The second value is the NCBI taxonomy identifier ([http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ '''NCBI taxonomy browser''']). The third value is the name of the user attribute. All three values are seperated by a colon ":".<br />
<br />
The data rows should always be two columns, where the columns are separated by a tab. The first value in a data row is the search string (what should be used to search iRefIndex). The values in the first column will appear in the search box at the end of the operation. The second column contains the user attribute. <br />
<br />
*the file name of the batch file should contain the prefix "INDEX_THIS_" to be considered for the indexing.<br />
<br />
Example file name<br />
INDEX_THIS_Sample_batch4.txt<br />
<br />
*The attribute do not appear as a separate attribute, but should instead look in the i.query field.<br />
<br />
==View tools==<br />
<br />
===Toggle selected multi-edges===<br />
iRefScape creates multiple edges between nodes to represent multiple evidences. If an interaction between two proteins has evidence from both MINT and IntAct, there will be 2 edges; one for MINT and one for IntAct. Although this provides more information for the user, sometime the user may prefer to collapse these edges to a single edge to facilitate viewing. When this action is performed on a network, all but a randomly selected edge between each node is hidden. The edges which are hidden has the i.flag=1 and the one remaining has i.flag=0. Therefore, while this process is random by default, the user can control which edges to keep and which to hide by editing the i.flag edge attribute before using the '''toggle multi-edge''' option.<br />
<br />
===Zoom to selected===<br />
This action brings the '''selected node(s)''' to the centre of the screen and makes the nodes as large as possible given that all selected nodes are visible. This action can also be performed manually using Cytoscape's zoom tool.<br />
<br />
===Select last iRefScape selection===<br />
This action shows the last selection '''performed by an iRefScape operation'''. This features does not record user selections or selections made by using Cytoscape tools (e.g filters).<br />
<br />
===Select nodes with different taxid than query node===<br />
Some interactions may involve proteins from multiple species. An interaction may truly occur between proteins from two species (e.g. an interaction between a Human protein and a virus protein). In other cases, this may be an artefact of how data was entered by the source database.<br />
<br />
===Select between nodes===<br />
This option highlights (selects) nodes interacting with at least two nodes that have been pre-selected by the user. The node attribute '''i.alive_degree''' will be recalculated to reflect the degree of each node with respect to this pre-selection.<br />
<br />
===Show spoke-represented complexes===<br />
Some complexes are represented as a set of binary interactions by some sources. This action attempts to highlight such complexes as a single unit by attaching them all to a single pseudonode. <br />
<br />
<br />
==Hide/Un-hide==<br />
<br />
===Hide selected nodes===<br />
This action hides the selected nodes. This operation is performed in a independent thread and more efficient than hiding using Cytoscape's 'hide node' utility for large networks.<br />
<br />
===Hide nodes (except pseudonodes)===<br />
This action hides all select nodes which represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Hide nodes not selected===<br />
Hides all nodes which are not currently selected<br />
<br />
===Hide nodes not selected (except pseudonodes)===<br />
Hides all nodes which are not currently selected and that represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Un-hide all===<br />
Un-hides all nodes which are hidden by the user.<br />
<br />
==Safe mode==<br />
This option is only available when using JAVA 1.5 and will not appear for Java 1.6 or newer. Selecting this will un-dock the iRefScape window and handles errors and exceptions thrown due to bugs in JAVA 1.5. When this mode is activated not all graphic features will be available.<br />
<br />
<br />
<br />
<br />
<br />
== All iRefIndex Pages ==<br />
<br />
Follow this link for a listing of all iRefIndex related pages (archived and current).<br />
[[Category:iRefIndex]]</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefScape_plugin_menu&diff=3471iRefScape plugin menu2011-06-08T14:50:39Z<p>Sabry: /* iRefScape user searchable index */</p>
<hr />
<div>==Search tools==<br />
<br />
===Retrieve interactions for the selected nodes===<br />
To load all protein-protein interactions and complexes involving one or more '''selected nodes'''. This action is the same as performing a iteration=1 search using iRefScape for the selected nodes.<br />
<br />
===Expand one level===<br />
To load all protein-protein interactions and complexes involving at least one of the nodes in the current network. The behaviour is same as performing iteration=1 search using iRefScape for all the nodes. <br />
<br />
===Load interactions between neighbours===<br />
To complete the interactions between the currently loaded nodes. When a search & load operation is performed in iRefScape, the network returned contains all the proteins interacting with the query and the corresponding interactions. This does not return interactions between the neighbours of the query. This operation is the same as performing an iteration=0 search using iRefScape for all the nodes.<br />
This action has no effect for networks for which this operation has already been performed using the option presented at the end of the search.<br />
<br />
===Clear load history (Reload everything next time)===<br />
This will clear the iRefScape cache memory containing currently loaded nodes and edges. IRefScape keeps track of what is loaded to avoid reloading and thus increase efficiency. Therefore, if a search is performed twice,the network will not be re-loaded unless the user has requested that results be shown in a new view or they have selected this menu option. If the user wishes to reload the network then this option has to be used. When using other methods of expanding the network like “Expand one level” iRefScape handles the cache clearing automatically.<br />
<br />
===Reset node degree===<br />
This option resets the i.alive_degree of nodes. i.alive_degree provides how many nodes with a certain attribute type is connected to each node (set using filters). <br />
<br />
==Loading user variables (this section is being edited)==<br />
User variables can be attached to nodes and be browsed using the attribute browser. This file can not be used as a searchable index (can not be used as a search type). please see section [http://irefindex.uio.no/wiki/README_Cytoscape_plugin_menu#iRefScape_user_searchable_index'''iRefScape_user_searchable_index'''] for details on searchable indices. <br />
<br />
There are three ways to load own variables for the user. <br />
#Use the Cytoscape attribute loading feature ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual'''])<br />
#Use a use attribute file with iRefScape (described in this section)<br />
#Include the attribute with the batch search file.(Described in section [http://irefindex.uio.no/wiki/README_Cytoscape_plugin_menu#Attribute_batch_file '''Attribute_batch_file''']).<br />
<br />
The iRefScape user attribute loader is provided as a complementing feature to the Cytoscape node attribute loading ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual''']). For most of the attribute loading operations the Cytoscape node attribute loader is sufficient and easier to use. However, when the iRefScape node attribute file is used, this can be used by using the menu entry iRefScape-> Search tools > Load user variables. In addition the file will be available for subsequent operations.<br />
<br />
===iRefScape user variable file format===<br />
The first line of the file provides instructions and this line is compulsory.<br />
Example. <br />
#i.rog New_attribute<br />
<br />
<br />
The first line always starts with a hash ("#") and immediately followed by the iReFscape variable name. This iRefScape variable name is used to locate the nodes via the new attribute will be attached. Then a tab is used as a column separator, followed by the name of the user attribute name.This user attribute name should be unique( not already used). In the above example the user attribute to use is the i.rog and the user attribute name is "New_attribute".<br />
<br />
From the second line onwards, the attributes with the mapping attribute are provided.<br />
Example <br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
<br />
The first column provides the iRefScape attribute to use and the second column provides the user attribute. Multiple attributes should be separated with a pipe ("|"). The example line shown would locate the node with i.rog=4399398 and attach the "TENC1|UniProtKB:Q63HR2|" value to it with the attribute name "New_attribute"<br />
<br />
*Each column is separated by a TAB.<br />
*Each line ends with a new line character ("\n")<br />
*The file should be constructed using a plain text editor (e.g. Kate, notepad) and word processing software like Microsoft word should not be used to construct this file.<br />
* The file extension is ".txt"<br />
* Sample file "ONE__EXT__ROG_#Name_5_.iruv" can be found in the iRefScape installation directory (iRefIndex directory)<br />
*The file name should have the format _rog_'''USER_VARIABLE_NAME'''.iruv (The text in bold is supplied by the user. e.g., _rog_myAttribute.iruv ).<br />
<br />
Sample file<br />
#i.rog New_name<br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
452957 GFI1B|UniProtKB:Q5VTD9|<br />
561552 TENC1|UniProtKB:Q63HR2-4|<br />
534065 GFI1B_MOUSE|UniProtKB:O70237|<br />
<br />
==iRefScape search with batch file==<br />
When there are many search queries, it is convenient to construct a batch file and load this to iRefScape. There are 3 type of batch files;<br />
#Simple batch file (recommended for users just wanting to search for a list of things)<br />
#Attribute batch file (Attach additional attributes) <br />
#User index batch file (Explained in section [http://irefindex.uio.no/wiki/README_Cytoscape_plugin_menu#iRefScape_user_searchable_index '''iRefScape_user_searchable_index'''])<br />
<br />
=== Simple batch file ===<br />
<br />
Example file content:<br />
#geneID:3702<br />
814707<br />
814714<br />
814714<br />
817659<br />
818662<br />
<br />
*The first line starts with a hash ("#") and this line is compulsory.<br />
*Immediately after the hash (no space in between) the iRefScape attribute name should be provided. Please see below for accepted list of identifier with the corresponding label.<br />
<br />
{| {{table}}<br />
| align="center" style="background:#f0f0f0;"|'''Label to use in the batch file'''<br />
| align="center" style="background:#f0f0f0;"|'''Description'''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
|-<br />
| rog||iROGID, the integer reference redundant object group identifier([http://irefindex.uio.no/wiki/Protein_identifier_mapping \'\'\'details of mapper files to locate the iRGOID can be found here)\'\'\']||||||<br />
|-<br />
| geneID||NCBI Gene ID, this is always an integer||||||<br />
|-<br />
| UniProt_Ac||UniProt/KB accession||||||<br />
|-<br />
| RefSeq_Ac||RefSeq Accession||||||<br />
|-<br />
| UniProt_ID||UniProt identifier||||||<br />
|-<br />
| geneSymbol||NCBI Gene symbol||||||<br />
|-<br />
| PMID||PubMed identifier ||||||<br />
|-<br />
| src_intxn_id||Interaction identifiers used by source databases||||||<br />
|-<br />
| omim||OMIM identifier ([http://www.ncbi.nlm.nih.gov/omim \'\'\'OMIM home page\'\'\'])||||||<br />
|-<br />
| digid||diseases group identifier ([http://irefindex.uio.no/wiki/DiG:_Disease_groups \'\'\'DiG home page\'\'\'])||||||<br />
|-<br />
| <br />
|}<br />
<br />
<!--<br />
==Only variables==<br />
Users can load there own variables for proteins which are mapped to a ROGID. The file should follow the format given below;<br />
#Should be a plain text file with exactly two columns and each line ending with a new line character (pressing enter).<br />
#First column should contain the ROGID<br />
#Second column should contain the user attribute/variable. <br />
#The file name should have the format _rog_'''USER_VARIABLE_NAME'''.iruv (The text in bold is supplied by the user. e.g., _rog_myAttribute.iruv ).<br />
<br />
<pre><br />
e.g<br />
#rog USER_VARIABLE<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
q6/pRFyay7gQ6bb2rzvKYgfkeaE9606 2<br />
8sODZSppCsuEgRmhSHp3UjwOf2M9606 3<br />
obze7v7i2yTIIcJjd7laIriNFg89606 4<br />
Ty0OLkmhoUPjUuLQQv5ykN057oM9606 5<br />
4bhW4sEt1YhYwHnHCyDNV3vvThs9606 6<br />
Al8M+JdB4H+QnwITh8KcicdI2x49606 6<br />
rkL/SGL1Enj6KoFkPbbcoJ5vKJE9606 6<br />
<br />
</pre><br />
--><br />
<br />
== Attribute batch file ==<br />
Users can attach additional attributes when performing batch queries (instead of loading the attributes after the search).<br />
<br />
The example shown below attaches an additional index "NOONAN_SYNDROME_TYPE" to the matching nodes.<br />
Example indexable batch file<br />
#geneSymbol:9606:NOONAN_SYNDROME_TYPE<br />
PTPN11 NS1<br />
SHOC2 NS2<br />
KRAS NS3<br />
SOS1 NS4<br />
RAF1 NS5<br />
NRAS NS6<br />
NF1 NFNS<br />
<br />
#The first line is compulsory and contains controlling information. the fist value after the hash ('#') is the iRefindex attribute type to be used(please see [http://irefindex.uio.no/wiki/README_Cytoscape_plugin_menu#Simple_batch_file '''Simple_batch_file'''] for attribute types). The second value is the NCBI taxonomy identifier ([http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ '''NCBI taxonomy browser''']). The third value is the name of the user attribute. All three values are seperated by a colon ":". It is possible to include multiple attributes in the same file. To do this first the attribute name should be defined in the first line and additional columns should be used to include the values. (Please not that if the batch file is also used as the template to construct user searchable index, only one user attribute is allowed in the file)<br />
<br />
== iRefScape user searchable index ==<br />
Users can construct their own indices to be used as search type. The easiest way to include a index is to use the advanced batch file mode. This process will;<br />
#Find the iROGID for the user variable<br />
#Construct searchable index.<br />
<br />
The example shown below constructs an index, where the user can perfume search using the Noonan syndrom type. <br />
Example indexable batch file<br />
#geneSymbol:9606:NOONAN_SYNDROME_TYPE<br />
PTPN11 NS1<br />
SHOC2 NS2<br />
KRAS NS3<br />
SOS1 NS4<br />
RAF1 NS5<br />
NRAS NS6<br />
NF1 NFNS<br />
<br />
#The first line is compulsory and contains controlling information. the fist value after the hash ('#') is the iRefindex attribute type to be used(please see [http://irefindex.uio.no/wiki/README_Cytoscape_plugin_menu#Simple_batch_file '''Simple_batch_file'''] for attribute types). The second value is the NCBI taxonomy identifier ([http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ '''NCBI taxonomy browser''']). The third value is the name of the user attribute. All three values are seperated by a colon ":".<br />
<br />
The data rows should always be two columns, where the columns are separated by a tab. The first value in a data row is the search string (what should be used to search iRefIndex). The values in the first column will appear in the search box at the end of the operation. The second column contains the user attribute. <br />
<br />
*the file name of the batch file should contain the prefix "INDEX_THIS_" to be considered for the indexing.<br />
<br />
Example file name<br />
INDEX_THIS_Sample_batch4.txt<br />
<br />
*The attribute do not appear as a separate attribute, but should instead look in the i.query field.<br />
<br />
==View tools==<br />
<br />
===Toggle selected multi-edges===<br />
iRefScape creates multiple edges between nodes to represent multiple evidences. If an interaction between two proteins has evidence from both MINT and IntAct, there will be 2 edges; one for MINT and one for IntAct. Although this provides more information for the user, sometime the user may prefer to collapse these edges to a single edge to facilitate viewing. When this action is performed on a network, all but a randomly selected edge between each node is hidden. The edges which are hidden has the i.flag=1 and the one remaining has i.flag=0. Therefore, while this process is random by default, the user can control which edges to keep and which to hide by editing the i.flag edge attribute before using the '''toggle multi-edge''' option.<br />
<br />
===Zoom to selected===<br />
This action brings the '''selected node(s)''' to the centre of the screen and makes the nodes as large as possible given that all selected nodes are visible. This action can also be performed manually using Cytoscape's zoom tool.<br />
<br />
===Select last iRefScape selection===<br />
This action shows the last selection '''performed by an iRefScape operation'''. This features does not record user selections or selections made by using Cytoscape tools (e.g filters).<br />
<br />
===Select nodes with different taxid than query node===<br />
Some interactions may involve proteins from multiple species. An interaction may truly occur between proteins from two species (e.g. an interaction between a Human protein and a virus protein). In other cases, this may be an artefact of how data was entered by the source database.<br />
<br />
===Select between nodes===<br />
This option highlights (selects) nodes interacting with at least two nodes that have been pre-selected by the user. The node attribute '''i.alive_degree''' will be recalculated to reflect the degree of each node with respect to this pre-selection.<br />
<br />
===Show spoke-represented complexes===<br />
Some complexes are represented as a set of binary interactions by some sources. This action attempts to highlight such complexes as a single unit by attaching them all to a single pseudonode. <br />
<br />
<br />
==Hide/Un-hide==<br />
<br />
===Hide selected nodes===<br />
This action hides the selected nodes. This operation is performed in a independent thread and more efficient than hiding using Cytoscape's 'hide node' utility for large networks.<br />
<br />
===Hide nodes (except pseudonodes)===<br />
This action hides all select nodes which represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Hide nodes not selected===<br />
Hides all nodes which are not currently selected<br />
<br />
===Hide nodes not selected (except pseudonodes)===<br />
Hides all nodes which are not currently selected and that represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Un-hide all===<br />
Un-hides all nodes which are hidden by the user.<br />
<br />
==Safe mode==<br />
This option is only available when using JAVA 1.5 and will not appear for Java 1.6 or newer. Selecting this will un-dock the iRefScape window and handles errors and exceptions thrown due to bugs in JAVA 1.5. When this mode is activated not all graphic features will be available.<br />
<br />
<br />
<br />
<br />
<br />
== All iRefIndex Pages ==<br />
<br />
Follow this link for a listing of all iRefIndex related pages (archived and current).<br />
[[Category:iRefIndex]]</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefScape_plugin_menu&diff=3470iRefScape plugin menu2011-06-08T14:49:52Z<p>Sabry: /* Attribute batch file */</p>
<hr />
<div>==Search tools==<br />
<br />
===Retrieve interactions for the selected nodes===<br />
To load all protein-protein interactions and complexes involving one or more '''selected nodes'''. This action is the same as performing a iteration=1 search using iRefScape for the selected nodes.<br />
<br />
===Expand one level===<br />
To load all protein-protein interactions and complexes involving at least one of the nodes in the current network. The behaviour is same as performing iteration=1 search using iRefScape for all the nodes. <br />
<br />
===Load interactions between neighbours===<br />
To complete the interactions between the currently loaded nodes. When a search & load operation is performed in iRefScape, the network returned contains all the proteins interacting with the query and the corresponding interactions. This does not return interactions between the neighbours of the query. This operation is the same as performing an iteration=0 search using iRefScape for all the nodes.<br />
This action has no effect for networks for which this operation has already been performed using the option presented at the end of the search.<br />
<br />
===Clear load history (Reload everything next time)===<br />
This will clear the iRefScape cache memory containing currently loaded nodes and edges. IRefScape keeps track of what is loaded to avoid reloading and thus increase efficiency. Therefore, if a search is performed twice,the network will not be re-loaded unless the user has requested that results be shown in a new view or they have selected this menu option. If the user wishes to reload the network then this option has to be used. When using other methods of expanding the network like “Expand one level” iRefScape handles the cache clearing automatically.<br />
<br />
===Reset node degree===<br />
This option resets the i.alive_degree of nodes. i.alive_degree provides how many nodes with a certain attribute type is connected to each node (set using filters). <br />
<br />
==Loading user variables (this section is being edited)==<br />
User variables can be attached to nodes and be browsed using the attribute browser. This file can not be used as a searchable index (can not be used as a search type). please see section [http://irefindex.uio.no/wiki/README_Cytoscape_plugin_menu#iRefScape_user_searchable_index'''iRefScape_user_searchable_index'''] for details on searchable indices. <br />
<br />
There are three ways to load own variables for the user. <br />
#Use the Cytoscape attribute loading feature ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual'''])<br />
#Use a use attribute file with iRefScape (described in this section)<br />
#Include the attribute with the batch search file.(Described in section [http://irefindex.uio.no/wiki/README_Cytoscape_plugin_menu#Attribute_batch_file '''Attribute_batch_file''']).<br />
<br />
The iRefScape user attribute loader is provided as a complementing feature to the Cytoscape node attribute loading ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual''']). For most of the attribute loading operations the Cytoscape node attribute loader is sufficient and easier to use. However, when the iRefScape node attribute file is used, this can be used by using the menu entry iRefScape-> Search tools > Load user variables. In addition the file will be available for subsequent operations.<br />
<br />
===iRefScape user variable file format===<br />
The first line of the file provides instructions and this line is compulsory.<br />
Example. <br />
#i.rog New_attribute<br />
<br />
<br />
The first line always starts with a hash ("#") and immediately followed by the iReFscape variable name. This iRefScape variable name is used to locate the nodes via the new attribute will be attached. Then a tab is used as a column separator, followed by the name of the user attribute name.This user attribute name should be unique( not already used). In the above example the user attribute to use is the i.rog and the user attribute name is "New_attribute".<br />
<br />
From the second line onwards, the attributes with the mapping attribute are provided.<br />
Example <br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
<br />
The first column provides the iRefScape attribute to use and the second column provides the user attribute. Multiple attributes should be separated with a pipe ("|"). The example line shown would locate the node with i.rog=4399398 and attach the "TENC1|UniProtKB:Q63HR2|" value to it with the attribute name "New_attribute"<br />
<br />
*Each column is separated by a TAB.<br />
*Each line ends with a new line character ("\n")<br />
*The file should be constructed using a plain text editor (e.g. Kate, notepad) and word processing software like Microsoft word should not be used to construct this file.<br />
* The file extension is ".txt"<br />
* Sample file "ONE__EXT__ROG_#Name_5_.iruv" can be found in the iRefScape installation directory (iRefIndex directory)<br />
*The file name should have the format _rog_'''USER_VARIABLE_NAME'''.iruv (The text in bold is supplied by the user. e.g., _rog_myAttribute.iruv ).<br />
<br />
Sample file<br />
#i.rog New_name<br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
452957 GFI1B|UniProtKB:Q5VTD9|<br />
561552 TENC1|UniProtKB:Q63HR2-4|<br />
534065 GFI1B_MOUSE|UniProtKB:O70237|<br />
<br />
==iRefScape search with batch file==<br />
When there are many search queries, it is convenient to construct a batch file and load this to iRefScape. There are 3 type of batch files;<br />
#Simple batch file (recommended for users just wanting to search for a list of things)<br />
#Attribute batch file (Attach additional attributes) <br />
#User index batch file (Explained in section [http://irefindex.uio.no/wiki/README_Cytoscape_plugin_menu#iRefScape_user_searchable_index '''iRefScape_user_searchable_index'''])<br />
<br />
=== Simple batch file ===<br />
<br />
Example file content:<br />
#geneID:3702<br />
814707<br />
814714<br />
814714<br />
817659<br />
818662<br />
<br />
*The first line starts with a hash ("#") and this line is compulsory.<br />
*Immediately after the hash (no space in between) the iRefScape attribute name should be provided. Please see below for accepted list of identifier with the corresponding label.<br />
<br />
{| {{table}}<br />
| align="center" style="background:#f0f0f0;"|'''Label to use in the batch file'''<br />
| align="center" style="background:#f0f0f0;"|'''Description'''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
|-<br />
| rog||iROGID, the integer reference redundant object group identifier([http://irefindex.uio.no/wiki/Protein_identifier_mapping \'\'\'details of mapper files to locate the iRGOID can be found here)\'\'\']||||||<br />
|-<br />
| geneID||NCBI Gene ID, this is always an integer||||||<br />
|-<br />
| UniProt_Ac||UniProt/KB accession||||||<br />
|-<br />
| RefSeq_Ac||RefSeq Accession||||||<br />
|-<br />
| UniProt_ID||UniProt identifier||||||<br />
|-<br />
| geneSymbol||NCBI Gene symbol||||||<br />
|-<br />
| PMID||PubMed identifier ||||||<br />
|-<br />
| src_intxn_id||Interaction identifiers used by source databases||||||<br />
|-<br />
| omim||OMIM identifier ([http://www.ncbi.nlm.nih.gov/omim \'\'\'OMIM home page\'\'\'])||||||<br />
|-<br />
| digid||diseases group identifier ([http://irefindex.uio.no/wiki/DiG:_Disease_groups \'\'\'DiG home page\'\'\'])||||||<br />
|-<br />
| <br />
|}<br />
<br />
<!--<br />
==Only variables==<br />
Users can load there own variables for proteins which are mapped to a ROGID. The file should follow the format given below;<br />
#Should be a plain text file with exactly two columns and each line ending with a new line character (pressing enter).<br />
#First column should contain the ROGID<br />
#Second column should contain the user attribute/variable. <br />
#The file name should have the format _rog_'''USER_VARIABLE_NAME'''.iruv (The text in bold is supplied by the user. e.g., _rog_myAttribute.iruv ).<br />
<br />
<pre><br />
e.g<br />
#rog USER_VARIABLE<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
q6/pRFyay7gQ6bb2rzvKYgfkeaE9606 2<br />
8sODZSppCsuEgRmhSHp3UjwOf2M9606 3<br />
obze7v7i2yTIIcJjd7laIriNFg89606 4<br />
Ty0OLkmhoUPjUuLQQv5ykN057oM9606 5<br />
4bhW4sEt1YhYwHnHCyDNV3vvThs9606 6<br />
Al8M+JdB4H+QnwITh8KcicdI2x49606 6<br />
rkL/SGL1Enj6KoFkPbbcoJ5vKJE9606 6<br />
<br />
</pre><br />
--><br />
<br />
== Attribute batch file ==<br />
Users can attach additional attributes when performing batch queries (instead of loading the attributes after the search).<br />
<br />
The example shown below attaches an additional index "NOONAN_SYNDROME_TYPE" to the matching nodes.<br />
Example indexable batch file<br />
#geneSymbol:9606:NOONAN_SYNDROME_TYPE<br />
PTPN11 NS1<br />
SHOC2 NS2<br />
KRAS NS3<br />
SOS1 NS4<br />
RAF1 NS5<br />
NRAS NS6<br />
NF1 NFNS<br />
<br />
#The first line is compulsory and contains controlling information. the fist value after the hash ('#') is the iRefindex attribute type to be used(please see [http://irefindex.uio.no/wiki/README_Cytoscape_plugin_menu#Simple_batch_file '''Simple_batch_file'''] for attribute types). The second value is the NCBI taxonomy identifier ([http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ '''NCBI taxonomy browser''']). The third value is the name of the user attribute. All three values are seperated by a colon ":". It is possible to include multiple attributes in the same file. To do this first the attribute name should be defined in the first line and additional columns should be used to include the values. (Please not that if the batch file is also used as the template to construct user searchable index, only one user attribute is allowed in the file)<br />
<br />
== iRefScape user searchable index ==<br />
Users can construct their own indices to be used as search type. The easiest way to include a index is to use the advanced batch file mode. This process will;<br />
#Find the iROGID for the user variable<br />
#Construct searchable index.<br />
<br />
The example shown below constructs an index, where the user can perfume search using the Noonan syndrom type. <br />
Example indexable batch file<br />
#geneSymbol:9606:NOONAN_SYNDROME_TYPE<br />
PTPN11 NS1<br />
SHOC2 NS2<br />
KRAS NS3<br />
SOS1 NS4<br />
RAF1 NS5<br />
NRAS NS6<br />
NF1 NFNS<br />
<br />
#The first line is compulsory and contains controlling information. the fist value after the hash ('#') is the iRefindex attribute type to be used(please see xxx for attribute types). The second value is the NCBI taxonomy identifier ([http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ '''NCBI taxonomy browser''']). The third value is the name of the user attribute. All three values are seperated by a colon ":".<br />
<br />
The data rows should always be two columns, where the columns are separated by a tab. The first value in a data row is the search string (what should be used to search iRefIndex). The values in the first column will appear in the search box at the end of the operation. The second column contains the user attribute. <br />
<br />
*the file name of the batch file should contain the prefix "INDEX_THIS_" to be considered for the indexing.<br />
<br />
Example file name<br />
INDEX_THIS_Sample_batch4.txt<br />
<br />
*The attribute do not appear as a separate attribute, but should instead look in the i.query field.<br />
<br />
==View tools==<br />
<br />
===Toggle selected multi-edges===<br />
iRefScape creates multiple edges between nodes to represent multiple evidences. If an interaction between two proteins has evidence from both MINT and IntAct, there will be 2 edges; one for MINT and one for IntAct. Although this provides more information for the user, sometime the user may prefer to collapse these edges to a single edge to facilitate viewing. When this action is performed on a network, all but a randomly selected edge between each node is hidden. The edges which are hidden has the i.flag=1 and the one remaining has i.flag=0. Therefore, while this process is random by default, the user can control which edges to keep and which to hide by editing the i.flag edge attribute before using the '''toggle multi-edge''' option.<br />
<br />
===Zoom to selected===<br />
This action brings the '''selected node(s)''' to the centre of the screen and makes the nodes as large as possible given that all selected nodes are visible. This action can also be performed manually using Cytoscape's zoom tool.<br />
<br />
===Select last iRefScape selection===<br />
This action shows the last selection '''performed by an iRefScape operation'''. This features does not record user selections or selections made by using Cytoscape tools (e.g filters).<br />
<br />
===Select nodes with different taxid than query node===<br />
Some interactions may involve proteins from multiple species. An interaction may truly occur between proteins from two species (e.g. an interaction between a Human protein and a virus protein). In other cases, this may be an artefact of how data was entered by the source database.<br />
<br />
===Select between nodes===<br />
This option highlights (selects) nodes interacting with at least two nodes that have been pre-selected by the user. The node attribute '''i.alive_degree''' will be recalculated to reflect the degree of each node with respect to this pre-selection.<br />
<br />
===Show spoke-represented complexes===<br />
Some complexes are represented as a set of binary interactions by some sources. This action attempts to highlight such complexes as a single unit by attaching them all to a single pseudonode. <br />
<br />
<br />
==Hide/Un-hide==<br />
<br />
===Hide selected nodes===<br />
This action hides the selected nodes. This operation is performed in a independent thread and more efficient than hiding using Cytoscape's 'hide node' utility for large networks.<br />
<br />
===Hide nodes (except pseudonodes)===<br />
This action hides all select nodes which represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Hide nodes not selected===<br />
Hides all nodes which are not currently selected<br />
<br />
===Hide nodes not selected (except pseudonodes)===<br />
Hides all nodes which are not currently selected and that represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Un-hide all===<br />
Un-hides all nodes which are hidden by the user.<br />
<br />
==Safe mode==<br />
This option is only available when using JAVA 1.5 and will not appear for Java 1.6 or newer. Selecting this will un-dock the iRefScape window and handles errors and exceptions thrown due to bugs in JAVA 1.5. When this mode is activated not all graphic features will be available.<br />
<br />
<br />
<br />
<br />
<br />
== All iRefIndex Pages ==<br />
<br />
Follow this link for a listing of all iRefIndex related pages (archived and current).<br />
[[Category:iRefIndex]]</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefScape_plugin_menu&diff=3469iRefScape plugin menu2011-06-08T14:48:49Z<p>Sabry: /* iRefScape search with batch file */</p>
<hr />
<div>==Search tools==<br />
<br />
===Retrieve interactions for the selected nodes===<br />
To load all protein-protein interactions and complexes involving one or more '''selected nodes'''. This action is the same as performing a iteration=1 search using iRefScape for the selected nodes.<br />
<br />
===Expand one level===<br />
To load all protein-protein interactions and complexes involving at least one of the nodes in the current network. The behaviour is same as performing iteration=1 search using iRefScape for all the nodes. <br />
<br />
===Load interactions between neighbours===<br />
To complete the interactions between the currently loaded nodes. When a search & load operation is performed in iRefScape, the network returned contains all the proteins interacting with the query and the corresponding interactions. This does not return interactions between the neighbours of the query. This operation is the same as performing an iteration=0 search using iRefScape for all the nodes.<br />
This action has no effect for networks for which this operation has already been performed using the option presented at the end of the search.<br />
<br />
===Clear load history (Reload everything next time)===<br />
This will clear the iRefScape cache memory containing currently loaded nodes and edges. IRefScape keeps track of what is loaded to avoid reloading and thus increase efficiency. Therefore, if a search is performed twice,the network will not be re-loaded unless the user has requested that results be shown in a new view or they have selected this menu option. If the user wishes to reload the network then this option has to be used. When using other methods of expanding the network like “Expand one level” iRefScape handles the cache clearing automatically.<br />
<br />
===Reset node degree===<br />
This option resets the i.alive_degree of nodes. i.alive_degree provides how many nodes with a certain attribute type is connected to each node (set using filters). <br />
<br />
==Loading user variables (this section is being edited)==<br />
User variables can be attached to nodes and be browsed using the attribute browser. This file can not be used as a searchable index (can not be used as a search type). please see section [http://irefindex.uio.no/wiki/README_Cytoscape_plugin_menu#iRefScape_user_searchable_index'''iRefScape_user_searchable_index'''] for details on searchable indices. <br />
<br />
There are three ways to load own variables for the user. <br />
#Use the Cytoscape attribute loading feature ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual'''])<br />
#Use a use attribute file with iRefScape (described in this section)<br />
#Include the attribute with the batch search file.(Described in section [http://irefindex.uio.no/wiki/README_Cytoscape_plugin_menu#Attribute_batch_file '''Attribute_batch_file''']).<br />
<br />
The iRefScape user attribute loader is provided as a complementing feature to the Cytoscape node attribute loading ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual''']). For most of the attribute loading operations the Cytoscape node attribute loader is sufficient and easier to use. However, when the iRefScape node attribute file is used, this can be used by using the menu entry iRefScape-> Search tools > Load user variables. In addition the file will be available for subsequent operations.<br />
<br />
===iRefScape user variable file format===<br />
The first line of the file provides instructions and this line is compulsory.<br />
Example. <br />
#i.rog New_attribute<br />
<br />
<br />
The first line always starts with a hash ("#") and immediately followed by the iReFscape variable name. This iRefScape variable name is used to locate the nodes via the new attribute will be attached. Then a tab is used as a column separator, followed by the name of the user attribute name.This user attribute name should be unique( not already used). In the above example the user attribute to use is the i.rog and the user attribute name is "New_attribute".<br />
<br />
From the second line onwards, the attributes with the mapping attribute are provided.<br />
Example <br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
<br />
The first column provides the iRefScape attribute to use and the second column provides the user attribute. Multiple attributes should be separated with a pipe ("|"). The example line shown would locate the node with i.rog=4399398 and attach the "TENC1|UniProtKB:Q63HR2|" value to it with the attribute name "New_attribute"<br />
<br />
*Each column is separated by a TAB.<br />
*Each line ends with a new line character ("\n")<br />
*The file should be constructed using a plain text editor (e.g. Kate, notepad) and word processing software like Microsoft word should not be used to construct this file.<br />
* The file extension is ".txt"<br />
* Sample file "ONE__EXT__ROG_#Name_5_.iruv" can be found in the iRefScape installation directory (iRefIndex directory)<br />
*The file name should have the format _rog_'''USER_VARIABLE_NAME'''.iruv (The text in bold is supplied by the user. e.g., _rog_myAttribute.iruv ).<br />
<br />
Sample file<br />
#i.rog New_name<br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
452957 GFI1B|UniProtKB:Q5VTD9|<br />
561552 TENC1|UniProtKB:Q63HR2-4|<br />
534065 GFI1B_MOUSE|UniProtKB:O70237|<br />
<br />
==iRefScape search with batch file==<br />
When there are many search queries, it is convenient to construct a batch file and load this to iRefScape. There are 3 type of batch files;<br />
#Simple batch file (recommended for users just wanting to search for a list of things)<br />
#Attribute batch file (Attach additional attributes) <br />
#User index batch file (Explained in section [http://irefindex.uio.no/wiki/README_Cytoscape_plugin_menu#iRefScape_user_searchable_index '''iRefScape_user_searchable_index'''])<br />
<br />
=== Simple batch file ===<br />
<br />
Example file content:<br />
#geneID:3702<br />
814707<br />
814714<br />
814714<br />
817659<br />
818662<br />
<br />
*The first line starts with a hash ("#") and this line is compulsory.<br />
*Immediately after the hash (no space in between) the iRefScape attribute name should be provided. Please see below for accepted list of identifier with the corresponding label.<br />
<br />
{| {{table}}<br />
| align="center" style="background:#f0f0f0;"|'''Label to use in the batch file'''<br />
| align="center" style="background:#f0f0f0;"|'''Description'''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
|-<br />
| rog||iROGID, the integer reference redundant object group identifier([http://irefindex.uio.no/wiki/Protein_identifier_mapping \'\'\'details of mapper files to locate the iRGOID can be found here)\'\'\']||||||<br />
|-<br />
| geneID||NCBI Gene ID, this is always an integer||||||<br />
|-<br />
| UniProt_Ac||UniProt/KB accession||||||<br />
|-<br />
| RefSeq_Ac||RefSeq Accession||||||<br />
|-<br />
| UniProt_ID||UniProt identifier||||||<br />
|-<br />
| geneSymbol||NCBI Gene symbol||||||<br />
|-<br />
| PMID||PubMed identifier ||||||<br />
|-<br />
| src_intxn_id||Interaction identifiers used by source databases||||||<br />
|-<br />
| omim||OMIM identifier ([http://www.ncbi.nlm.nih.gov/omim \'\'\'OMIM home page\'\'\'])||||||<br />
|-<br />
| digid||diseases group identifier ([http://irefindex.uio.no/wiki/DiG:_Disease_groups \'\'\'DiG home page\'\'\'])||||||<br />
|-<br />
| <br />
|}<br />
<br />
<!--<br />
==Only variables==<br />
Users can load there own variables for proteins which are mapped to a ROGID. The file should follow the format given below;<br />
#Should be a plain text file with exactly two columns and each line ending with a new line character (pressing enter).<br />
#First column should contain the ROGID<br />
#Second column should contain the user attribute/variable. <br />
#The file name should have the format _rog_'''USER_VARIABLE_NAME'''.iruv (The text in bold is supplied by the user. e.g., _rog_myAttribute.iruv ).<br />
<br />
<pre><br />
e.g<br />
#rog USER_VARIABLE<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
q6/pRFyay7gQ6bb2rzvKYgfkeaE9606 2<br />
8sODZSppCsuEgRmhSHp3UjwOf2M9606 3<br />
obze7v7i2yTIIcJjd7laIriNFg89606 4<br />
Ty0OLkmhoUPjUuLQQv5ykN057oM9606 5<br />
4bhW4sEt1YhYwHnHCyDNV3vvThs9606 6<br />
Al8M+JdB4H+QnwITh8KcicdI2x49606 6<br />
rkL/SGL1Enj6KoFkPbbcoJ5vKJE9606 6<br />
<br />
</pre><br />
--><br />
<br />
== Attribute batch file ==<br />
Users can attach additional attributes when performing batch queries (instead of loading the attributes after the search).<br />
<br />
The example shown below attaches an additional index "NOONAN_SYNDROME_TYPE" to the matching nodes.<br />
Example indexable batch file<br />
#geneSymbol:9606:NOONAN_SYNDROME_TYPE<br />
PTPN11 NS1<br />
SHOC2 NS2<br />
KRAS NS3<br />
SOS1 NS4<br />
RAF1 NS5<br />
NRAS NS6<br />
NF1 NFNS<br />
<br />
#The first line is compulsory and contains controlling information. the fist value after the hash ('#') is the iRefindex attribute type to be used(please see xxx for attribute types). The second value is the NCBI taxonomy identifier ([http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ '''NCBI taxonomy browser''']). The third value is the name of the user attribute. All three values are seperated by a colon ":". It is possible to include multiple attributes in the same file. To do this first the attribute name should be defined in the first line and additional columns should be used to include the values. (Please not that if the batch file is also used as the template to construct user searchable index, only one user attribute is allowed in the file)<br />
<br />
== iRefScape user searchable index ==<br />
Users can construct their own indices to be used as search type. The easiest way to include a index is to use the advanced batch file mode. This process will;<br />
#Find the iROGID for the user variable<br />
#Construct searchable index.<br />
<br />
The example shown below constructs an index, where the user can perfume search using the Noonan syndrom type. <br />
Example indexable batch file<br />
#geneSymbol:9606:NOONAN_SYNDROME_TYPE<br />
PTPN11 NS1<br />
SHOC2 NS2<br />
KRAS NS3<br />
SOS1 NS4<br />
RAF1 NS5<br />
NRAS NS6<br />
NF1 NFNS<br />
<br />
#The first line is compulsory and contains controlling information. the fist value after the hash ('#') is the iRefindex attribute type to be used(please see xxx for attribute types). The second value is the NCBI taxonomy identifier ([http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ '''NCBI taxonomy browser''']). The third value is the name of the user attribute. All three values are seperated by a colon ":".<br />
<br />
The data rows should always be two columns, where the columns are separated by a tab. The first value in a data row is the search string (what should be used to search iRefIndex). The values in the first column will appear in the search box at the end of the operation. The second column contains the user attribute. <br />
<br />
*the file name of the batch file should contain the prefix "INDEX_THIS_" to be considered for the indexing.<br />
<br />
Example file name<br />
INDEX_THIS_Sample_batch4.txt<br />
<br />
*The attribute do not appear as a separate attribute, but should instead look in the i.query field.<br />
<br />
==View tools==<br />
<br />
===Toggle selected multi-edges===<br />
iRefScape creates multiple edges between nodes to represent multiple evidences. If an interaction between two proteins has evidence from both MINT and IntAct, there will be 2 edges; one for MINT and one for IntAct. Although this provides more information for the user, sometime the user may prefer to collapse these edges to a single edge to facilitate viewing. When this action is performed on a network, all but a randomly selected edge between each node is hidden. The edges which are hidden has the i.flag=1 and the one remaining has i.flag=0. Therefore, while this process is random by default, the user can control which edges to keep and which to hide by editing the i.flag edge attribute before using the '''toggle multi-edge''' option.<br />
<br />
===Zoom to selected===<br />
This action brings the '''selected node(s)''' to the centre of the screen and makes the nodes as large as possible given that all selected nodes are visible. This action can also be performed manually using Cytoscape's zoom tool.<br />
<br />
===Select last iRefScape selection===<br />
This action shows the last selection '''performed by an iRefScape operation'''. This features does not record user selections or selections made by using Cytoscape tools (e.g filters).<br />
<br />
===Select nodes with different taxid than query node===<br />
Some interactions may involve proteins from multiple species. An interaction may truly occur between proteins from two species (e.g. an interaction between a Human protein and a virus protein). In other cases, this may be an artefact of how data was entered by the source database.<br />
<br />
===Select between nodes===<br />
This option highlights (selects) nodes interacting with at least two nodes that have been pre-selected by the user. The node attribute '''i.alive_degree''' will be recalculated to reflect the degree of each node with respect to this pre-selection.<br />
<br />
===Show spoke-represented complexes===<br />
Some complexes are represented as a set of binary interactions by some sources. This action attempts to highlight such complexes as a single unit by attaching them all to a single pseudonode. <br />
<br />
<br />
==Hide/Un-hide==<br />
<br />
===Hide selected nodes===<br />
This action hides the selected nodes. This operation is performed in a independent thread and more efficient than hiding using Cytoscape's 'hide node' utility for large networks.<br />
<br />
===Hide nodes (except pseudonodes)===<br />
This action hides all select nodes which represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Hide nodes not selected===<br />
Hides all nodes which are not currently selected<br />
<br />
===Hide nodes not selected (except pseudonodes)===<br />
Hides all nodes which are not currently selected and that represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Un-hide all===<br />
Un-hides all nodes which are hidden by the user.<br />
<br />
==Safe mode==<br />
This option is only available when using JAVA 1.5 and will not appear for Java 1.6 or newer. Selecting this will un-dock the iRefScape window and handles errors and exceptions thrown due to bugs in JAVA 1.5. When this mode is activated not all graphic features will be available.<br />
<br />
<br />
<br />
<br />
<br />
== All iRefIndex Pages ==<br />
<br />
Follow this link for a listing of all iRefIndex related pages (archived and current).<br />
[[Category:iRefIndex]]</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefScape_plugin_menu&diff=3468iRefScape plugin menu2011-06-08T14:47:53Z<p>Sabry: /* Loading user variables (this section is being edited) */</p>
<hr />
<div>==Search tools==<br />
<br />
===Retrieve interactions for the selected nodes===<br />
To load all protein-protein interactions and complexes involving one or more '''selected nodes'''. This action is the same as performing a iteration=1 search using iRefScape for the selected nodes.<br />
<br />
===Expand one level===<br />
To load all protein-protein interactions and complexes involving at least one of the nodes in the current network. The behaviour is same as performing iteration=1 search using iRefScape for all the nodes. <br />
<br />
===Load interactions between neighbours===<br />
To complete the interactions between the currently loaded nodes. When a search & load operation is performed in iRefScape, the network returned contains all the proteins interacting with the query and the corresponding interactions. This does not return interactions between the neighbours of the query. This operation is the same as performing an iteration=0 search using iRefScape for all the nodes.<br />
This action has no effect for networks for which this operation has already been performed using the option presented at the end of the search.<br />
<br />
===Clear load history (Reload everything next time)===<br />
This will clear the iRefScape cache memory containing currently loaded nodes and edges. IRefScape keeps track of what is loaded to avoid reloading and thus increase efficiency. Therefore, if a search is performed twice,the network will not be re-loaded unless the user has requested that results be shown in a new view or they have selected this menu option. If the user wishes to reload the network then this option has to be used. When using other methods of expanding the network like “Expand one level” iRefScape handles the cache clearing automatically.<br />
<br />
===Reset node degree===<br />
This option resets the i.alive_degree of nodes. i.alive_degree provides how many nodes with a certain attribute type is connected to each node (set using filters). <br />
<br />
==Loading user variables (this section is being edited)==<br />
User variables can be attached to nodes and be browsed using the attribute browser. This file can not be used as a searchable index (can not be used as a search type). please see section [http://irefindex.uio.no/wiki/README_Cytoscape_plugin_menu#iRefScape_user_searchable_index'''iRefScape_user_searchable_index'''] for details on searchable indices. <br />
<br />
There are three ways to load own variables for the user. <br />
#Use the Cytoscape attribute loading feature ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual'''])<br />
#Use a use attribute file with iRefScape (described in this section)<br />
#Include the attribute with the batch search file.(Described in section [http://irefindex.uio.no/wiki/README_Cytoscape_plugin_menu#Attribute_batch_file '''Attribute_batch_file''']).<br />
<br />
The iRefScape user attribute loader is provided as a complementing feature to the Cytoscape node attribute loading ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual''']). For most of the attribute loading operations the Cytoscape node attribute loader is sufficient and easier to use. However, when the iRefScape node attribute file is used, this can be used by using the menu entry iRefScape-> Search tools > Load user variables. In addition the file will be available for subsequent operations.<br />
<br />
===iRefScape user variable file format===<br />
The first line of the file provides instructions and this line is compulsory.<br />
Example. <br />
#i.rog New_attribute<br />
<br />
<br />
The first line always starts with a hash ("#") and immediately followed by the iReFscape variable name. This iRefScape variable name is used to locate the nodes via the new attribute will be attached. Then a tab is used as a column separator, followed by the name of the user attribute name.This user attribute name should be unique( not already used). In the above example the user attribute to use is the i.rog and the user attribute name is "New_attribute".<br />
<br />
From the second line onwards, the attributes with the mapping attribute are provided.<br />
Example <br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
<br />
The first column provides the iRefScape attribute to use and the second column provides the user attribute. Multiple attributes should be separated with a pipe ("|"). The example line shown would locate the node with i.rog=4399398 and attach the "TENC1|UniProtKB:Q63HR2|" value to it with the attribute name "New_attribute"<br />
<br />
*Each column is separated by a TAB.<br />
*Each line ends with a new line character ("\n")<br />
*The file should be constructed using a plain text editor (e.g. Kate, notepad) and word processing software like Microsoft word should not be used to construct this file.<br />
* The file extension is ".txt"<br />
* Sample file "ONE__EXT__ROG_#Name_5_.iruv" can be found in the iRefScape installation directory (iRefIndex directory)<br />
*The file name should have the format _rog_'''USER_VARIABLE_NAME'''.iruv (The text in bold is supplied by the user. e.g., _rog_myAttribute.iruv ).<br />
<br />
Sample file<br />
#i.rog New_name<br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
452957 GFI1B|UniProtKB:Q5VTD9|<br />
561552 TENC1|UniProtKB:Q63HR2-4|<br />
534065 GFI1B_MOUSE|UniProtKB:O70237|<br />
<br />
==iRefScape search with batch file==<br />
When there are many search queries, it is convenient to construct a batch file and load this to iRefScape. There are 3 type of batch files;<br />
#Simple batch file (recommended for users just wanting to search for a list of things)<br />
#Attribute batch file (Attach additional attributes) <br />
#User index batch file (please refer XXX)<br />
<br />
=== Simple batch file ===<br />
<br />
Example file content:<br />
#geneID:3702<br />
814707<br />
814714<br />
814714<br />
817659<br />
818662<br />
<br />
*The first line starts with a hash ("#") and this line is compulsory.<br />
*Immediately after the hash (no space in between) the iRefScape attribute name should be provided. Please see below for accepted list of identifier with the corresponding label.<br />
<br />
{| {{table}}<br />
| align="center" style="background:#f0f0f0;"|'''Label to use in the batch file'''<br />
| align="center" style="background:#f0f0f0;"|'''Description'''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
|-<br />
| rog||iROGID, the integer reference redundant object group identifier([http://irefindex.uio.no/wiki/Protein_identifier_mapping \'\'\'details of mapper files to locate the iRGOID can be found here)\'\'\']||||||<br />
|-<br />
| geneID||NCBI Gene ID, this is always an integer||||||<br />
|-<br />
| UniProt_Ac||UniProt/KB accession||||||<br />
|-<br />
| RefSeq_Ac||RefSeq Accession||||||<br />
|-<br />
| UniProt_ID||UniProt identifier||||||<br />
|-<br />
| geneSymbol||NCBI Gene symbol||||||<br />
|-<br />
| PMID||PubMed identifier ||||||<br />
|-<br />
| src_intxn_id||Interaction identifiers used by source databases||||||<br />
|-<br />
| omim||OMIM identifier ([http://www.ncbi.nlm.nih.gov/omim \'\'\'OMIM home page\'\'\'])||||||<br />
|-<br />
| digid||diseases group identifier ([http://irefindex.uio.no/wiki/DiG:_Disease_groups \'\'\'DiG home page\'\'\'])||||||<br />
|-<br />
| <br />
|}<br />
<br />
<!--<br />
==Only variables==<br />
Users can load there own variables for proteins which are mapped to a ROGID. The file should follow the format given below;<br />
#Should be a plain text file with exactly two columns and each line ending with a new line character (pressing enter).<br />
#First column should contain the ROGID<br />
#Second column should contain the user attribute/variable. <br />
#The file name should have the format _rog_'''USER_VARIABLE_NAME'''.iruv (The text in bold is supplied by the user. e.g., _rog_myAttribute.iruv ).<br />
<br />
<pre><br />
e.g<br />
#rog USER_VARIABLE<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
q6/pRFyay7gQ6bb2rzvKYgfkeaE9606 2<br />
8sODZSppCsuEgRmhSHp3UjwOf2M9606 3<br />
obze7v7i2yTIIcJjd7laIriNFg89606 4<br />
Ty0OLkmhoUPjUuLQQv5ykN057oM9606 5<br />
4bhW4sEt1YhYwHnHCyDNV3vvThs9606 6<br />
Al8M+JdB4H+QnwITh8KcicdI2x49606 6<br />
rkL/SGL1Enj6KoFkPbbcoJ5vKJE9606 6<br />
<br />
</pre><br />
--><br />
<br />
== Attribute batch file ==<br />
Users can attach additional attributes when performing batch queries (instead of loading the attributes after the search).<br />
<br />
The example shown below attaches an additional index "NOONAN_SYNDROME_TYPE" to the matching nodes.<br />
Example indexable batch file<br />
#geneSymbol:9606:NOONAN_SYNDROME_TYPE<br />
PTPN11 NS1<br />
SHOC2 NS2<br />
KRAS NS3<br />
SOS1 NS4<br />
RAF1 NS5<br />
NRAS NS6<br />
NF1 NFNS<br />
<br />
#The first line is compulsory and contains controlling information. the fist value after the hash ('#') is the iRefindex attribute type to be used(please see xxx for attribute types). The second value is the NCBI taxonomy identifier ([http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ '''NCBI taxonomy browser''']). The third value is the name of the user attribute. All three values are seperated by a colon ":". It is possible to include multiple attributes in the same file. To do this first the attribute name should be defined in the first line and additional columns should be used to include the values. (Please not that if the batch file is also used as the template to construct user searchable index, only one user attribute is allowed in the file)<br />
<br />
== iRefScape user searchable index ==<br />
Users can construct their own indices to be used as search type. The easiest way to include a index is to use the advanced batch file mode. This process will;<br />
#Find the iROGID for the user variable<br />
#Construct searchable index.<br />
<br />
The example shown below constructs an index, where the user can perfume search using the Noonan syndrom type. <br />
Example indexable batch file<br />
#geneSymbol:9606:NOONAN_SYNDROME_TYPE<br />
PTPN11 NS1<br />
SHOC2 NS2<br />
KRAS NS3<br />
SOS1 NS4<br />
RAF1 NS5<br />
NRAS NS6<br />
NF1 NFNS<br />
<br />
#The first line is compulsory and contains controlling information. the fist value after the hash ('#') is the iRefindex attribute type to be used(please see xxx for attribute types). The second value is the NCBI taxonomy identifier ([http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ '''NCBI taxonomy browser''']). The third value is the name of the user attribute. All three values are seperated by a colon ":".<br />
<br />
The data rows should always be two columns, where the columns are separated by a tab. The first value in a data row is the search string (what should be used to search iRefIndex). The values in the first column will appear in the search box at the end of the operation. The second column contains the user attribute. <br />
<br />
*the file name of the batch file should contain the prefix "INDEX_THIS_" to be considered for the indexing.<br />
<br />
Example file name<br />
INDEX_THIS_Sample_batch4.txt<br />
<br />
*The attribute do not appear as a separate attribute, but should instead look in the i.query field.<br />
<br />
==View tools==<br />
<br />
===Toggle selected multi-edges===<br />
iRefScape creates multiple edges between nodes to represent multiple evidences. If an interaction between two proteins has evidence from both MINT and IntAct, there will be 2 edges; one for MINT and one for IntAct. Although this provides more information for the user, sometime the user may prefer to collapse these edges to a single edge to facilitate viewing. When this action is performed on a network, all but a randomly selected edge between each node is hidden. The edges which are hidden has the i.flag=1 and the one remaining has i.flag=0. Therefore, while this process is random by default, the user can control which edges to keep and which to hide by editing the i.flag edge attribute before using the '''toggle multi-edge''' option.<br />
<br />
===Zoom to selected===<br />
This action brings the '''selected node(s)''' to the centre of the screen and makes the nodes as large as possible given that all selected nodes are visible. This action can also be performed manually using Cytoscape's zoom tool.<br />
<br />
===Select last iRefScape selection===<br />
This action shows the last selection '''performed by an iRefScape operation'''. This features does not record user selections or selections made by using Cytoscape tools (e.g filters).<br />
<br />
===Select nodes with different taxid than query node===<br />
Some interactions may involve proteins from multiple species. An interaction may truly occur between proteins from two species (e.g. an interaction between a Human protein and a virus protein). In other cases, this may be an artefact of how data was entered by the source database.<br />
<br />
===Select between nodes===<br />
This option highlights (selects) nodes interacting with at least two nodes that have been pre-selected by the user. The node attribute '''i.alive_degree''' will be recalculated to reflect the degree of each node with respect to this pre-selection.<br />
<br />
===Show spoke-represented complexes===<br />
Some complexes are represented as a set of binary interactions by some sources. This action attempts to highlight such complexes as a single unit by attaching them all to a single pseudonode. <br />
<br />
<br />
==Hide/Un-hide==<br />
<br />
===Hide selected nodes===<br />
This action hides the selected nodes. This operation is performed in a independent thread and more efficient than hiding using Cytoscape's 'hide node' utility for large networks.<br />
<br />
===Hide nodes (except pseudonodes)===<br />
This action hides all select nodes which represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Hide nodes not selected===<br />
Hides all nodes which are not currently selected<br />
<br />
===Hide nodes not selected (except pseudonodes)===<br />
Hides all nodes which are not currently selected and that represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Un-hide all===<br />
Un-hides all nodes which are hidden by the user.<br />
<br />
==Safe mode==<br />
This option is only available when using JAVA 1.5 and will not appear for Java 1.6 or newer. Selecting this will un-dock the iRefScape window and handles errors and exceptions thrown due to bugs in JAVA 1.5. When this mode is activated not all graphic features will be available.<br />
<br />
<br />
<br />
<br />
<br />
== All iRefIndex Pages ==<br />
<br />
Follow this link for a listing of all iRefIndex related pages (archived and current).<br />
[[Category:iRefIndex]]</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefScape_plugin_menu&diff=3467iRefScape plugin menu2011-06-08T14:45:10Z<p>Sabry: /* Loading user variables (this section is being edited) */</p>
<hr />
<div>==Search tools==<br />
<br />
===Retrieve interactions for the selected nodes===<br />
To load all protein-protein interactions and complexes involving one or more '''selected nodes'''. This action is the same as performing a iteration=1 search using iRefScape for the selected nodes.<br />
<br />
===Expand one level===<br />
To load all protein-protein interactions and complexes involving at least one of the nodes in the current network. The behaviour is same as performing iteration=1 search using iRefScape for all the nodes. <br />
<br />
===Load interactions between neighbours===<br />
To complete the interactions between the currently loaded nodes. When a search & load operation is performed in iRefScape, the network returned contains all the proteins interacting with the query and the corresponding interactions. This does not return interactions between the neighbours of the query. This operation is the same as performing an iteration=0 search using iRefScape for all the nodes.<br />
This action has no effect for networks for which this operation has already been performed using the option presented at the end of the search.<br />
<br />
===Clear load history (Reload everything next time)===<br />
This will clear the iRefScape cache memory containing currently loaded nodes and edges. IRefScape keeps track of what is loaded to avoid reloading and thus increase efficiency. Therefore, if a search is performed twice,the network will not be re-loaded unless the user has requested that results be shown in a new view or they have selected this menu option. If the user wishes to reload the network then this option has to be used. When using other methods of expanding the network like “Expand one level” iRefScape handles the cache clearing automatically.<br />
<br />
===Reset node degree===<br />
This option resets the i.alive_degree of nodes. i.alive_degree provides how many nodes with a certain attribute type is connected to each node (set using filters). <br />
<br />
==Loading user variables (this section is being edited)==<br />
User variables can be attached to nodes and be browsed using the attribute browser. This file can not be used as a searchable index (can not be used as a search type). please see section [http://irefindex.uio.no/wiki/README_Cytoscape_plugin_menu#iRefScape_user_searchable_index'''iRefScape_user_searchable_index'''] for details on searchable indices. <br />
<br />
There are three ways to load own variables for the user. <br />
#Use the Cytoscape attribute loading feature ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual'''])<br />
#Use a use attribute file with iRefScape (described in this section)<br />
#Include the attribute with the batch search file.(Described in section [http://irefindex.uio.no/wiki/README_Cytoscape_plugin_menu#Attribute_batch_file '''Attribute_batch_file''']).<br />
<br />
The iRefScape user attribute loader is provided as a complementing feature to the Cytoscape node attribute loading ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual''']). For most of the attribute loading operations the Cytoscape node attribute loader is sufficient and easier to use. However, when the iRefScape node attribute file is used, this can be used by just using the menu entry XXX. In addition the file will be available for subsequent operations.<br />
<br />
===iRefScape user variable file format===<br />
The first line of the file provides instructions and this line is compulsory.<br />
Example. <br />
#i.rog New_attribute<br />
<br />
<br />
The first line always starts with a hash ("#") and immediately followed by the iReFscape variable name. This iRefScape variable name is used to locate the nodes via the new attribute will be attached. Then a tab is used as a column separator, followed by the name of the user attribute name.This user attribute name should be unique( not already used). In the above example the user attribute to use is the i.rog and the user attribute name is "New_attribute".<br />
<br />
From the second line onwards, the attributes with the mapping attribute are provided.<br />
Example <br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
<br />
The first column provides the iRefScape attribute to use and the second column provides the user attribute. Multiple attributes should be separated with a pipe ("|"). The example line shown would locate the node with i.rog=4399398 and attach the "TENC1|UniProtKB:Q63HR2|" value to it with the attribute name "New_attribute"<br />
<br />
*Each column is separated by a TAB.<br />
*Each line ends with a new line character ("\n")<br />
*The file should be constructed using a plain text editor (e.g. Kate, notepad) and word processing software like Microsoft word should not be used to construct this file.<br />
* The file extension is ".txt"<br />
* Sample file "ONE__EXT__ROG_#Name_5_.iruv" can be found in the iRefScape installation directory (iRefIndex directory)<br />
*The file name should have the format _rog_'''USER_VARIABLE_NAME'''.iruv (The text in bold is supplied by the user. e.g., _rog_myAttribute.iruv ).<br />
<br />
Sample file<br />
#i.rog New_name<br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
452957 GFI1B|UniProtKB:Q5VTD9|<br />
561552 TENC1|UniProtKB:Q63HR2-4|<br />
534065 GFI1B_MOUSE|UniProtKB:O70237|<br />
<br />
==iRefScape search with batch file==<br />
When there are many search queries, it is convenient to construct a batch file and load this to iRefScape. There are 3 type of batch files;<br />
#Simple batch file (recommended for users just wanting to search for a list of things)<br />
#Attribute batch file (Attach additional attributes) <br />
#User index batch file (please refer XXX)<br />
<br />
=== Simple batch file ===<br />
<br />
Example file content:<br />
#geneID:3702<br />
814707<br />
814714<br />
814714<br />
817659<br />
818662<br />
<br />
*The first line starts with a hash ("#") and this line is compulsory.<br />
*Immediately after the hash (no space in between) the iRefScape attribute name should be provided. Please see below for accepted list of identifier with the corresponding label.<br />
<br />
{| {{table}}<br />
| align="center" style="background:#f0f0f0;"|'''Label to use in the batch file'''<br />
| align="center" style="background:#f0f0f0;"|'''Description'''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
|-<br />
| rog||iROGID, the integer reference redundant object group identifier([http://irefindex.uio.no/wiki/Protein_identifier_mapping \'\'\'details of mapper files to locate the iRGOID can be found here)\'\'\']||||||<br />
|-<br />
| geneID||NCBI Gene ID, this is always an integer||||||<br />
|-<br />
| UniProt_Ac||UniProt/KB accession||||||<br />
|-<br />
| RefSeq_Ac||RefSeq Accession||||||<br />
|-<br />
| UniProt_ID||UniProt identifier||||||<br />
|-<br />
| geneSymbol||NCBI Gene symbol||||||<br />
|-<br />
| PMID||PubMed identifier ||||||<br />
|-<br />
| src_intxn_id||Interaction identifiers used by source databases||||||<br />
|-<br />
| omim||OMIM identifier ([http://www.ncbi.nlm.nih.gov/omim \'\'\'OMIM home page\'\'\'])||||||<br />
|-<br />
| digid||diseases group identifier ([http://irefindex.uio.no/wiki/DiG:_Disease_groups \'\'\'DiG home page\'\'\'])||||||<br />
|-<br />
| <br />
|}<br />
<br />
<!--<br />
==Only variables==<br />
Users can load there own variables for proteins which are mapped to a ROGID. The file should follow the format given below;<br />
#Should be a plain text file with exactly two columns and each line ending with a new line character (pressing enter).<br />
#First column should contain the ROGID<br />
#Second column should contain the user attribute/variable. <br />
#The file name should have the format _rog_'''USER_VARIABLE_NAME'''.iruv (The text in bold is supplied by the user. e.g., _rog_myAttribute.iruv ).<br />
<br />
<pre><br />
e.g<br />
#rog USER_VARIABLE<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
q6/pRFyay7gQ6bb2rzvKYgfkeaE9606 2<br />
8sODZSppCsuEgRmhSHp3UjwOf2M9606 3<br />
obze7v7i2yTIIcJjd7laIriNFg89606 4<br />
Ty0OLkmhoUPjUuLQQv5ykN057oM9606 5<br />
4bhW4sEt1YhYwHnHCyDNV3vvThs9606 6<br />
Al8M+JdB4H+QnwITh8KcicdI2x49606 6<br />
rkL/SGL1Enj6KoFkPbbcoJ5vKJE9606 6<br />
<br />
</pre><br />
--><br />
<br />
== Attribute batch file ==<br />
Users can attach additional attributes when performing batch queries (instead of loading the attributes after the search).<br />
<br />
The example shown below attaches an additional index "NOONAN_SYNDROME_TYPE" to the matching nodes.<br />
Example indexable batch file<br />
#geneSymbol:9606:NOONAN_SYNDROME_TYPE<br />
PTPN11 NS1<br />
SHOC2 NS2<br />
KRAS NS3<br />
SOS1 NS4<br />
RAF1 NS5<br />
NRAS NS6<br />
NF1 NFNS<br />
<br />
#The first line is compulsory and contains controlling information. the fist value after the hash ('#') is the iRefindex attribute type to be used(please see xxx for attribute types). The second value is the NCBI taxonomy identifier ([http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ '''NCBI taxonomy browser''']). The third value is the name of the user attribute. All three values are seperated by a colon ":". It is possible to include multiple attributes in the same file. To do this first the attribute name should be defined in the first line and additional columns should be used to include the values. (Please not that if the batch file is also used as the template to construct user searchable index, only one user attribute is allowed in the file)<br />
<br />
== iRefScape user searchable index ==<br />
Users can construct their own indices to be used as search type. The easiest way to include a index is to use the advanced batch file mode. This process will;<br />
#Find the iROGID for the user variable<br />
#Construct searchable index.<br />
<br />
The example shown below constructs an index, where the user can perfume search using the Noonan syndrom type. <br />
Example indexable batch file<br />
#geneSymbol:9606:NOONAN_SYNDROME_TYPE<br />
PTPN11 NS1<br />
SHOC2 NS2<br />
KRAS NS3<br />
SOS1 NS4<br />
RAF1 NS5<br />
NRAS NS6<br />
NF1 NFNS<br />
<br />
#The first line is compulsory and contains controlling information. the fist value after the hash ('#') is the iRefindex attribute type to be used(please see xxx for attribute types). The second value is the NCBI taxonomy identifier ([http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ '''NCBI taxonomy browser''']). The third value is the name of the user attribute. All three values are seperated by a colon ":".<br />
<br />
The data rows should always be two columns, where the columns are separated by a tab. The first value in a data row is the search string (what should be used to search iRefIndex). The values in the first column will appear in the search box at the end of the operation. The second column contains the user attribute. <br />
<br />
*the file name of the batch file should contain the prefix "INDEX_THIS_" to be considered for the indexing.<br />
<br />
Example file name<br />
INDEX_THIS_Sample_batch4.txt<br />
<br />
*The attribute do not appear as a separate attribute, but should instead look in the i.query field.<br />
<br />
==View tools==<br />
<br />
===Toggle selected multi-edges===<br />
iRefScape creates multiple edges between nodes to represent multiple evidences. If an interaction between two proteins has evidence from both MINT and IntAct, there will be 2 edges; one for MINT and one for IntAct. Although this provides more information for the user, sometime the user may prefer to collapse these edges to a single edge to facilitate viewing. When this action is performed on a network, all but a randomly selected edge between each node is hidden. The edges which are hidden has the i.flag=1 and the one remaining has i.flag=0. Therefore, while this process is random by default, the user can control which edges to keep and which to hide by editing the i.flag edge attribute before using the '''toggle multi-edge''' option.<br />
<br />
===Zoom to selected===<br />
This action brings the '''selected node(s)''' to the centre of the screen and makes the nodes as large as possible given that all selected nodes are visible. This action can also be performed manually using Cytoscape's zoom tool.<br />
<br />
===Select last iRefScape selection===<br />
This action shows the last selection '''performed by an iRefScape operation'''. This features does not record user selections or selections made by using Cytoscape tools (e.g filters).<br />
<br />
===Select nodes with different taxid than query node===<br />
Some interactions may involve proteins from multiple species. An interaction may truly occur between proteins from two species (e.g. an interaction between a Human protein and a virus protein). In other cases, this may be an artefact of how data was entered by the source database.<br />
<br />
===Select between nodes===<br />
This option highlights (selects) nodes interacting with at least two nodes that have been pre-selected by the user. The node attribute '''i.alive_degree''' will be recalculated to reflect the degree of each node with respect to this pre-selection.<br />
<br />
===Show spoke-represented complexes===<br />
Some complexes are represented as a set of binary interactions by some sources. This action attempts to highlight such complexes as a single unit by attaching them all to a single pseudonode. <br />
<br />
<br />
==Hide/Un-hide==<br />
<br />
===Hide selected nodes===<br />
This action hides the selected nodes. This operation is performed in a independent thread and more efficient than hiding using Cytoscape's 'hide node' utility for large networks.<br />
<br />
===Hide nodes (except pseudonodes)===<br />
This action hides all select nodes which represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Hide nodes not selected===<br />
Hides all nodes which are not currently selected<br />
<br />
===Hide nodes not selected (except pseudonodes)===<br />
Hides all nodes which are not currently selected and that represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Un-hide all===<br />
Un-hides all nodes which are hidden by the user.<br />
<br />
==Safe mode==<br />
This option is only available when using JAVA 1.5 and will not appear for Java 1.6 or newer. Selecting this will un-dock the iRefScape window and handles errors and exceptions thrown due to bugs in JAVA 1.5. When this mode is activated not all graphic features will be available.<br />
<br />
<br />
<br />
<br />
<br />
== All iRefIndex Pages ==<br />
<br />
Follow this link for a listing of all iRefIndex related pages (archived and current).<br />
[[Category:iRefIndex]]</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefScape_plugin_menu&diff=3466iRefScape plugin menu2011-06-08T14:44:17Z<p>Sabry: /* Loading user variables (this section is being edited) */</p>
<hr />
<div>==Search tools==<br />
<br />
===Retrieve interactions for the selected nodes===<br />
To load all protein-protein interactions and complexes involving one or more '''selected nodes'''. This action is the same as performing a iteration=1 search using iRefScape for the selected nodes.<br />
<br />
===Expand one level===<br />
To load all protein-protein interactions and complexes involving at least one of the nodes in the current network. The behaviour is same as performing iteration=1 search using iRefScape for all the nodes. <br />
<br />
===Load interactions between neighbours===<br />
To complete the interactions between the currently loaded nodes. When a search & load operation is performed in iRefScape, the network returned contains all the proteins interacting with the query and the corresponding interactions. This does not return interactions between the neighbours of the query. This operation is the same as performing an iteration=0 search using iRefScape for all the nodes.<br />
This action has no effect for networks for which this operation has already been performed using the option presented at the end of the search.<br />
<br />
===Clear load history (Reload everything next time)===<br />
This will clear the iRefScape cache memory containing currently loaded nodes and edges. IRefScape keeps track of what is loaded to avoid reloading and thus increase efficiency. Therefore, if a search is performed twice,the network will not be re-loaded unless the user has requested that results be shown in a new view or they have selected this menu option. If the user wishes to reload the network then this option has to be used. When using other methods of expanding the network like “Expand one level” iRefScape handles the cache clearing automatically.<br />
<br />
===Reset node degree===<br />
This option resets the i.alive_degree of nodes. i.alive_degree provides how many nodes with a certain attribute type is connected to each node (set using filters). <br />
<br />
==Loading user variables (this section is being edited)==<br />
User variables can be attached to nodes and be browsed using the attribute browser. This file can not be used as a searchable index (can not be used as a search type). please see section [http://irefindex.uio.no/wiki/README_Cytoscape_plugin_menu#iRefScape_user_searchable_index'''iRefScape_user_searchable_index'''] for details on searchable indices. <br />
<br />
There are three ways to load own variables for the user. <br />
#Use the Cytoscape attribute loading feature ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual'''])<br />
#Use a use attribute file with iRefScape (described in this section)<br />
#Include the attribute with the batch search file.(described in XXX).<br />
<br />
The iRefScape user attribute loader is provided as a complementing feature to the Cytoscape node attribute loading ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual''']). For most of the attribute loading operations the Cytoscape node attribute loader is sufficient and easier to use. However, when the iRefScape node attribute file is used, this can be used by just using the menu entry XXX. In addition the file will be available for subsequent operations.<br />
<br />
===iRefScape user variable file format===<br />
The first line of the file provides instructions and this line is compulsory.<br />
Example. <br />
#i.rog New_attribute<br />
<br />
<br />
The first line always starts with a hash ("#") and immediately followed by the iReFscape variable name. This iRefScape variable name is used to locate the nodes via the new attribute will be attached. Then a tab is used as a column separator, followed by the name of the user attribute name.This user attribute name should be unique( not already used). In the above example the user attribute to use is the i.rog and the user attribute name is "New_attribute".<br />
<br />
From the second line onwards, the attributes with the mapping attribute are provided.<br />
Example <br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
<br />
The first column provides the iRefScape attribute to use and the second column provides the user attribute. Multiple attributes should be separated with a pipe ("|"). The example line shown would locate the node with i.rog=4399398 and attach the "TENC1|UniProtKB:Q63HR2|" value to it with the attribute name "New_attribute"<br />
<br />
*Each column is separated by a TAB.<br />
*Each line ends with a new line character ("\n")<br />
*The file should be constructed using a plain text editor (e.g. Kate, notepad) and word processing software like Microsoft word should not be used to construct this file.<br />
* The file extension is ".txt"<br />
* Sample file "ONE__EXT__ROG_#Name_5_.iruv" can be found in the iRefScape installation directory (iRefIndex directory)<br />
*The file name should have the format _rog_'''USER_VARIABLE_NAME'''.iruv (The text in bold is supplied by the user. e.g., _rog_myAttribute.iruv ).<br />
<br />
Sample file<br />
#i.rog New_name<br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
452957 GFI1B|UniProtKB:Q5VTD9|<br />
561552 TENC1|UniProtKB:Q63HR2-4|<br />
534065 GFI1B_MOUSE|UniProtKB:O70237|<br />
<br />
==iRefScape search with batch file==<br />
When there are many search queries, it is convenient to construct a batch file and load this to iRefScape. There are 3 type of batch files;<br />
#Simple batch file (recommended for users just wanting to search for a list of things)<br />
#Attribute batch file (Attach additional attributes) <br />
#User index batch file (please refer XXX)<br />
<br />
=== Simple batch file ===<br />
<br />
Example file content:<br />
#geneID:3702<br />
814707<br />
814714<br />
814714<br />
817659<br />
818662<br />
<br />
*The first line starts with a hash ("#") and this line is compulsory.<br />
*Immediately after the hash (no space in between) the iRefScape attribute name should be provided. Please see below for accepted list of identifier with the corresponding label.<br />
<br />
{| {{table}}<br />
| align="center" style="background:#f0f0f0;"|'''Label to use in the batch file'''<br />
| align="center" style="background:#f0f0f0;"|'''Description'''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
|-<br />
| rog||iROGID, the integer reference redundant object group identifier([http://irefindex.uio.no/wiki/Protein_identifier_mapping \'\'\'details of mapper files to locate the iRGOID can be found here)\'\'\']||||||<br />
|-<br />
| geneID||NCBI Gene ID, this is always an integer||||||<br />
|-<br />
| UniProt_Ac||UniProt/KB accession||||||<br />
|-<br />
| RefSeq_Ac||RefSeq Accession||||||<br />
|-<br />
| UniProt_ID||UniProt identifier||||||<br />
|-<br />
| geneSymbol||NCBI Gene symbol||||||<br />
|-<br />
| PMID||PubMed identifier ||||||<br />
|-<br />
| src_intxn_id||Interaction identifiers used by source databases||||||<br />
|-<br />
| omim||OMIM identifier ([http://www.ncbi.nlm.nih.gov/omim \'\'\'OMIM home page\'\'\'])||||||<br />
|-<br />
| digid||diseases group identifier ([http://irefindex.uio.no/wiki/DiG:_Disease_groups \'\'\'DiG home page\'\'\'])||||||<br />
|-<br />
| <br />
|}<br />
<br />
<!--<br />
==Only variables==<br />
Users can load there own variables for proteins which are mapped to a ROGID. The file should follow the format given below;<br />
#Should be a plain text file with exactly two columns and each line ending with a new line character (pressing enter).<br />
#First column should contain the ROGID<br />
#Second column should contain the user attribute/variable. <br />
#The file name should have the format _rog_'''USER_VARIABLE_NAME'''.iruv (The text in bold is supplied by the user. e.g., _rog_myAttribute.iruv ).<br />
<br />
<pre><br />
e.g<br />
#rog USER_VARIABLE<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
q6/pRFyay7gQ6bb2rzvKYgfkeaE9606 2<br />
8sODZSppCsuEgRmhSHp3UjwOf2M9606 3<br />
obze7v7i2yTIIcJjd7laIriNFg89606 4<br />
Ty0OLkmhoUPjUuLQQv5ykN057oM9606 5<br />
4bhW4sEt1YhYwHnHCyDNV3vvThs9606 6<br />
Al8M+JdB4H+QnwITh8KcicdI2x49606 6<br />
rkL/SGL1Enj6KoFkPbbcoJ5vKJE9606 6<br />
<br />
</pre><br />
--><br />
<br />
== Attribute batch file ==<br />
Users can attach additional attributes when performing batch queries (instead of loading the attributes after the search).<br />
<br />
The example shown below attaches an additional index "NOONAN_SYNDROME_TYPE" to the matching nodes.<br />
Example indexable batch file<br />
#geneSymbol:9606:NOONAN_SYNDROME_TYPE<br />
PTPN11 NS1<br />
SHOC2 NS2<br />
KRAS NS3<br />
SOS1 NS4<br />
RAF1 NS5<br />
NRAS NS6<br />
NF1 NFNS<br />
<br />
#The first line is compulsory and contains controlling information. the fist value after the hash ('#') is the iRefindex attribute type to be used(please see xxx for attribute types). The second value is the NCBI taxonomy identifier ([http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ '''NCBI taxonomy browser''']). The third value is the name of the user attribute. All three values are seperated by a colon ":". It is possible to include multiple attributes in the same file. To do this first the attribute name should be defined in the first line and additional columns should be used to include the values. (Please not that if the batch file is also used as the template to construct user searchable index, only one user attribute is allowed in the file)<br />
<br />
== iRefScape user searchable index ==<br />
Users can construct their own indices to be used as search type. The easiest way to include a index is to use the advanced batch file mode. This process will;<br />
#Find the iROGID for the user variable<br />
#Construct searchable index.<br />
<br />
The example shown below constructs an index, where the user can perfume search using the Noonan syndrom type. <br />
Example indexable batch file<br />
#geneSymbol:9606:NOONAN_SYNDROME_TYPE<br />
PTPN11 NS1<br />
SHOC2 NS2<br />
KRAS NS3<br />
SOS1 NS4<br />
RAF1 NS5<br />
NRAS NS6<br />
NF1 NFNS<br />
<br />
#The first line is compulsory and contains controlling information. the fist value after the hash ('#') is the iRefindex attribute type to be used(please see xxx for attribute types). The second value is the NCBI taxonomy identifier ([http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ '''NCBI taxonomy browser''']). The third value is the name of the user attribute. All three values are seperated by a colon ":".<br />
<br />
The data rows should always be two columns, where the columns are separated by a tab. The first value in a data row is the search string (what should be used to search iRefIndex). The values in the first column will appear in the search box at the end of the operation. The second column contains the user attribute. <br />
<br />
*the file name of the batch file should contain the prefix "INDEX_THIS_" to be considered for the indexing.<br />
<br />
Example file name<br />
INDEX_THIS_Sample_batch4.txt<br />
<br />
*The attribute do not appear as a separate attribute, but should instead look in the i.query field.<br />
<br />
==View tools==<br />
<br />
===Toggle selected multi-edges===<br />
iRefScape creates multiple edges between nodes to represent multiple evidences. If an interaction between two proteins has evidence from both MINT and IntAct, there will be 2 edges; one for MINT and one for IntAct. Although this provides more information for the user, sometime the user may prefer to collapse these edges to a single edge to facilitate viewing. When this action is performed on a network, all but a randomly selected edge between each node is hidden. The edges which are hidden has the i.flag=1 and the one remaining has i.flag=0. Therefore, while this process is random by default, the user can control which edges to keep and which to hide by editing the i.flag edge attribute before using the '''toggle multi-edge''' option.<br />
<br />
===Zoom to selected===<br />
This action brings the '''selected node(s)''' to the centre of the screen and makes the nodes as large as possible given that all selected nodes are visible. This action can also be performed manually using Cytoscape's zoom tool.<br />
<br />
===Select last iRefScape selection===<br />
This action shows the last selection '''performed by an iRefScape operation'''. This features does not record user selections or selections made by using Cytoscape tools (e.g filters).<br />
<br />
===Select nodes with different taxid than query node===<br />
Some interactions may involve proteins from multiple species. An interaction may truly occur between proteins from two species (e.g. an interaction between a Human protein and a virus protein). In other cases, this may be an artefact of how data was entered by the source database.<br />
<br />
===Select between nodes===<br />
This option highlights (selects) nodes interacting with at least two nodes that have been pre-selected by the user. The node attribute '''i.alive_degree''' will be recalculated to reflect the degree of each node with respect to this pre-selection.<br />
<br />
===Show spoke-represented complexes===<br />
Some complexes are represented as a set of binary interactions by some sources. This action attempts to highlight such complexes as a single unit by attaching them all to a single pseudonode. <br />
<br />
<br />
==Hide/Un-hide==<br />
<br />
===Hide selected nodes===<br />
This action hides the selected nodes. This operation is performed in a independent thread and more efficient than hiding using Cytoscape's 'hide node' utility for large networks.<br />
<br />
===Hide nodes (except pseudonodes)===<br />
This action hides all select nodes which represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Hide nodes not selected===<br />
Hides all nodes which are not currently selected<br />
<br />
===Hide nodes not selected (except pseudonodes)===<br />
Hides all nodes which are not currently selected and that represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Un-hide all===<br />
Un-hides all nodes which are hidden by the user.<br />
<br />
==Safe mode==<br />
This option is only available when using JAVA 1.5 and will not appear for Java 1.6 or newer. Selecting this will un-dock the iRefScape window and handles errors and exceptions thrown due to bugs in JAVA 1.5. When this mode is activated not all graphic features will be available.<br />
<br />
<br />
<br />
<br />
<br />
== All iRefIndex Pages ==<br />
<br />
Follow this link for a listing of all iRefIndex related pages (archived and current).<br />
[[Category:iRefIndex]]</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefScape_plugin_menu&diff=3465iRefScape plugin menu2011-06-08T14:43:29Z<p>Sabry: /* iRefScape user searchable index */</p>
<hr />
<div>==Search tools==<br />
<br />
===Retrieve interactions for the selected nodes===<br />
To load all protein-protein interactions and complexes involving one or more '''selected nodes'''. This action is the same as performing a iteration=1 search using iRefScape for the selected nodes.<br />
<br />
===Expand one level===<br />
To load all protein-protein interactions and complexes involving at least one of the nodes in the current network. The behaviour is same as performing iteration=1 search using iRefScape for all the nodes. <br />
<br />
===Load interactions between neighbours===<br />
To complete the interactions between the currently loaded nodes. When a search & load operation is performed in iRefScape, the network returned contains all the proteins interacting with the query and the corresponding interactions. This does not return interactions between the neighbours of the query. This operation is the same as performing an iteration=0 search using iRefScape for all the nodes.<br />
This action has no effect for networks for which this operation has already been performed using the option presented at the end of the search.<br />
<br />
===Clear load history (Reload everything next time)===<br />
This will clear the iRefScape cache memory containing currently loaded nodes and edges. IRefScape keeps track of what is loaded to avoid reloading and thus increase efficiency. Therefore, if a search is performed twice,the network will not be re-loaded unless the user has requested that results be shown in a new view or they have selected this menu option. If the user wishes to reload the network then this option has to be used. When using other methods of expanding the network like “Expand one level” iRefScape handles the cache clearing automatically.<br />
<br />
===Reset node degree===<br />
This option resets the i.alive_degree of nodes. i.alive_degree provides how many nodes with a certain attribute type is connected to each node (set using filters). <br />
<br />
==Loading user variables (this section is being edited)==<br />
User variables can be attached to nodes and be browsed using the attribute browser. This file can not be used as a searchable index (can not be used as a search type). please see section XXX for details on searchable indices. <br />
<br />
There are three ways to load own variables for the user. <br />
#Use the Cytoscape attribute loading feature ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual'''])<br />
#Use a use attribute file with iRefScape (described in this section)<br />
#Include the attribute with the batch search file.(described in XXX).<br />
<br />
The iRefScape user attribute loader is provided as a complementing feature to the Cytoscape node attribute loading ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual''']). For most of the attribute loading operations the Cytoscape node attribute loader is sufficient and easier to use. However, when the iRefScape node attribute file is used, this can be used by just using the menu entry XXX. In addition the file will be available for subsequent operations.<br />
<br />
===iRefScape user variable file format===<br />
The first line of the file provides instructions and this line is compulsory.<br />
Example. <br />
#i.rog New_attribute<br />
<br />
<br />
The first line always starts with a hash ("#") and immediately followed by the iReFscape variable name. This iRefScape variable name is used to locate the nodes via the new attribute will be attached. Then a tab is used as a column separator, followed by the name of the user attribute name.This user attribute name should be unique( not already used). In the above example the user attribute to use is the i.rog and the user attribute name is "New_attribute".<br />
<br />
From the second line onwards, the attributes with the mapping attribute are provided.<br />
Example <br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
<br />
The first column provides the iRefScape attribute to use and the second column provides the user attribute. Multiple attributes should be separated with a pipe ("|"). The example line shown would locate the node with i.rog=4399398 and attach the "TENC1|UniProtKB:Q63HR2|" value to it with the attribute name "New_attribute"<br />
<br />
*Each column is separated by a TAB.<br />
*Each line ends with a new line character ("\n")<br />
*The file should be constructed using a plain text editor (e.g. Kate, notepad) and word processing software like Microsoft word should not be used to construct this file.<br />
* The file extension is ".txt"<br />
* Sample file "ONE__EXT__ROG_#Name_5_.iruv" can be found in the iRefScape installation directory (iRefIndex directory)<br />
*The file name should have the format _rog_'''USER_VARIABLE_NAME'''.iruv (The text in bold is supplied by the user. e.g., _rog_myAttribute.iruv ).<br />
<br />
Sample file<br />
#i.rog New_name<br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
452957 GFI1B|UniProtKB:Q5VTD9|<br />
561552 TENC1|UniProtKB:Q63HR2-4|<br />
534065 GFI1B_MOUSE|UniProtKB:O70237|<br />
<br />
==iRefScape search with batch file==<br />
When there are many search queries, it is convenient to construct a batch file and load this to iRefScape. There are 3 type of batch files;<br />
#Simple batch file (recommended for users just wanting to search for a list of things)<br />
#Attribute batch file (Attach additional attributes) <br />
#User index batch file (please refer XXX)<br />
<br />
=== Simple batch file ===<br />
<br />
Example file content:<br />
#geneID:3702<br />
814707<br />
814714<br />
814714<br />
817659<br />
818662<br />
<br />
*The first line starts with a hash ("#") and this line is compulsory.<br />
*Immediately after the hash (no space in between) the iRefScape attribute name should be provided. Please see below for accepted list of identifier with the corresponding label.<br />
<br />
{| {{table}}<br />
| align="center" style="background:#f0f0f0;"|'''Label to use in the batch file'''<br />
| align="center" style="background:#f0f0f0;"|'''Description'''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
|-<br />
| rog||iROGID, the integer reference redundant object group identifier([http://irefindex.uio.no/wiki/Protein_identifier_mapping \'\'\'details of mapper files to locate the iRGOID can be found here)\'\'\']||||||<br />
|-<br />
| geneID||NCBI Gene ID, this is always an integer||||||<br />
|-<br />
| UniProt_Ac||UniProt/KB accession||||||<br />
|-<br />
| RefSeq_Ac||RefSeq Accession||||||<br />
|-<br />
| UniProt_ID||UniProt identifier||||||<br />
|-<br />
| geneSymbol||NCBI Gene symbol||||||<br />
|-<br />
| PMID||PubMed identifier ||||||<br />
|-<br />
| src_intxn_id||Interaction identifiers used by source databases||||||<br />
|-<br />
| omim||OMIM identifier ([http://www.ncbi.nlm.nih.gov/omim \'\'\'OMIM home page\'\'\'])||||||<br />
|-<br />
| digid||diseases group identifier ([http://irefindex.uio.no/wiki/DiG:_Disease_groups \'\'\'DiG home page\'\'\'])||||||<br />
|-<br />
| <br />
|}<br />
<br />
<!--<br />
==Only variables==<br />
Users can load there own variables for proteins which are mapped to a ROGID. The file should follow the format given below;<br />
#Should be a plain text file with exactly two columns and each line ending with a new line character (pressing enter).<br />
#First column should contain the ROGID<br />
#Second column should contain the user attribute/variable. <br />
#The file name should have the format _rog_'''USER_VARIABLE_NAME'''.iruv (The text in bold is supplied by the user. e.g., _rog_myAttribute.iruv ).<br />
<br />
<pre><br />
e.g<br />
#rog USER_VARIABLE<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
q6/pRFyay7gQ6bb2rzvKYgfkeaE9606 2<br />
8sODZSppCsuEgRmhSHp3UjwOf2M9606 3<br />
obze7v7i2yTIIcJjd7laIriNFg89606 4<br />
Ty0OLkmhoUPjUuLQQv5ykN057oM9606 5<br />
4bhW4sEt1YhYwHnHCyDNV3vvThs9606 6<br />
Al8M+JdB4H+QnwITh8KcicdI2x49606 6<br />
rkL/SGL1Enj6KoFkPbbcoJ5vKJE9606 6<br />
<br />
</pre><br />
--><br />
<br />
== Attribute batch file ==<br />
Users can attach additional attributes when performing batch queries (instead of loading the attributes after the search).<br />
<br />
The example shown below attaches an additional index "NOONAN_SYNDROME_TYPE" to the matching nodes.<br />
Example indexable batch file<br />
#geneSymbol:9606:NOONAN_SYNDROME_TYPE<br />
PTPN11 NS1<br />
SHOC2 NS2<br />
KRAS NS3<br />
SOS1 NS4<br />
RAF1 NS5<br />
NRAS NS6<br />
NF1 NFNS<br />
<br />
#The first line is compulsory and contains controlling information. the fist value after the hash ('#') is the iRefindex attribute type to be used(please see xxx for attribute types). The second value is the NCBI taxonomy identifier ([http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ '''NCBI taxonomy browser''']). The third value is the name of the user attribute. All three values are seperated by a colon ":". It is possible to include multiple attributes in the same file. To do this first the attribute name should be defined in the first line and additional columns should be used to include the values. (Please not that if the batch file is also used as the template to construct user searchable index, only one user attribute is allowed in the file)<br />
<br />
== iRefScape user searchable index ==<br />
Users can construct their own indices to be used as search type. The easiest way to include a index is to use the advanced batch file mode. This process will;<br />
#Find the iROGID for the user variable<br />
#Construct searchable index.<br />
<br />
The example shown below constructs an index, where the user can perfume search using the Noonan syndrom type. <br />
Example indexable batch file<br />
#geneSymbol:9606:NOONAN_SYNDROME_TYPE<br />
PTPN11 NS1<br />
SHOC2 NS2<br />
KRAS NS3<br />
SOS1 NS4<br />
RAF1 NS5<br />
NRAS NS6<br />
NF1 NFNS<br />
<br />
#The first line is compulsory and contains controlling information. the fist value after the hash ('#') is the iRefindex attribute type to be used(please see xxx for attribute types). The second value is the NCBI taxonomy identifier ([http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ '''NCBI taxonomy browser''']). The third value is the name of the user attribute. All three values are seperated by a colon ":".<br />
<br />
The data rows should always be two columns, where the columns are separated by a tab. The first value in a data row is the search string (what should be used to search iRefIndex). The values in the first column will appear in the search box at the end of the operation. The second column contains the user attribute. <br />
<br />
*the file name of the batch file should contain the prefix "INDEX_THIS_" to be considered for the indexing.<br />
<br />
Example file name<br />
INDEX_THIS_Sample_batch4.txt<br />
<br />
*The attribute do not appear as a separate attribute, but should instead look in the i.query field.<br />
<br />
==View tools==<br />
<br />
===Toggle selected multi-edges===<br />
iRefScape creates multiple edges between nodes to represent multiple evidences. If an interaction between two proteins has evidence from both MINT and IntAct, there will be 2 edges; one for MINT and one for IntAct. Although this provides more information for the user, sometime the user may prefer to collapse these edges to a single edge to facilitate viewing. When this action is performed on a network, all but a randomly selected edge between each node is hidden. The edges which are hidden has the i.flag=1 and the one remaining has i.flag=0. Therefore, while this process is random by default, the user can control which edges to keep and which to hide by editing the i.flag edge attribute before using the '''toggle multi-edge''' option.<br />
<br />
===Zoom to selected===<br />
This action brings the '''selected node(s)''' to the centre of the screen and makes the nodes as large as possible given that all selected nodes are visible. This action can also be performed manually using Cytoscape's zoom tool.<br />
<br />
===Select last iRefScape selection===<br />
This action shows the last selection '''performed by an iRefScape operation'''. This features does not record user selections or selections made by using Cytoscape tools (e.g filters).<br />
<br />
===Select nodes with different taxid than query node===<br />
Some interactions may involve proteins from multiple species. An interaction may truly occur between proteins from two species (e.g. an interaction between a Human protein and a virus protein). In other cases, this may be an artefact of how data was entered by the source database.<br />
<br />
===Select between nodes===<br />
This option highlights (selects) nodes interacting with at least two nodes that have been pre-selected by the user. The node attribute '''i.alive_degree''' will be recalculated to reflect the degree of each node with respect to this pre-selection.<br />
<br />
===Show spoke-represented complexes===<br />
Some complexes are represented as a set of binary interactions by some sources. This action attempts to highlight such complexes as a single unit by attaching them all to a single pseudonode. <br />
<br />
<br />
==Hide/Un-hide==<br />
<br />
===Hide selected nodes===<br />
This action hides the selected nodes. This operation is performed in a independent thread and more efficient than hiding using Cytoscape's 'hide node' utility for large networks.<br />
<br />
===Hide nodes (except pseudonodes)===<br />
This action hides all select nodes which represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Hide nodes not selected===<br />
Hides all nodes which are not currently selected<br />
<br />
===Hide nodes not selected (except pseudonodes)===<br />
Hides all nodes which are not currently selected and that represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Un-hide all===<br />
Un-hides all nodes which are hidden by the user.<br />
<br />
==Safe mode==<br />
This option is only available when using JAVA 1.5 and will not appear for Java 1.6 or newer. Selecting this will un-dock the iRefScape window and handles errors and exceptions thrown due to bugs in JAVA 1.5. When this mode is activated not all graphic features will be available.<br />
<br />
<br />
<br />
<br />
<br />
== All iRefIndex Pages ==<br />
<br />
Follow this link for a listing of all iRefIndex related pages (archived and current).<br />
[[Category:iRefIndex]]</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefScape_plugin_menu&diff=3464iRefScape plugin menu2011-06-08T14:41:35Z<p>Sabry: /* Attribute batch file */</p>
<hr />
<div>==Search tools==<br />
<br />
===Retrieve interactions for the selected nodes===<br />
To load all protein-protein interactions and complexes involving one or more '''selected nodes'''. This action is the same as performing a iteration=1 search using iRefScape for the selected nodes.<br />
<br />
===Expand one level===<br />
To load all protein-protein interactions and complexes involving at least one of the nodes in the current network. The behaviour is same as performing iteration=1 search using iRefScape for all the nodes. <br />
<br />
===Load interactions between neighbours===<br />
To complete the interactions between the currently loaded nodes. When a search & load operation is performed in iRefScape, the network returned contains all the proteins interacting with the query and the corresponding interactions. This does not return interactions between the neighbours of the query. This operation is the same as performing an iteration=0 search using iRefScape for all the nodes.<br />
This action has no effect for networks for which this operation has already been performed using the option presented at the end of the search.<br />
<br />
===Clear load history (Reload everything next time)===<br />
This will clear the iRefScape cache memory containing currently loaded nodes and edges. IRefScape keeps track of what is loaded to avoid reloading and thus increase efficiency. Therefore, if a search is performed twice,the network will not be re-loaded unless the user has requested that results be shown in a new view or they have selected this menu option. If the user wishes to reload the network then this option has to be used. When using other methods of expanding the network like “Expand one level” iRefScape handles the cache clearing automatically.<br />
<br />
===Reset node degree===<br />
This option resets the i.alive_degree of nodes. i.alive_degree provides how many nodes with a certain attribute type is connected to each node (set using filters). <br />
<br />
==Loading user variables (this section is being edited)==<br />
User variables can be attached to nodes and be browsed using the attribute browser. This file can not be used as a searchable index (can not be used as a search type). please see section XXX for details on searchable indices. <br />
<br />
There are three ways to load own variables for the user. <br />
#Use the Cytoscape attribute loading feature ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual'''])<br />
#Use a use attribute file with iRefScape (described in this section)<br />
#Include the attribute with the batch search file.(described in XXX).<br />
<br />
The iRefScape user attribute loader is provided as a complementing feature to the Cytoscape node attribute loading ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual''']). For most of the attribute loading operations the Cytoscape node attribute loader is sufficient and easier to use. However, when the iRefScape node attribute file is used, this can be used by just using the menu entry XXX. In addition the file will be available for subsequent operations.<br />
<br />
===iRefScape user variable file format===<br />
The first line of the file provides instructions and this line is compulsory.<br />
Example. <br />
#i.rog New_attribute<br />
<br />
<br />
The first line always starts with a hash ("#") and immediately followed by the iReFscape variable name. This iRefScape variable name is used to locate the nodes via the new attribute will be attached. Then a tab is used as a column separator, followed by the name of the user attribute name.This user attribute name should be unique( not already used). In the above example the user attribute to use is the i.rog and the user attribute name is "New_attribute".<br />
<br />
From the second line onwards, the attributes with the mapping attribute are provided.<br />
Example <br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
<br />
The first column provides the iRefScape attribute to use and the second column provides the user attribute. Multiple attributes should be separated with a pipe ("|"). The example line shown would locate the node with i.rog=4399398 and attach the "TENC1|UniProtKB:Q63HR2|" value to it with the attribute name "New_attribute"<br />
<br />
*Each column is separated by a TAB.<br />
*Each line ends with a new line character ("\n")<br />
*The file should be constructed using a plain text editor (e.g. Kate, notepad) and word processing software like Microsoft word should not be used to construct this file.<br />
* The file extension is ".txt"<br />
* Sample file "ONE__EXT__ROG_#Name_5_.iruv" can be found in the iRefScape installation directory (iRefIndex directory)<br />
*The file name should have the format _rog_'''USER_VARIABLE_NAME'''.iruv (The text in bold is supplied by the user. e.g., _rog_myAttribute.iruv ).<br />
<br />
Sample file<br />
#i.rog New_name<br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
452957 GFI1B|UniProtKB:Q5VTD9|<br />
561552 TENC1|UniProtKB:Q63HR2-4|<br />
534065 GFI1B_MOUSE|UniProtKB:O70237|<br />
<br />
==iRefScape search with batch file==<br />
When there are many search queries, it is convenient to construct a batch file and load this to iRefScape. There are 3 type of batch files;<br />
#Simple batch file (recommended for users just wanting to search for a list of things)<br />
#Attribute batch file (Attach additional attributes) <br />
#User index batch file (please refer XXX)<br />
<br />
=== Simple batch file ===<br />
<br />
Example file content:<br />
#geneID:3702<br />
814707<br />
814714<br />
814714<br />
817659<br />
818662<br />
<br />
*The first line starts with a hash ("#") and this line is compulsory.<br />
*Immediately after the hash (no space in between) the iRefScape attribute name should be provided. Please see below for accepted list of identifier with the corresponding label.<br />
<br />
{| {{table}}<br />
| align="center" style="background:#f0f0f0;"|'''Label to use in the batch file'''<br />
| align="center" style="background:#f0f0f0;"|'''Description'''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
|-<br />
| rog||iROGID, the integer reference redundant object group identifier([http://irefindex.uio.no/wiki/Protein_identifier_mapping \'\'\'details of mapper files to locate the iRGOID can be found here)\'\'\']||||||<br />
|-<br />
| geneID||NCBI Gene ID, this is always an integer||||||<br />
|-<br />
| UniProt_Ac||UniProt/KB accession||||||<br />
|-<br />
| RefSeq_Ac||RefSeq Accession||||||<br />
|-<br />
| UniProt_ID||UniProt identifier||||||<br />
|-<br />
| geneSymbol||NCBI Gene symbol||||||<br />
|-<br />
| PMID||PubMed identifier ||||||<br />
|-<br />
| src_intxn_id||Interaction identifiers used by source databases||||||<br />
|-<br />
| omim||OMIM identifier ([http://www.ncbi.nlm.nih.gov/omim \'\'\'OMIM home page\'\'\'])||||||<br />
|-<br />
| digid||diseases group identifier ([http://irefindex.uio.no/wiki/DiG:_Disease_groups \'\'\'DiG home page\'\'\'])||||||<br />
|-<br />
| <br />
|}<br />
<br />
<!--<br />
==Only variables==<br />
Users can load there own variables for proteins which are mapped to a ROGID. The file should follow the format given below;<br />
#Should be a plain text file with exactly two columns and each line ending with a new line character (pressing enter).<br />
#First column should contain the ROGID<br />
#Second column should contain the user attribute/variable. <br />
#The file name should have the format _rog_'''USER_VARIABLE_NAME'''.iruv (The text in bold is supplied by the user. e.g., _rog_myAttribute.iruv ).<br />
<br />
<pre><br />
e.g<br />
#rog USER_VARIABLE<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
q6/pRFyay7gQ6bb2rzvKYgfkeaE9606 2<br />
8sODZSppCsuEgRmhSHp3UjwOf2M9606 3<br />
obze7v7i2yTIIcJjd7laIriNFg89606 4<br />
Ty0OLkmhoUPjUuLQQv5ykN057oM9606 5<br />
4bhW4sEt1YhYwHnHCyDNV3vvThs9606 6<br />
Al8M+JdB4H+QnwITh8KcicdI2x49606 6<br />
rkL/SGL1Enj6KoFkPbbcoJ5vKJE9606 6<br />
<br />
</pre><br />
--><br />
<br />
== Attribute batch file ==<br />
Users can attach additional attributes when performing batch queries (instead of loading the attributes after the search).<br />
<br />
The example shown below attaches an additional index "NOONAN_SYNDROME_TYPE" to the matching nodes.<br />
Example indexable batch file<br />
#geneSymbol:9606:NOONAN_SYNDROME_TYPE<br />
PTPN11 NS1<br />
SHOC2 NS2<br />
KRAS NS3<br />
SOS1 NS4<br />
RAF1 NS5<br />
NRAS NS6<br />
NF1 NFNS<br />
<br />
#The first line is compulsory and contains controlling information. the fist value after the hash ('#') is the iRefindex attribute type to be used(please see xxx for attribute types). The second value is the NCBI taxonomy identifier ([http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ '''NCBI taxonomy browser''']). The third value is the name of the user attribute. All three values are seperated by a colon ":". It is possible to include multiple attributes in the same file. To do this first the attribute name should be defined in the first line and additional columns should be used to include the values. (Please not that if the batch file is also used as the template to construct user searchable index, only one user attribute is allowed in the file)<br />
<br />
== iRefScape user searchable index ==<br />
Users can construct their own indices to be used as search type. The easiest way to include a index is to use the advanced batch file mode. This process will;<br />
#Find the iROGID for the user variable<br />
#Construct searchable index.<br />
<br />
The example shown below constructs an index, where the user can perfume search using the Noonan syndrom type. <br />
Example indexable batch file<br />
#geneSymbol:9606:NOONAN_SYNDROME_TYPE<br />
PTPN11 NS1<br />
SHOC2 NS2<br />
KRAS NS3<br />
SOS1 NS4<br />
RAF1 NS5<br />
NRAS NS6<br />
NF1 NFNS<br />
<br />
#The first line is compulsory and contains controlling information. the fist value after the hash ('#') is the iRefindex attribute type to be used(please see xxx for attribute types). The second value is the NCBI taxonomy identifier ([http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ '''NCBI taxonomy browser''']). The third value is the name of the user attribute. All three values are seperated by a colon ":".<br />
<br />
The data rows should always be two columns, where the columns are separated by a tab. The first value in a data row is the search string (what should be used to search iRefIndex). The values in the first column will appear in the search box at the end of the operation. The second column contains the user attribute. <br />
<br />
<br />
<br />
The attribute do not appear as a separate attribute, but should instead look in the i.query field.<br />
<br />
==View tools==<br />
<br />
===Toggle selected multi-edges===<br />
iRefScape creates multiple edges between nodes to represent multiple evidences. If an interaction between two proteins has evidence from both MINT and IntAct, there will be 2 edges; one for MINT and one for IntAct. Although this provides more information for the user, sometime the user may prefer to collapse these edges to a single edge to facilitate viewing. When this action is performed on a network, all but a randomly selected edge between each node is hidden. The edges which are hidden has the i.flag=1 and the one remaining has i.flag=0. Therefore, while this process is random by default, the user can control which edges to keep and which to hide by editing the i.flag edge attribute before using the '''toggle multi-edge''' option.<br />
<br />
===Zoom to selected===<br />
This action brings the '''selected node(s)''' to the centre of the screen and makes the nodes as large as possible given that all selected nodes are visible. This action can also be performed manually using Cytoscape's zoom tool.<br />
<br />
===Select last iRefScape selection===<br />
This action shows the last selection '''performed by an iRefScape operation'''. This features does not record user selections or selections made by using Cytoscape tools (e.g filters).<br />
<br />
===Select nodes with different taxid than query node===<br />
Some interactions may involve proteins from multiple species. An interaction may truly occur between proteins from two species (e.g. an interaction between a Human protein and a virus protein). In other cases, this may be an artefact of how data was entered by the source database.<br />
<br />
===Select between nodes===<br />
This option highlights (selects) nodes interacting with at least two nodes that have been pre-selected by the user. The node attribute '''i.alive_degree''' will be recalculated to reflect the degree of each node with respect to this pre-selection.<br />
<br />
===Show spoke-represented complexes===<br />
Some complexes are represented as a set of binary interactions by some sources. This action attempts to highlight such complexes as a single unit by attaching them all to a single pseudonode. <br />
<br />
<br />
==Hide/Un-hide==<br />
<br />
===Hide selected nodes===<br />
This action hides the selected nodes. This operation is performed in a independent thread and more efficient than hiding using Cytoscape's 'hide node' utility for large networks.<br />
<br />
===Hide nodes (except pseudonodes)===<br />
This action hides all select nodes which represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Hide nodes not selected===<br />
Hides all nodes which are not currently selected<br />
<br />
===Hide nodes not selected (except pseudonodes)===<br />
Hides all nodes which are not currently selected and that represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Un-hide all===<br />
Un-hides all nodes which are hidden by the user.<br />
<br />
==Safe mode==<br />
This option is only available when using JAVA 1.5 and will not appear for Java 1.6 or newer. Selecting this will un-dock the iRefScape window and handles errors and exceptions thrown due to bugs in JAVA 1.5. When this mode is activated not all graphic features will be available.<br />
<br />
<br />
<br />
<br />
<br />
== All iRefIndex Pages ==<br />
<br />
Follow this link for a listing of all iRefIndex related pages (archived and current).<br />
[[Category:iRefIndex]]</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefScape_plugin_menu&diff=3463iRefScape plugin menu2011-06-08T14:36:40Z<p>Sabry: /* Simple batch file */</p>
<hr />
<div>==Search tools==<br />
<br />
===Retrieve interactions for the selected nodes===<br />
To load all protein-protein interactions and complexes involving one or more '''selected nodes'''. This action is the same as performing a iteration=1 search using iRefScape for the selected nodes.<br />
<br />
===Expand one level===<br />
To load all protein-protein interactions and complexes involving at least one of the nodes in the current network. The behaviour is same as performing iteration=1 search using iRefScape for all the nodes. <br />
<br />
===Load interactions between neighbours===<br />
To complete the interactions between the currently loaded nodes. When a search & load operation is performed in iRefScape, the network returned contains all the proteins interacting with the query and the corresponding interactions. This does not return interactions between the neighbours of the query. This operation is the same as performing an iteration=0 search using iRefScape for all the nodes.<br />
This action has no effect for networks for which this operation has already been performed using the option presented at the end of the search.<br />
<br />
===Clear load history (Reload everything next time)===<br />
This will clear the iRefScape cache memory containing currently loaded nodes and edges. IRefScape keeps track of what is loaded to avoid reloading and thus increase efficiency. Therefore, if a search is performed twice,the network will not be re-loaded unless the user has requested that results be shown in a new view or they have selected this menu option. If the user wishes to reload the network then this option has to be used. When using other methods of expanding the network like “Expand one level” iRefScape handles the cache clearing automatically.<br />
<br />
===Reset node degree===<br />
This option resets the i.alive_degree of nodes. i.alive_degree provides how many nodes with a certain attribute type is connected to each node (set using filters). <br />
<br />
==Loading user variables (this section is being edited)==<br />
User variables can be attached to nodes and be browsed using the attribute browser. This file can not be used as a searchable index (can not be used as a search type). please see section XXX for details on searchable indices. <br />
<br />
There are three ways to load own variables for the user. <br />
#Use the Cytoscape attribute loading feature ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual'''])<br />
#Use a use attribute file with iRefScape (described in this section)<br />
#Include the attribute with the batch search file.(described in XXX).<br />
<br />
The iRefScape user attribute loader is provided as a complementing feature to the Cytoscape node attribute loading ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual''']). For most of the attribute loading operations the Cytoscape node attribute loader is sufficient and easier to use. However, when the iRefScape node attribute file is used, this can be used by just using the menu entry XXX. In addition the file will be available for subsequent operations.<br />
<br />
===iRefScape user variable file format===<br />
The first line of the file provides instructions and this line is compulsory.<br />
Example. <br />
#i.rog New_attribute<br />
<br />
<br />
The first line always starts with a hash ("#") and immediately followed by the iReFscape variable name. This iRefScape variable name is used to locate the nodes via the new attribute will be attached. Then a tab is used as a column separator, followed by the name of the user attribute name.This user attribute name should be unique( not already used). In the above example the user attribute to use is the i.rog and the user attribute name is "New_attribute".<br />
<br />
From the second line onwards, the attributes with the mapping attribute are provided.<br />
Example <br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
<br />
The first column provides the iRefScape attribute to use and the second column provides the user attribute. Multiple attributes should be separated with a pipe ("|"). The example line shown would locate the node with i.rog=4399398 and attach the "TENC1|UniProtKB:Q63HR2|" value to it with the attribute name "New_attribute"<br />
<br />
*Each column is separated by a TAB.<br />
*Each line ends with a new line character ("\n")<br />
*The file should be constructed using a plain text editor (e.g. Kate, notepad) and word processing software like Microsoft word should not be used to construct this file.<br />
* The file extension is ".txt"<br />
* Sample file "ONE__EXT__ROG_#Name_5_.iruv" can be found in the iRefScape installation directory (iRefIndex directory)<br />
*The file name should have the format _rog_'''USER_VARIABLE_NAME'''.iruv (The text in bold is supplied by the user. e.g., _rog_myAttribute.iruv ).<br />
<br />
Sample file<br />
#i.rog New_name<br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
452957 GFI1B|UniProtKB:Q5VTD9|<br />
561552 TENC1|UniProtKB:Q63HR2-4|<br />
534065 GFI1B_MOUSE|UniProtKB:O70237|<br />
<br />
==iRefScape search with batch file==<br />
When there are many search queries, it is convenient to construct a batch file and load this to iRefScape. There are 3 type of batch files;<br />
#Simple batch file (recommended for users just wanting to search for a list of things)<br />
#Attribute batch file (Attach additional attributes) <br />
#User index batch file (please refer XXX)<br />
<br />
=== Simple batch file ===<br />
<br />
Example file content:<br />
#geneID:3702<br />
814707<br />
814714<br />
814714<br />
817659<br />
818662<br />
<br />
*The first line starts with a hash ("#") and this line is compulsory.<br />
*Immediately after the hash (no space in between) the iRefScape attribute name should be provided. Please see below for accepted list of identifier with the corresponding label.<br />
<br />
{| {{table}}<br />
| align="center" style="background:#f0f0f0;"|'''Label to use in the batch file'''<br />
| align="center" style="background:#f0f0f0;"|'''Description'''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
|-<br />
| rog||iROGID, the integer reference redundant object group identifier([http://irefindex.uio.no/wiki/Protein_identifier_mapping \'\'\'details of mapper files to locate the iRGOID can be found here)\'\'\']||||||<br />
|-<br />
| geneID||NCBI Gene ID, this is always an integer||||||<br />
|-<br />
| UniProt_Ac||UniProt/KB accession||||||<br />
|-<br />
| RefSeq_Ac||RefSeq Accession||||||<br />
|-<br />
| UniProt_ID||UniProt identifier||||||<br />
|-<br />
| geneSymbol||NCBI Gene symbol||||||<br />
|-<br />
| PMID||PubMed identifier ||||||<br />
|-<br />
| src_intxn_id||Interaction identifiers used by source databases||||||<br />
|-<br />
| omim||OMIM identifier ([http://www.ncbi.nlm.nih.gov/omim \'\'\'OMIM home page\'\'\'])||||||<br />
|-<br />
| digid||diseases group identifier ([http://irefindex.uio.no/wiki/DiG:_Disease_groups \'\'\'DiG home page\'\'\'])||||||<br />
|-<br />
| <br />
|}<br />
<br />
<!--<br />
==Only variables==<br />
Users can load there own variables for proteins which are mapped to a ROGID. The file should follow the format given below;<br />
#Should be a plain text file with exactly two columns and each line ending with a new line character (pressing enter).<br />
#First column should contain the ROGID<br />
#Second column should contain the user attribute/variable. <br />
#The file name should have the format _rog_'''USER_VARIABLE_NAME'''.iruv (The text in bold is supplied by the user. e.g., _rog_myAttribute.iruv ).<br />
<br />
<pre><br />
e.g<br />
#rog USER_VARIABLE<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
q6/pRFyay7gQ6bb2rzvKYgfkeaE9606 2<br />
8sODZSppCsuEgRmhSHp3UjwOf2M9606 3<br />
obze7v7i2yTIIcJjd7laIriNFg89606 4<br />
Ty0OLkmhoUPjUuLQQv5ykN057oM9606 5<br />
4bhW4sEt1YhYwHnHCyDNV3vvThs9606 6<br />
Al8M+JdB4H+QnwITh8KcicdI2x49606 6<br />
rkL/SGL1Enj6KoFkPbbcoJ5vKJE9606 6<br />
<br />
</pre><br />
--><br />
<br />
== Attribute batch file ==<br />
<br />
== iRefScape user searchable index ==<br />
Users can construct their own indices to be used as search type. The easiest way to include a index is to use the advanced batch file mode. This process will;<br />
#Find the iROGID for the user variable<br />
#Construct searchable index.<br />
<br />
The example shown below constructs an index, where the user can perfume search using the Noonan syndrom type. <br />
Example indexable batch file<br />
#geneSymbol:9606:NOONAN_SYNDROME_TYPE<br />
PTPN11 NS1<br />
SHOC2 NS2<br />
KRAS NS3<br />
SOS1 NS4<br />
RAF1 NS5<br />
NRAS NS6<br />
NF1 NFNS<br />
<br />
#The first line is compulsory and contains controlling information. the fist value after the hash ('#') is the iRefindex attribute type to be used(please see xxx for attribute types). The second value is the NCBI taxonomy identifier ([http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ '''NCBI taxonomy browser''']). The third value is the name of the user attribute. All three values are seperated by a colon ":".<br />
<br />
The data rows should always be two columns, where the columns are separated by a tab. The first value in a data row is the search string (what should be used to search iRefIndex). The values in the first column will appear in the search box at the end of the operation. The second column contains the user attribute. <br />
<br />
<br />
<br />
The attribute do not appear as a separate attribute, but should instead look in the i.query field.<br />
<br />
==View tools==<br />
<br />
===Toggle selected multi-edges===<br />
iRefScape creates multiple edges between nodes to represent multiple evidences. If an interaction between two proteins has evidence from both MINT and IntAct, there will be 2 edges; one for MINT and one for IntAct. Although this provides more information for the user, sometime the user may prefer to collapse these edges to a single edge to facilitate viewing. When this action is performed on a network, all but a randomly selected edge between each node is hidden. The edges which are hidden has the i.flag=1 and the one remaining has i.flag=0. Therefore, while this process is random by default, the user can control which edges to keep and which to hide by editing the i.flag edge attribute before using the '''toggle multi-edge''' option.<br />
<br />
===Zoom to selected===<br />
This action brings the '''selected node(s)''' to the centre of the screen and makes the nodes as large as possible given that all selected nodes are visible. This action can also be performed manually using Cytoscape's zoom tool.<br />
<br />
===Select last iRefScape selection===<br />
This action shows the last selection '''performed by an iRefScape operation'''. This features does not record user selections or selections made by using Cytoscape tools (e.g filters).<br />
<br />
===Select nodes with different taxid than query node===<br />
Some interactions may involve proteins from multiple species. An interaction may truly occur between proteins from two species (e.g. an interaction between a Human protein and a virus protein). In other cases, this may be an artefact of how data was entered by the source database.<br />
<br />
===Select between nodes===<br />
This option highlights (selects) nodes interacting with at least two nodes that have been pre-selected by the user. The node attribute '''i.alive_degree''' will be recalculated to reflect the degree of each node with respect to this pre-selection.<br />
<br />
===Show spoke-represented complexes===<br />
Some complexes are represented as a set of binary interactions by some sources. This action attempts to highlight such complexes as a single unit by attaching them all to a single pseudonode. <br />
<br />
<br />
==Hide/Un-hide==<br />
<br />
===Hide selected nodes===<br />
This action hides the selected nodes. This operation is performed in a independent thread and more efficient than hiding using Cytoscape's 'hide node' utility for large networks.<br />
<br />
===Hide nodes (except pseudonodes)===<br />
This action hides all select nodes which represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Hide nodes not selected===<br />
Hides all nodes which are not currently selected<br />
<br />
===Hide nodes not selected (except pseudonodes)===<br />
Hides all nodes which are not currently selected and that represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Un-hide all===<br />
Un-hides all nodes which are hidden by the user.<br />
<br />
==Safe mode==<br />
This option is only available when using JAVA 1.5 and will not appear for Java 1.6 or newer. Selecting this will un-dock the iRefScape window and handles errors and exceptions thrown due to bugs in JAVA 1.5. When this mode is activated not all graphic features will be available.<br />
<br />
<br />
<br />
<br />
<br />
== All iRefIndex Pages ==<br />
<br />
Follow this link for a listing of all iRefIndex related pages (archived and current).<br />
[[Category:iRefIndex]]</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefScape_plugin_menu&diff=3462iRefScape plugin menu2011-06-08T14:36:15Z<p>Sabry: /* Attribute batch file */</p>
<hr />
<div>==Search tools==<br />
<br />
===Retrieve interactions for the selected nodes===<br />
To load all protein-protein interactions and complexes involving one or more '''selected nodes'''. This action is the same as performing a iteration=1 search using iRefScape for the selected nodes.<br />
<br />
===Expand one level===<br />
To load all protein-protein interactions and complexes involving at least one of the nodes in the current network. The behaviour is same as performing iteration=1 search using iRefScape for all the nodes. <br />
<br />
===Load interactions between neighbours===<br />
To complete the interactions between the currently loaded nodes. When a search & load operation is performed in iRefScape, the network returned contains all the proteins interacting with the query and the corresponding interactions. This does not return interactions between the neighbours of the query. This operation is the same as performing an iteration=0 search using iRefScape for all the nodes.<br />
This action has no effect for networks for which this operation has already been performed using the option presented at the end of the search.<br />
<br />
===Clear load history (Reload everything next time)===<br />
This will clear the iRefScape cache memory containing currently loaded nodes and edges. IRefScape keeps track of what is loaded to avoid reloading and thus increase efficiency. Therefore, if a search is performed twice,the network will not be re-loaded unless the user has requested that results be shown in a new view or they have selected this menu option. If the user wishes to reload the network then this option has to be used. When using other methods of expanding the network like “Expand one level” iRefScape handles the cache clearing automatically.<br />
<br />
===Reset node degree===<br />
This option resets the i.alive_degree of nodes. i.alive_degree provides how many nodes with a certain attribute type is connected to each node (set using filters). <br />
<br />
==Loading user variables (this section is being edited)==<br />
User variables can be attached to nodes and be browsed using the attribute browser. This file can not be used as a searchable index (can not be used as a search type). please see section XXX for details on searchable indices. <br />
<br />
There are three ways to load own variables for the user. <br />
#Use the Cytoscape attribute loading feature ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual'''])<br />
#Use a use attribute file with iRefScape (described in this section)<br />
#Include the attribute with the batch search file.(described in XXX).<br />
<br />
The iRefScape user attribute loader is provided as a complementing feature to the Cytoscape node attribute loading ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual''']). For most of the attribute loading operations the Cytoscape node attribute loader is sufficient and easier to use. However, when the iRefScape node attribute file is used, this can be used by just using the menu entry XXX. In addition the file will be available for subsequent operations.<br />
<br />
===iRefScape user variable file format===<br />
The first line of the file provides instructions and this line is compulsory.<br />
Example. <br />
#i.rog New_attribute<br />
<br />
<br />
The first line always starts with a hash ("#") and immediately followed by the iReFscape variable name. This iRefScape variable name is used to locate the nodes via the new attribute will be attached. Then a tab is used as a column separator, followed by the name of the user attribute name.This user attribute name should be unique( not already used). In the above example the user attribute to use is the i.rog and the user attribute name is "New_attribute".<br />
<br />
From the second line onwards, the attributes with the mapping attribute are provided.<br />
Example <br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
<br />
The first column provides the iRefScape attribute to use and the second column provides the user attribute. Multiple attributes should be separated with a pipe ("|"). The example line shown would locate the node with i.rog=4399398 and attach the "TENC1|UniProtKB:Q63HR2|" value to it with the attribute name "New_attribute"<br />
<br />
*Each column is separated by a TAB.<br />
*Each line ends with a new line character ("\n")<br />
*The file should be constructed using a plain text editor (e.g. Kate, notepad) and word processing software like Microsoft word should not be used to construct this file.<br />
* The file extension is ".txt"<br />
* Sample file "ONE__EXT__ROG_#Name_5_.iruv" can be found in the iRefScape installation directory (iRefIndex directory)<br />
*The file name should have the format _rog_'''USER_VARIABLE_NAME'''.iruv (The text in bold is supplied by the user. e.g., _rog_myAttribute.iruv ).<br />
<br />
Sample file<br />
#i.rog New_name<br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
452957 GFI1B|UniProtKB:Q5VTD9|<br />
561552 TENC1|UniProtKB:Q63HR2-4|<br />
534065 GFI1B_MOUSE|UniProtKB:O70237|<br />
<br />
==iRefScape search with batch file==<br />
When there are many search queries, it is convenient to construct a batch file and load this to iRefScape. There are 3 type of batch files;<br />
#Simple batch file (recommended for users just wanting to search for a list of things)<br />
#Attribute batch file (Attach additional attributes) <br />
#User index batch file (please refer XXX)<br />
<br />
=== Simple batch file ===<br />
<br />
Example file content:<br />
#geneID:3702<br />
814707<br />
814714<br />
814714<br />
817659<br />
818662<br />
<br />
*The first line starts with a hash ("#") and this line is compulsory.<br />
*Immediately after the hash (no space in between) the iRefScape attribute name should be provided. Please see below for accepted list of identifier with the corresponding label.<br />
<br />
{| {{table}}<br />
| align="center" style="background:#f0f0f0;"|'''Label to use in the batch file'''<br />
| align="center" style="background:#f0f0f0;"|'''Description'''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
|-<br />
| rog||iROGID, the integer reference redundant object group identifier([http://irefindex.uio.no/wiki/Protein_identifier_mapping \'\'\'details of mapper files to locate the iRGOID can be found here)\'\'\']||||||<br />
|-<br />
| geneID||NCBI Gene ID, this is always an integer||||||<br />
|-<br />
| UniProt_Ac||UniProt/KB accession||||||<br />
|-<br />
| RefSeq_Ac||RefSeq Accession||||||<br />
|-<br />
| UniProt_ID||UniProt identifier||||||<br />
|-<br />
| geneSymbol||NCBI Gene symbol||||||<br />
|-<br />
| PMID||PubMed identifier ||||||<br />
|-<br />
| src_intxn_id||Interaction identifiers used by source databases||||||<br />
|-<br />
| omim||OMIM identifier ([http://www.ncbi.nlm.nih.gov/omim \'\'\'OMIM home page\'\'\'])||||||<br />
|-<br />
| digid||diseases group identifier ([http://irefindex.uio.no/wiki/DiG:_Disease_groups \'\'\'DiG home page\'\'\'])||||||<br />
|-<br />
| <br />
|}<br />
<br />
<!--<br />
==Only variables==<br />
Users can load there own variables for proteins which are mapped to a ROGID. The file should follow the format given below;<br />
#Should be a plain text file with exactly two columns and each line ending with a new line character (pressing enter).<br />
#First column should contain the ROGID<br />
#Second column should contain the user attribute/variable. <br />
#The file name should have the format _rog_'''USER_VARIABLE_NAME'''.iruv (The text in bold is supplied by the user. e.g., _rog_myAttribute.iruv ).<br />
<br />
<pre><br />
e.g<br />
#rog USER_VARIABLE<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
q6/pRFyay7gQ6bb2rzvKYgfkeaE9606 2<br />
8sODZSppCsuEgRmhSHp3UjwOf2M9606 3<br />
obze7v7i2yTIIcJjd7laIriNFg89606 4<br />
Ty0OLkmhoUPjUuLQQv5ykN057oM9606 5<br />
4bhW4sEt1YhYwHnHCyDNV3vvThs9606 6<br />
Al8M+JdB4H+QnwITh8KcicdI2x49606 6<br />
rkL/SGL1Enj6KoFkPbbcoJ5vKJE9606 6<br />
<br />
</pre><br />
--><br />
<br />
== iRefScape user searchable index ==<br />
Users can construct their own indices to be used as search type. The easiest way to include a index is to use the advanced batch file mode. This process will;<br />
#Find the iROGID for the user variable<br />
#Construct searchable index.<br />
<br />
The example shown below constructs an index, where the user can perfume search using the Noonan syndrom type. <br />
Example indexable batch file<br />
#geneSymbol:9606:NOONAN_SYNDROME_TYPE<br />
PTPN11 NS1<br />
SHOC2 NS2<br />
KRAS NS3<br />
SOS1 NS4<br />
RAF1 NS5<br />
NRAS NS6<br />
NF1 NFNS<br />
<br />
#The first line is compulsory and contains controlling information. the fist value after the hash ('#') is the iRefindex attribute type to be used(please see xxx for attribute types). The second value is the NCBI taxonomy identifier ([http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ '''NCBI taxonomy browser''']). The third value is the name of the user attribute. All three values are seperated by a colon ":".<br />
<br />
The data rows should always be two columns, where the columns are separated by a tab. The first value in a data row is the search string (what should be used to search iRefIndex). The values in the first column will appear in the search box at the end of the operation. The second column contains the user attribute. <br />
<br />
<br />
<br />
The attribute do not appear as a separate attribute, but should instead look in the i.query field.<br />
<br />
==View tools==<br />
<br />
===Toggle selected multi-edges===<br />
iRefScape creates multiple edges between nodes to represent multiple evidences. If an interaction between two proteins has evidence from both MINT and IntAct, there will be 2 edges; one for MINT and one for IntAct. Although this provides more information for the user, sometime the user may prefer to collapse these edges to a single edge to facilitate viewing. When this action is performed on a network, all but a randomly selected edge between each node is hidden. The edges which are hidden has the i.flag=1 and the one remaining has i.flag=0. Therefore, while this process is random by default, the user can control which edges to keep and which to hide by editing the i.flag edge attribute before using the '''toggle multi-edge''' option.<br />
<br />
===Zoom to selected===<br />
This action brings the '''selected node(s)''' to the centre of the screen and makes the nodes as large as possible given that all selected nodes are visible. This action can also be performed manually using Cytoscape's zoom tool.<br />
<br />
===Select last iRefScape selection===<br />
This action shows the last selection '''performed by an iRefScape operation'''. This features does not record user selections or selections made by using Cytoscape tools (e.g filters).<br />
<br />
===Select nodes with different taxid than query node===<br />
Some interactions may involve proteins from multiple species. An interaction may truly occur between proteins from two species (e.g. an interaction between a Human protein and a virus protein). In other cases, this may be an artefact of how data was entered by the source database.<br />
<br />
===Select between nodes===<br />
This option highlights (selects) nodes interacting with at least two nodes that have been pre-selected by the user. The node attribute '''i.alive_degree''' will be recalculated to reflect the degree of each node with respect to this pre-selection.<br />
<br />
===Show spoke-represented complexes===<br />
Some complexes are represented as a set of binary interactions by some sources. This action attempts to highlight such complexes as a single unit by attaching them all to a single pseudonode. <br />
<br />
<br />
==Hide/Un-hide==<br />
<br />
===Hide selected nodes===<br />
This action hides the selected nodes. This operation is performed in a independent thread and more efficient than hiding using Cytoscape's 'hide node' utility for large networks.<br />
<br />
===Hide nodes (except pseudonodes)===<br />
This action hides all select nodes which represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Hide nodes not selected===<br />
Hides all nodes which are not currently selected<br />
<br />
===Hide nodes not selected (except pseudonodes)===<br />
Hides all nodes which are not currently selected and that represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Un-hide all===<br />
Un-hides all nodes which are hidden by the user.<br />
<br />
==Safe mode==<br />
This option is only available when using JAVA 1.5 and will not appear for Java 1.6 or newer. Selecting this will un-dock the iRefScape window and handles errors and exceptions thrown due to bugs in JAVA 1.5. When this mode is activated not all graphic features will be available.<br />
<br />
<br />
<br />
<br />
<br />
== All iRefIndex Pages ==<br />
<br />
Follow this link for a listing of all iRefIndex related pages (archived and current).<br />
[[Category:iRefIndex]]</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefScape_plugin_menu&diff=3461iRefScape plugin menu2011-06-08T14:35:56Z<p>Sabry: /* iRefScape search with batch file */</p>
<hr />
<div>==Search tools==<br />
<br />
===Retrieve interactions for the selected nodes===<br />
To load all protein-protein interactions and complexes involving one or more '''selected nodes'''. This action is the same as performing a iteration=1 search using iRefScape for the selected nodes.<br />
<br />
===Expand one level===<br />
To load all protein-protein interactions and complexes involving at least one of the nodes in the current network. The behaviour is same as performing iteration=1 search using iRefScape for all the nodes. <br />
<br />
===Load interactions between neighbours===<br />
To complete the interactions between the currently loaded nodes. When a search & load operation is performed in iRefScape, the network returned contains all the proteins interacting with the query and the corresponding interactions. This does not return interactions between the neighbours of the query. This operation is the same as performing an iteration=0 search using iRefScape for all the nodes.<br />
This action has no effect for networks for which this operation has already been performed using the option presented at the end of the search.<br />
<br />
===Clear load history (Reload everything next time)===<br />
This will clear the iRefScape cache memory containing currently loaded nodes and edges. IRefScape keeps track of what is loaded to avoid reloading and thus increase efficiency. Therefore, if a search is performed twice,the network will not be re-loaded unless the user has requested that results be shown in a new view or they have selected this menu option. If the user wishes to reload the network then this option has to be used. When using other methods of expanding the network like “Expand one level” iRefScape handles the cache clearing automatically.<br />
<br />
===Reset node degree===<br />
This option resets the i.alive_degree of nodes. i.alive_degree provides how many nodes with a certain attribute type is connected to each node (set using filters). <br />
<br />
==Loading user variables (this section is being edited)==<br />
User variables can be attached to nodes and be browsed using the attribute browser. This file can not be used as a searchable index (can not be used as a search type). please see section XXX for details on searchable indices. <br />
<br />
There are three ways to load own variables for the user. <br />
#Use the Cytoscape attribute loading feature ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual'''])<br />
#Use a use attribute file with iRefScape (described in this section)<br />
#Include the attribute with the batch search file.(described in XXX).<br />
<br />
The iRefScape user attribute loader is provided as a complementing feature to the Cytoscape node attribute loading ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual''']). For most of the attribute loading operations the Cytoscape node attribute loader is sufficient and easier to use. However, when the iRefScape node attribute file is used, this can be used by just using the menu entry XXX. In addition the file will be available for subsequent operations.<br />
<br />
===iRefScape user variable file format===<br />
The first line of the file provides instructions and this line is compulsory.<br />
Example. <br />
#i.rog New_attribute<br />
<br />
<br />
The first line always starts with a hash ("#") and immediately followed by the iReFscape variable name. This iRefScape variable name is used to locate the nodes via the new attribute will be attached. Then a tab is used as a column separator, followed by the name of the user attribute name.This user attribute name should be unique( not already used). In the above example the user attribute to use is the i.rog and the user attribute name is "New_attribute".<br />
<br />
From the second line onwards, the attributes with the mapping attribute are provided.<br />
Example <br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
<br />
The first column provides the iRefScape attribute to use and the second column provides the user attribute. Multiple attributes should be separated with a pipe ("|"). The example line shown would locate the node with i.rog=4399398 and attach the "TENC1|UniProtKB:Q63HR2|" value to it with the attribute name "New_attribute"<br />
<br />
*Each column is separated by a TAB.<br />
*Each line ends with a new line character ("\n")<br />
*The file should be constructed using a plain text editor (e.g. Kate, notepad) and word processing software like Microsoft word should not be used to construct this file.<br />
* The file extension is ".txt"<br />
* Sample file "ONE__EXT__ROG_#Name_5_.iruv" can be found in the iRefScape installation directory (iRefIndex directory)<br />
*The file name should have the format _rog_'''USER_VARIABLE_NAME'''.iruv (The text in bold is supplied by the user. e.g., _rog_myAttribute.iruv ).<br />
<br />
Sample file<br />
#i.rog New_name<br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
452957 GFI1B|UniProtKB:Q5VTD9|<br />
561552 TENC1|UniProtKB:Q63HR2-4|<br />
534065 GFI1B_MOUSE|UniProtKB:O70237|<br />
<br />
==iRefScape search with batch file==<br />
When there are many search queries, it is convenient to construct a batch file and load this to iRefScape. There are 3 type of batch files;<br />
#Simple batch file (recommended for users just wanting to search for a list of things)<br />
#Attribute batch file (Attach additional attributes) <br />
#User index batch file (please refer XXX)<br />
<br />
=== Simple batch file ===<br />
<br />
Example file content:<br />
#geneID:3702<br />
814707<br />
814714<br />
814714<br />
817659<br />
818662<br />
<br />
*The first line starts with a hash ("#") and this line is compulsory.<br />
*Immediately after the hash (no space in between) the iRefScape attribute name should be provided. Please see below for accepted list of identifier with the corresponding label.<br />
<br />
{| {{table}}<br />
| align="center" style="background:#f0f0f0;"|'''Label to use in the batch file'''<br />
| align="center" style="background:#f0f0f0;"|'''Description'''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
|-<br />
| rog||iROGID, the integer reference redundant object group identifier([http://irefindex.uio.no/wiki/Protein_identifier_mapping \'\'\'details of mapper files to locate the iRGOID can be found here)\'\'\']||||||<br />
|-<br />
| geneID||NCBI Gene ID, this is always an integer||||||<br />
|-<br />
| UniProt_Ac||UniProt/KB accession||||||<br />
|-<br />
| RefSeq_Ac||RefSeq Accession||||||<br />
|-<br />
| UniProt_ID||UniProt identifier||||||<br />
|-<br />
| geneSymbol||NCBI Gene symbol||||||<br />
|-<br />
| PMID||PubMed identifier ||||||<br />
|-<br />
| src_intxn_id||Interaction identifiers used by source databases||||||<br />
|-<br />
| omim||OMIM identifier ([http://www.ncbi.nlm.nih.gov/omim \'\'\'OMIM home page\'\'\'])||||||<br />
|-<br />
| digid||diseases group identifier ([http://irefindex.uio.no/wiki/DiG:_Disease_groups \'\'\'DiG home page\'\'\'])||||||<br />
|-<br />
| <br />
|}<br />
<br />
<!--<br />
==Only variables==<br />
Users can load there own variables for proteins which are mapped to a ROGID. The file should follow the format given below;<br />
#Should be a plain text file with exactly two columns and each line ending with a new line character (pressing enter).<br />
#First column should contain the ROGID<br />
#Second column should contain the user attribute/variable. <br />
#The file name should have the format _rog_'''USER_VARIABLE_NAME'''.iruv (The text in bold is supplied by the user. e.g., _rog_myAttribute.iruv ).<br />
<br />
<pre><br />
e.g<br />
#rog USER_VARIABLE<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
q6/pRFyay7gQ6bb2rzvKYgfkeaE9606 2<br />
8sODZSppCsuEgRmhSHp3UjwOf2M9606 3<br />
obze7v7i2yTIIcJjd7laIriNFg89606 4<br />
Ty0OLkmhoUPjUuLQQv5ykN057oM9606 5<br />
4bhW4sEt1YhYwHnHCyDNV3vvThs9606 6<br />
Al8M+JdB4H+QnwITh8KcicdI2x49606 6<br />
rkL/SGL1Enj6KoFkPbbcoJ5vKJE9606 6<br />
<br />
</pre><br />
--><br />
<br />
== Attribute batch file ==<br />
<br />
== iRefScape user searchable index ==<br />
Users can construct their own indices to be used as search type. The easiest way to include a index is to use the advanced batch file mode. This process will;<br />
#Find the iROGID for the user variable<br />
#Construct searchable index.<br />
<br />
The example shown below constructs an index, where the user can perfume search using the Noonan syndrom type. <br />
Example indexable batch file<br />
#geneSymbol:9606:NOONAN_SYNDROME_TYPE<br />
PTPN11 NS1<br />
SHOC2 NS2<br />
KRAS NS3<br />
SOS1 NS4<br />
RAF1 NS5<br />
NRAS NS6<br />
NF1 NFNS<br />
<br />
#The first line is compulsory and contains controlling information. the fist value after the hash ('#') is the iRefindex attribute type to be used(please see xxx for attribute types). The second value is the NCBI taxonomy identifier ([http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ '''NCBI taxonomy browser''']). The third value is the name of the user attribute. All three values are seperated by a colon ":".<br />
<br />
The data rows should always be two columns, where the columns are separated by a tab. The first value in a data row is the search string (what should be used to search iRefIndex). The values in the first column will appear in the search box at the end of the operation. The second column contains the user attribute. <br />
<br />
<br />
<br />
The attribute do not appear as a separate attribute, but should instead look in the i.query field.<br />
<br />
==View tools==<br />
<br />
===Toggle selected multi-edges===<br />
iRefScape creates multiple edges between nodes to represent multiple evidences. If an interaction between two proteins has evidence from both MINT and IntAct, there will be 2 edges; one for MINT and one for IntAct. Although this provides more information for the user, sometime the user may prefer to collapse these edges to a single edge to facilitate viewing. When this action is performed on a network, all but a randomly selected edge between each node is hidden. The edges which are hidden has the i.flag=1 and the one remaining has i.flag=0. Therefore, while this process is random by default, the user can control which edges to keep and which to hide by editing the i.flag edge attribute before using the '''toggle multi-edge''' option.<br />
<br />
===Zoom to selected===<br />
This action brings the '''selected node(s)''' to the centre of the screen and makes the nodes as large as possible given that all selected nodes are visible. This action can also be performed manually using Cytoscape's zoom tool.<br />
<br />
===Select last iRefScape selection===<br />
This action shows the last selection '''performed by an iRefScape operation'''. This features does not record user selections or selections made by using Cytoscape tools (e.g filters).<br />
<br />
===Select nodes with different taxid than query node===<br />
Some interactions may involve proteins from multiple species. An interaction may truly occur between proteins from two species (e.g. an interaction between a Human protein and a virus protein). In other cases, this may be an artefact of how data was entered by the source database.<br />
<br />
===Select between nodes===<br />
This option highlights (selects) nodes interacting with at least two nodes that have been pre-selected by the user. The node attribute '''i.alive_degree''' will be recalculated to reflect the degree of each node with respect to this pre-selection.<br />
<br />
===Show spoke-represented complexes===<br />
Some complexes are represented as a set of binary interactions by some sources. This action attempts to highlight such complexes as a single unit by attaching them all to a single pseudonode. <br />
<br />
<br />
==Hide/Un-hide==<br />
<br />
===Hide selected nodes===<br />
This action hides the selected nodes. This operation is performed in a independent thread and more efficient than hiding using Cytoscape's 'hide node' utility for large networks.<br />
<br />
===Hide nodes (except pseudonodes)===<br />
This action hides all select nodes which represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Hide nodes not selected===<br />
Hides all nodes which are not currently selected<br />
<br />
===Hide nodes not selected (except pseudonodes)===<br />
Hides all nodes which are not currently selected and that represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Un-hide all===<br />
Un-hides all nodes which are hidden by the user.<br />
<br />
==Safe mode==<br />
This option is only available when using JAVA 1.5 and will not appear for Java 1.6 or newer. Selecting this will un-dock the iRefScape window and handles errors and exceptions thrown due to bugs in JAVA 1.5. When this mode is activated not all graphic features will be available.<br />
<br />
<br />
<br />
<br />
<br />
== All iRefIndex Pages ==<br />
<br />
Follow this link for a listing of all iRefIndex related pages (archived and current).<br />
[[Category:iRefIndex]]</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefScape_plugin_menu&diff=3460iRefScape plugin menu2011-06-08T14:34:33Z<p>Sabry: /* iReFscape user searchable index */</p>
<hr />
<div>==Search tools==<br />
<br />
===Retrieve interactions for the selected nodes===<br />
To load all protein-protein interactions and complexes involving one or more '''selected nodes'''. This action is the same as performing a iteration=1 search using iRefScape for the selected nodes.<br />
<br />
===Expand one level===<br />
To load all protein-protein interactions and complexes involving at least one of the nodes in the current network. The behaviour is same as performing iteration=1 search using iRefScape for all the nodes. <br />
<br />
===Load interactions between neighbours===<br />
To complete the interactions between the currently loaded nodes. When a search & load operation is performed in iRefScape, the network returned contains all the proteins interacting with the query and the corresponding interactions. This does not return interactions between the neighbours of the query. This operation is the same as performing an iteration=0 search using iRefScape for all the nodes.<br />
This action has no effect for networks for which this operation has already been performed using the option presented at the end of the search.<br />
<br />
===Clear load history (Reload everything next time)===<br />
This will clear the iRefScape cache memory containing currently loaded nodes and edges. IRefScape keeps track of what is loaded to avoid reloading and thus increase efficiency. Therefore, if a search is performed twice,the network will not be re-loaded unless the user has requested that results be shown in a new view or they have selected this menu option. If the user wishes to reload the network then this option has to be used. When using other methods of expanding the network like “Expand one level” iRefScape handles the cache clearing automatically.<br />
<br />
===Reset node degree===<br />
This option resets the i.alive_degree of nodes. i.alive_degree provides how many nodes with a certain attribute type is connected to each node (set using filters). <br />
<br />
==Loading user variables (this section is being edited)==<br />
User variables can be attached to nodes and be browsed using the attribute browser. This file can not be used as a searchable index (can not be used as a search type). please see section XXX for details on searchable indices. <br />
<br />
There are three ways to load own variables for the user. <br />
#Use the Cytoscape attribute loading feature ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual'''])<br />
#Use a use attribute file with iRefScape (described in this section)<br />
#Include the attribute with the batch search file.(described in XXX).<br />
<br />
The iRefScape user attribute loader is provided as a complementing feature to the Cytoscape node attribute loading ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual''']). For most of the attribute loading operations the Cytoscape node attribute loader is sufficient and easier to use. However, when the iRefScape node attribute file is used, this can be used by just using the menu entry XXX. In addition the file will be available for subsequent operations.<br />
<br />
===iRefScape user variable file format===<br />
The first line of the file provides instructions and this line is compulsory.<br />
Example. <br />
#i.rog New_attribute<br />
<br />
<br />
The first line always starts with a hash ("#") and immediately followed by the iReFscape variable name. This iRefScape variable name is used to locate the nodes via the new attribute will be attached. Then a tab is used as a column separator, followed by the name of the user attribute name.This user attribute name should be unique( not already used). In the above example the user attribute to use is the i.rog and the user attribute name is "New_attribute".<br />
<br />
From the second line onwards, the attributes with the mapping attribute are provided.<br />
Example <br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
<br />
The first column provides the iRefScape attribute to use and the second column provides the user attribute. Multiple attributes should be separated with a pipe ("|"). The example line shown would locate the node with i.rog=4399398 and attach the "TENC1|UniProtKB:Q63HR2|" value to it with the attribute name "New_attribute"<br />
<br />
*Each column is separated by a TAB.<br />
*Each line ends with a new line character ("\n")<br />
*The file should be constructed using a plain text editor (e.g. Kate, notepad) and word processing software like Microsoft word should not be used to construct this file.<br />
* The file extension is ".txt"<br />
* Sample file "ONE__EXT__ROG_#Name_5_.iruv" can be found in the iRefScape installation directory (iRefIndex directory)<br />
*The file name should have the format _rog_'''USER_VARIABLE_NAME'''.iruv (The text in bold is supplied by the user. e.g., _rog_myAttribute.iruv ).<br />
<br />
Sample file<br />
#i.rog New_name<br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
452957 GFI1B|UniProtKB:Q5VTD9|<br />
561552 TENC1|UniProtKB:Q63HR2-4|<br />
534065 GFI1B_MOUSE|UniProtKB:O70237|<br />
<br />
==iRefScape search with batch file==<br />
When there are many search queries, it is convenient to construct a batch file and load this to iRefScape. There are 3 type of batch files;<br />
#Simple batch file (recommended for users just wanting to search for a list of things)<br />
#Attribute batch file (Attach additional attributes) <br />
#User index batch file (please refer XXX)<br />
<br />
=== Simple batch file ===<br />
<br />
Example file content:<br />
#geneID:3702<br />
814707<br />
814714<br />
814714<br />
817659<br />
818662<br />
<br />
*The first line starts with a hash ("#") and this line is compulsory.<br />
*Immediately after the hash (no space in between) the iRefScape attribute name should be provided. Please see below for accepted list of identifier with the corresponding label.<br />
<br />
{| {{table}}<br />
| align="center" style="background:#f0f0f0;"|'''Label to use in the batch file'''<br />
| align="center" style="background:#f0f0f0;"|'''Description'''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
|-<br />
| rog||iROGID, the integer reference redundant object group identifier([http://irefindex.uio.no/wiki/Protein_identifier_mapping \'\'\'details of mapper files to locate the iRGOID can be found here)\'\'\']||||||<br />
|-<br />
| geneID||NCBI Gene ID, this is always an integer||||||<br />
|-<br />
| UniProt_Ac||UniProt/KB accession||||||<br />
|-<br />
| RefSeq_Ac||RefSeq Accession||||||<br />
|-<br />
| UniProt_ID||UniProt identifier||||||<br />
|-<br />
| geneSymbol||NCBI Gene symbol||||||<br />
|-<br />
| PMID||PubMed identifier ||||||<br />
|-<br />
| src_intxn_id||Interaction identifiers used by source databases||||||<br />
|-<br />
| omim||OMIM identifier ([http://www.ncbi.nlm.nih.gov/omim \'\'\'OMIM home page\'\'\'])||||||<br />
|-<br />
| digid||diseases group identifier ([http://irefindex.uio.no/wiki/DiG:_Disease_groups \'\'\'DiG home page\'\'\'])||||||<br />
|-<br />
| <br />
|}<br />
<br />
<!--<br />
==Only variables==<br />
Users can load there own variables for proteins which are mapped to a ROGID. The file should follow the format given below;<br />
#Should be a plain text file with exactly two columns and each line ending with a new line character (pressing enter).<br />
#First column should contain the ROGID<br />
#Second column should contain the user attribute/variable. <br />
#The file name should have the format _rog_'''USER_VARIABLE_NAME'''.iruv (The text in bold is supplied by the user. e.g., _rog_myAttribute.iruv ).<br />
<br />
<pre><br />
e.g<br />
#rog USER_VARIABLE<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
q6/pRFyay7gQ6bb2rzvKYgfkeaE9606 2<br />
8sODZSppCsuEgRmhSHp3UjwOf2M9606 3<br />
obze7v7i2yTIIcJjd7laIriNFg89606 4<br />
Ty0OLkmhoUPjUuLQQv5ykN057oM9606 5<br />
4bhW4sEt1YhYwHnHCyDNV3vvThs9606 6<br />
Al8M+JdB4H+QnwITh8KcicdI2x49606 6<br />
rkL/SGL1Enj6KoFkPbbcoJ5vKJE9606 6<br />
<br />
</pre><br />
--><br />
<br />
== iRefScape user searchable index ==<br />
Users can construct their own indices to be used as search type. The easiest way to include a index is to use the advanced batch file mode. This process will;<br />
#Find the iROGID for the user variable<br />
#Construct searchable index.<br />
<br />
The example shown below constructs an index, where the user can perfume search using the Noonan syndrom type. <br />
Example indexable batch file<br />
#geneSymbol:9606:NOONAN_SYNDROME_TYPE<br />
PTPN11 NS1<br />
SHOC2 NS2<br />
KRAS NS3<br />
SOS1 NS4<br />
RAF1 NS5<br />
NRAS NS6<br />
NF1 NFNS<br />
<br />
#The first line is compulsory and contains controlling information. the fist value after the hash ('#') is the iRefindex attribute type to be used(please see xxx for attribute types). The second value is the NCBI taxonomy identifier ([http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ '''NCBI taxonomy browser''']). The third value is the name of the user attribute. All three values are seperated by a colon ":".<br />
<br />
The data rows should always be two columns, where the columns are separated by a tab. The first value in a data row is the search string (what should be used to search iRefIndex). The values in the first column will appear in the search box at the end of the operation. The second column contains the user attribute. <br />
<br />
<br />
<br />
The attribute do not appear as a separate attribute, but should instead look in the i.query field.<br />
<br />
==View tools==<br />
<br />
===Toggle selected multi-edges===<br />
iRefScape creates multiple edges between nodes to represent multiple evidences. If an interaction between two proteins has evidence from both MINT and IntAct, there will be 2 edges; one for MINT and one for IntAct. Although this provides more information for the user, sometime the user may prefer to collapse these edges to a single edge to facilitate viewing. When this action is performed on a network, all but a randomly selected edge between each node is hidden. The edges which are hidden has the i.flag=1 and the one remaining has i.flag=0. Therefore, while this process is random by default, the user can control which edges to keep and which to hide by editing the i.flag edge attribute before using the '''toggle multi-edge''' option.<br />
<br />
===Zoom to selected===<br />
This action brings the '''selected node(s)''' to the centre of the screen and makes the nodes as large as possible given that all selected nodes are visible. This action can also be performed manually using Cytoscape's zoom tool.<br />
<br />
===Select last iRefScape selection===<br />
This action shows the last selection '''performed by an iRefScape operation'''. This features does not record user selections or selections made by using Cytoscape tools (e.g filters).<br />
<br />
===Select nodes with different taxid than query node===<br />
Some interactions may involve proteins from multiple species. An interaction may truly occur between proteins from two species (e.g. an interaction between a Human protein and a virus protein). In other cases, this may be an artefact of how data was entered by the source database.<br />
<br />
===Select between nodes===<br />
This option highlights (selects) nodes interacting with at least two nodes that have been pre-selected by the user. The node attribute '''i.alive_degree''' will be recalculated to reflect the degree of each node with respect to this pre-selection.<br />
<br />
===Show spoke-represented complexes===<br />
Some complexes are represented as a set of binary interactions by some sources. This action attempts to highlight such complexes as a single unit by attaching them all to a single pseudonode. <br />
<br />
<br />
==Hide/Un-hide==<br />
<br />
===Hide selected nodes===<br />
This action hides the selected nodes. This operation is performed in a independent thread and more efficient than hiding using Cytoscape's 'hide node' utility for large networks.<br />
<br />
===Hide nodes (except pseudonodes)===<br />
This action hides all select nodes which represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Hide nodes not selected===<br />
Hides all nodes which are not currently selected<br />
<br />
===Hide nodes not selected (except pseudonodes)===<br />
Hides all nodes which are not currently selected and that represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Un-hide all===<br />
Un-hides all nodes which are hidden by the user.<br />
<br />
==Safe mode==<br />
This option is only available when using JAVA 1.5 and will not appear for Java 1.6 or newer. Selecting this will un-dock the iRefScape window and handles errors and exceptions thrown due to bugs in JAVA 1.5. When this mode is activated not all graphic features will be available.<br />
<br />
<br />
<br />
<br />
<br />
== All iRefIndex Pages ==<br />
<br />
Follow this link for a listing of all iRefIndex related pages (archived and current).<br />
[[Category:iRefIndex]]</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefScape_plugin_menu&diff=3459iRefScape plugin menu2011-06-08T14:34:22Z<p>Sabry: /* iRefINdex user searchable index */</p>
<hr />
<div>==Search tools==<br />
<br />
===Retrieve interactions for the selected nodes===<br />
To load all protein-protein interactions and complexes involving one or more '''selected nodes'''. This action is the same as performing a iteration=1 search using iRefScape for the selected nodes.<br />
<br />
===Expand one level===<br />
To load all protein-protein interactions and complexes involving at least one of the nodes in the current network. The behaviour is same as performing iteration=1 search using iRefScape for all the nodes. <br />
<br />
===Load interactions between neighbours===<br />
To complete the interactions between the currently loaded nodes. When a search & load operation is performed in iRefScape, the network returned contains all the proteins interacting with the query and the corresponding interactions. This does not return interactions between the neighbours of the query. This operation is the same as performing an iteration=0 search using iRefScape for all the nodes.<br />
This action has no effect for networks for which this operation has already been performed using the option presented at the end of the search.<br />
<br />
===Clear load history (Reload everything next time)===<br />
This will clear the iRefScape cache memory containing currently loaded nodes and edges. IRefScape keeps track of what is loaded to avoid reloading and thus increase efficiency. Therefore, if a search is performed twice,the network will not be re-loaded unless the user has requested that results be shown in a new view or they have selected this menu option. If the user wishes to reload the network then this option has to be used. When using other methods of expanding the network like “Expand one level” iRefScape handles the cache clearing automatically.<br />
<br />
===Reset node degree===<br />
This option resets the i.alive_degree of nodes. i.alive_degree provides how many nodes with a certain attribute type is connected to each node (set using filters). <br />
<br />
==Loading user variables (this section is being edited)==<br />
User variables can be attached to nodes and be browsed using the attribute browser. This file can not be used as a searchable index (can not be used as a search type). please see section XXX for details on searchable indices. <br />
<br />
There are three ways to load own variables for the user. <br />
#Use the Cytoscape attribute loading feature ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual'''])<br />
#Use a use attribute file with iRefScape (described in this section)<br />
#Include the attribute with the batch search file.(described in XXX).<br />
<br />
The iRefScape user attribute loader is provided as a complementing feature to the Cytoscape node attribute loading ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual''']). For most of the attribute loading operations the Cytoscape node attribute loader is sufficient and easier to use. However, when the iRefScape node attribute file is used, this can be used by just using the menu entry XXX. In addition the file will be available for subsequent operations.<br />
<br />
===iRefScape user variable file format===<br />
The first line of the file provides instructions and this line is compulsory.<br />
Example. <br />
#i.rog New_attribute<br />
<br />
<br />
The first line always starts with a hash ("#") and immediately followed by the iReFscape variable name. This iRefScape variable name is used to locate the nodes via the new attribute will be attached. Then a tab is used as a column separator, followed by the name of the user attribute name.This user attribute name should be unique( not already used). In the above example the user attribute to use is the i.rog and the user attribute name is "New_attribute".<br />
<br />
From the second line onwards, the attributes with the mapping attribute are provided.<br />
Example <br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
<br />
The first column provides the iRefScape attribute to use and the second column provides the user attribute. Multiple attributes should be separated with a pipe ("|"). The example line shown would locate the node with i.rog=4399398 and attach the "TENC1|UniProtKB:Q63HR2|" value to it with the attribute name "New_attribute"<br />
<br />
*Each column is separated by a TAB.<br />
*Each line ends with a new line character ("\n")<br />
*The file should be constructed using a plain text editor (e.g. Kate, notepad) and word processing software like Microsoft word should not be used to construct this file.<br />
* The file extension is ".txt"<br />
* Sample file "ONE__EXT__ROG_#Name_5_.iruv" can be found in the iRefScape installation directory (iRefIndex directory)<br />
*The file name should have the format _rog_'''USER_VARIABLE_NAME'''.iruv (The text in bold is supplied by the user. e.g., _rog_myAttribute.iruv ).<br />
<br />
Sample file<br />
#i.rog New_name<br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
452957 GFI1B|UniProtKB:Q5VTD9|<br />
561552 TENC1|UniProtKB:Q63HR2-4|<br />
534065 GFI1B_MOUSE|UniProtKB:O70237|<br />
<br />
==iRefScape search with batch file==<br />
When there are many search queries, it is convenient to construct a batch file and load this to iRefScape. There are 3 type of batch files;<br />
#Simple batch file (recommended for users just wanting to search for a list of things)<br />
#Attribute batch file (Attach additional attributes) <br />
#User index batch file (please refer XXX)<br />
<br />
=== Simple batch file ===<br />
<br />
Example file content:<br />
#geneID:3702<br />
814707<br />
814714<br />
814714<br />
817659<br />
818662<br />
<br />
*The first line starts with a hash ("#") and this line is compulsory.<br />
*Immediately after the hash (no space in between) the iRefScape attribute name should be provided. Please see below for accepted list of identifier with the corresponding label.<br />
<br />
{| {{table}}<br />
| align="center" style="background:#f0f0f0;"|'''Label to use in the batch file'''<br />
| align="center" style="background:#f0f0f0;"|'''Description'''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
|-<br />
| rog||iROGID, the integer reference redundant object group identifier([http://irefindex.uio.no/wiki/Protein_identifier_mapping \'\'\'details of mapper files to locate the iRGOID can be found here)\'\'\']||||||<br />
|-<br />
| geneID||NCBI Gene ID, this is always an integer||||||<br />
|-<br />
| UniProt_Ac||UniProt/KB accession||||||<br />
|-<br />
| RefSeq_Ac||RefSeq Accession||||||<br />
|-<br />
| UniProt_ID||UniProt identifier||||||<br />
|-<br />
| geneSymbol||NCBI Gene symbol||||||<br />
|-<br />
| PMID||PubMed identifier ||||||<br />
|-<br />
| src_intxn_id||Interaction identifiers used by source databases||||||<br />
|-<br />
| omim||OMIM identifier ([http://www.ncbi.nlm.nih.gov/omim \'\'\'OMIM home page\'\'\'])||||||<br />
|-<br />
| digid||diseases group identifier ([http://irefindex.uio.no/wiki/DiG:_Disease_groups \'\'\'DiG home page\'\'\'])||||||<br />
|-<br />
| <br />
|}<br />
<br />
<!--<br />
==Only variables==<br />
Users can load there own variables for proteins which are mapped to a ROGID. The file should follow the format given below;<br />
#Should be a plain text file with exactly two columns and each line ending with a new line character (pressing enter).<br />
#First column should contain the ROGID<br />
#Second column should contain the user attribute/variable. <br />
#The file name should have the format _rog_'''USER_VARIABLE_NAME'''.iruv (The text in bold is supplied by the user. e.g., _rog_myAttribute.iruv ).<br />
<br />
<pre><br />
e.g<br />
#rog USER_VARIABLE<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
q6/pRFyay7gQ6bb2rzvKYgfkeaE9606 2<br />
8sODZSppCsuEgRmhSHp3UjwOf2M9606 3<br />
obze7v7i2yTIIcJjd7laIriNFg89606 4<br />
Ty0OLkmhoUPjUuLQQv5ykN057oM9606 5<br />
4bhW4sEt1YhYwHnHCyDNV3vvThs9606 6<br />
Al8M+JdB4H+QnwITh8KcicdI2x49606 6<br />
rkL/SGL1Enj6KoFkPbbcoJ5vKJE9606 6<br />
<br />
</pre><br />
--><br />
<br />
== iReFscape user searchable index ==<br />
Users can construct their own indices to be used as search type. The easiest way to include a index is to use the advanced batch file mode. This process will;<br />
#Find the iROGID for the user variable<br />
#Construct searchable index.<br />
<br />
The example shown below constructs an index, where the user can perfume search using the Noonan syndrom type. <br />
Example indexable batch file<br />
#geneSymbol:9606:NOONAN_SYNDROME_TYPE<br />
PTPN11 NS1<br />
SHOC2 NS2<br />
KRAS NS3<br />
SOS1 NS4<br />
RAF1 NS5<br />
NRAS NS6<br />
NF1 NFNS<br />
<br />
#The first line is compulsory and contains controlling information. the fist value after the hash ('#') is the iRefindex attribute type to be used(please see xxx for attribute types). The second value is the NCBI taxonomy identifier ([http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ '''NCBI taxonomy browser''']). The third value is the name of the user attribute. All three values are seperated by a colon ":".<br />
<br />
The data rows should always be two columns, where the columns are separated by a tab. The first value in a data row is the search string (what should be used to search iRefIndex). The values in the first column will appear in the search box at the end of the operation. The second column contains the user attribute. <br />
<br />
<br />
<br />
The attribute do not appear as a separate attribute, but should instead look in the i.query field.<br />
<br />
==View tools==<br />
<br />
===Toggle selected multi-edges===<br />
iRefScape creates multiple edges between nodes to represent multiple evidences. If an interaction between two proteins has evidence from both MINT and IntAct, there will be 2 edges; one for MINT and one for IntAct. Although this provides more information for the user, sometime the user may prefer to collapse these edges to a single edge to facilitate viewing. When this action is performed on a network, all but a randomly selected edge between each node is hidden. The edges which are hidden has the i.flag=1 and the one remaining has i.flag=0. Therefore, while this process is random by default, the user can control which edges to keep and which to hide by editing the i.flag edge attribute before using the '''toggle multi-edge''' option.<br />
<br />
===Zoom to selected===<br />
This action brings the '''selected node(s)''' to the centre of the screen and makes the nodes as large as possible given that all selected nodes are visible. This action can also be performed manually using Cytoscape's zoom tool.<br />
<br />
===Select last iRefScape selection===<br />
This action shows the last selection '''performed by an iRefScape operation'''. This features does not record user selections or selections made by using Cytoscape tools (e.g filters).<br />
<br />
===Select nodes with different taxid than query node===<br />
Some interactions may involve proteins from multiple species. An interaction may truly occur between proteins from two species (e.g. an interaction between a Human protein and a virus protein). In other cases, this may be an artefact of how data was entered by the source database.<br />
<br />
===Select between nodes===<br />
This option highlights (selects) nodes interacting with at least two nodes that have been pre-selected by the user. The node attribute '''i.alive_degree''' will be recalculated to reflect the degree of each node with respect to this pre-selection.<br />
<br />
===Show spoke-represented complexes===<br />
Some complexes are represented as a set of binary interactions by some sources. This action attempts to highlight such complexes as a single unit by attaching them all to a single pseudonode. <br />
<br />
<br />
==Hide/Un-hide==<br />
<br />
===Hide selected nodes===<br />
This action hides the selected nodes. This operation is performed in a independent thread and more efficient than hiding using Cytoscape's 'hide node' utility for large networks.<br />
<br />
===Hide nodes (except pseudonodes)===<br />
This action hides all select nodes which represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Hide nodes not selected===<br />
Hides all nodes which are not currently selected<br />
<br />
===Hide nodes not selected (except pseudonodes)===<br />
Hides all nodes which are not currently selected and that represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Un-hide all===<br />
Un-hides all nodes which are hidden by the user.<br />
<br />
==Safe mode==<br />
This option is only available when using JAVA 1.5 and will not appear for Java 1.6 or newer. Selecting this will un-dock the iRefScape window and handles errors and exceptions thrown due to bugs in JAVA 1.5. When this mode is activated not all graphic features will be available.<br />
<br />
<br />
<br />
<br />
<br />
== All iRefIndex Pages ==<br />
<br />
Follow this link for a listing of all iRefIndex related pages (archived and current).<br />
[[Category:iRefIndex]]</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefScape_plugin_menu&diff=3458iRefScape plugin menu2011-06-08T14:33:38Z<p>Sabry: /* iRefINdex user searchable index */</p>
<hr />
<div>==Search tools==<br />
<br />
===Retrieve interactions for the selected nodes===<br />
To load all protein-protein interactions and complexes involving one or more '''selected nodes'''. This action is the same as performing a iteration=1 search using iRefScape for the selected nodes.<br />
<br />
===Expand one level===<br />
To load all protein-protein interactions and complexes involving at least one of the nodes in the current network. The behaviour is same as performing iteration=1 search using iRefScape for all the nodes. <br />
<br />
===Load interactions between neighbours===<br />
To complete the interactions between the currently loaded nodes. When a search & load operation is performed in iRefScape, the network returned contains all the proteins interacting with the query and the corresponding interactions. This does not return interactions between the neighbours of the query. This operation is the same as performing an iteration=0 search using iRefScape for all the nodes.<br />
This action has no effect for networks for which this operation has already been performed using the option presented at the end of the search.<br />
<br />
===Clear load history (Reload everything next time)===<br />
This will clear the iRefScape cache memory containing currently loaded nodes and edges. IRefScape keeps track of what is loaded to avoid reloading and thus increase efficiency. Therefore, if a search is performed twice,the network will not be re-loaded unless the user has requested that results be shown in a new view or they have selected this menu option. If the user wishes to reload the network then this option has to be used. When using other methods of expanding the network like “Expand one level” iRefScape handles the cache clearing automatically.<br />
<br />
===Reset node degree===<br />
This option resets the i.alive_degree of nodes. i.alive_degree provides how many nodes with a certain attribute type is connected to each node (set using filters). <br />
<br />
==Loading user variables (this section is being edited)==<br />
User variables can be attached to nodes and be browsed using the attribute browser. This file can not be used as a searchable index (can not be used as a search type). please see section XXX for details on searchable indices. <br />
<br />
There are three ways to load own variables for the user. <br />
#Use the Cytoscape attribute loading feature ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual'''])<br />
#Use a use attribute file with iRefScape (described in this section)<br />
#Include the attribute with the batch search file.(described in XXX).<br />
<br />
The iRefScape user attribute loader is provided as a complementing feature to the Cytoscape node attribute loading ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual''']). For most of the attribute loading operations the Cytoscape node attribute loader is sufficient and easier to use. However, when the iRefScape node attribute file is used, this can be used by just using the menu entry XXX. In addition the file will be available for subsequent operations.<br />
<br />
===iRefScape user variable file format===<br />
The first line of the file provides instructions and this line is compulsory.<br />
Example. <br />
#i.rog New_attribute<br />
<br />
<br />
The first line always starts with a hash ("#") and immediately followed by the iReFscape variable name. This iRefScape variable name is used to locate the nodes via the new attribute will be attached. Then a tab is used as a column separator, followed by the name of the user attribute name.This user attribute name should be unique( not already used). In the above example the user attribute to use is the i.rog and the user attribute name is "New_attribute".<br />
<br />
From the second line onwards, the attributes with the mapping attribute are provided.<br />
Example <br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
<br />
The first column provides the iRefScape attribute to use and the second column provides the user attribute. Multiple attributes should be separated with a pipe ("|"). The example line shown would locate the node with i.rog=4399398 and attach the "TENC1|UniProtKB:Q63HR2|" value to it with the attribute name "New_attribute"<br />
<br />
*Each column is separated by a TAB.<br />
*Each line ends with a new line character ("\n")<br />
*The file should be constructed using a plain text editor (e.g. Kate, notepad) and word processing software like Microsoft word should not be used to construct this file.<br />
* The file extension is ".txt"<br />
* Sample file "ONE__EXT__ROG_#Name_5_.iruv" can be found in the iRefScape installation directory (iRefIndex directory)<br />
*The file name should have the format _rog_'''USER_VARIABLE_NAME'''.iruv (The text in bold is supplied by the user. e.g., _rog_myAttribute.iruv ).<br />
<br />
Sample file<br />
#i.rog New_name<br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
452957 GFI1B|UniProtKB:Q5VTD9|<br />
561552 TENC1|UniProtKB:Q63HR2-4|<br />
534065 GFI1B_MOUSE|UniProtKB:O70237|<br />
<br />
==iRefScape search with batch file==<br />
When there are many search queries, it is convenient to construct a batch file and load this to iRefScape. There are 3 type of batch files;<br />
#Simple batch file (recommended for users just wanting to search for a list of things)<br />
#Attribute batch file (Attach additional attributes) <br />
#User index batch file (please refer XXX)<br />
<br />
=== Simple batch file ===<br />
<br />
Example file content:<br />
#geneID:3702<br />
814707<br />
814714<br />
814714<br />
817659<br />
818662<br />
<br />
*The first line starts with a hash ("#") and this line is compulsory.<br />
*Immediately after the hash (no space in between) the iRefScape attribute name should be provided. Please see below for accepted list of identifier with the corresponding label.<br />
<br />
{| {{table}}<br />
| align="center" style="background:#f0f0f0;"|'''Label to use in the batch file'''<br />
| align="center" style="background:#f0f0f0;"|'''Description'''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
|-<br />
| rog||iROGID, the integer reference redundant object group identifier([http://irefindex.uio.no/wiki/Protein_identifier_mapping \'\'\'details of mapper files to locate the iRGOID can be found here)\'\'\']||||||<br />
|-<br />
| geneID||NCBI Gene ID, this is always an integer||||||<br />
|-<br />
| UniProt_Ac||UniProt/KB accession||||||<br />
|-<br />
| RefSeq_Ac||RefSeq Accession||||||<br />
|-<br />
| UniProt_ID||UniProt identifier||||||<br />
|-<br />
| geneSymbol||NCBI Gene symbol||||||<br />
|-<br />
| PMID||PubMed identifier ||||||<br />
|-<br />
| src_intxn_id||Interaction identifiers used by source databases||||||<br />
|-<br />
| omim||OMIM identifier ([http://www.ncbi.nlm.nih.gov/omim \'\'\'OMIM home page\'\'\'])||||||<br />
|-<br />
| digid||diseases group identifier ([http://irefindex.uio.no/wiki/DiG:_Disease_groups \'\'\'DiG home page\'\'\'])||||||<br />
|-<br />
| <br />
|}<br />
<br />
<!--<br />
==Only variables==<br />
Users can load there own variables for proteins which are mapped to a ROGID. The file should follow the format given below;<br />
#Should be a plain text file with exactly two columns and each line ending with a new line character (pressing enter).<br />
#First column should contain the ROGID<br />
#Second column should contain the user attribute/variable. <br />
#The file name should have the format _rog_'''USER_VARIABLE_NAME'''.iruv (The text in bold is supplied by the user. e.g., _rog_myAttribute.iruv ).<br />
<br />
<pre><br />
e.g<br />
#rog USER_VARIABLE<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
q6/pRFyay7gQ6bb2rzvKYgfkeaE9606 2<br />
8sODZSppCsuEgRmhSHp3UjwOf2M9606 3<br />
obze7v7i2yTIIcJjd7laIriNFg89606 4<br />
Ty0OLkmhoUPjUuLQQv5ykN057oM9606 5<br />
4bhW4sEt1YhYwHnHCyDNV3vvThs9606 6<br />
Al8M+JdB4H+QnwITh8KcicdI2x49606 6<br />
rkL/SGL1Enj6KoFkPbbcoJ5vKJE9606 6<br />
<br />
</pre><br />
--><br />
<br />
== iRefINdex user searchable index ==<br />
Users can construct their own indices to be used as search type. The easiest way to include a index is to use the advanced batch file mode. This process will;<br />
#Find the iROGID for the user variable<br />
#Construct searchable index.<br />
<br />
The example shown below constructs an index, where the user can perfume search using the Noonan syndrom type. <br />
Example indexable batch file<br />
#geneSymbol:9606:NOONAN_SYNDROME_TYPE<br />
PTPN11 NS1<br />
SHOC2 NS2<br />
KRAS NS3<br />
SOS1 NS4<br />
RAF1 NS5<br />
NRAS NS6<br />
NF1 NFNS<br />
<br />
#The first line is compulsory and contains controlling information. the fist value after the hash ('#') is the iRefindex attribute type to be used(please see xxx for attribute types). The second value is the NCBI taxonomy identifier ([http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ '''NCBI taxonomy browser''']). The third value is the name of the user attribute. All three values are seperated by a colon ":".<br />
<br />
The data rows should always be two columns, where the columns are separated by a tab. The first value in a data row is the search string (what should be used to search iRefIndex). The values in the first column will appear in the search box at the end of the operation. The second column contains the user attribute. <br />
<br />
<br />
<br />
The attribute do not appear as a separate attribute, but should instead look in the i.query field.<br />
<br />
==View tools==<br />
<br />
===Toggle selected multi-edges===<br />
iRefScape creates multiple edges between nodes to represent multiple evidences. If an interaction between two proteins has evidence from both MINT and IntAct, there will be 2 edges; one for MINT and one for IntAct. Although this provides more information for the user, sometime the user may prefer to collapse these edges to a single edge to facilitate viewing. When this action is performed on a network, all but a randomly selected edge between each node is hidden. The edges which are hidden has the i.flag=1 and the one remaining has i.flag=0. Therefore, while this process is random by default, the user can control which edges to keep and which to hide by editing the i.flag edge attribute before using the '''toggle multi-edge''' option.<br />
<br />
===Zoom to selected===<br />
This action brings the '''selected node(s)''' to the centre of the screen and makes the nodes as large as possible given that all selected nodes are visible. This action can also be performed manually using Cytoscape's zoom tool.<br />
<br />
===Select last iRefScape selection===<br />
This action shows the last selection '''performed by an iRefScape operation'''. This features does not record user selections or selections made by using Cytoscape tools (e.g filters).<br />
<br />
===Select nodes with different taxid than query node===<br />
Some interactions may involve proteins from multiple species. An interaction may truly occur between proteins from two species (e.g. an interaction between a Human protein and a virus protein). In other cases, this may be an artefact of how data was entered by the source database.<br />
<br />
===Select between nodes===<br />
This option highlights (selects) nodes interacting with at least two nodes that have been pre-selected by the user. The node attribute '''i.alive_degree''' will be recalculated to reflect the degree of each node with respect to this pre-selection.<br />
<br />
===Show spoke-represented complexes===<br />
Some complexes are represented as a set of binary interactions by some sources. This action attempts to highlight such complexes as a single unit by attaching them all to a single pseudonode. <br />
<br />
<br />
==Hide/Un-hide==<br />
<br />
===Hide selected nodes===<br />
This action hides the selected nodes. This operation is performed in a independent thread and more efficient than hiding using Cytoscape's 'hide node' utility for large networks.<br />
<br />
===Hide nodes (except pseudonodes)===<br />
This action hides all select nodes which represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Hide nodes not selected===<br />
Hides all nodes which are not currently selected<br />
<br />
===Hide nodes not selected (except pseudonodes)===<br />
Hides all nodes which are not currently selected and that represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Un-hide all===<br />
Un-hides all nodes which are hidden by the user.<br />
<br />
==Safe mode==<br />
This option is only available when using JAVA 1.5 and will not appear for Java 1.6 or newer. Selecting this will un-dock the iRefScape window and handles errors and exceptions thrown due to bugs in JAVA 1.5. When this mode is activated not all graphic features will be available.<br />
<br />
<br />
<br />
<br />
<br />
== All iRefIndex Pages ==<br />
<br />
Follow this link for a listing of all iRefIndex related pages (archived and current).<br />
[[Category:iRefIndex]]</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefScape_plugin_menu&diff=3457iRefScape plugin menu2011-06-08T14:17:09Z<p>Sabry: /* Simple batch file */</p>
<hr />
<div>==Search tools==<br />
<br />
===Retrieve interactions for the selected nodes===<br />
To load all protein-protein interactions and complexes involving one or more '''selected nodes'''. This action is the same as performing a iteration=1 search using iRefScape for the selected nodes.<br />
<br />
===Expand one level===<br />
To load all protein-protein interactions and complexes involving at least one of the nodes in the current network. The behaviour is same as performing iteration=1 search using iRefScape for all the nodes. <br />
<br />
===Load interactions between neighbours===<br />
To complete the interactions between the currently loaded nodes. When a search & load operation is performed in iRefScape, the network returned contains all the proteins interacting with the query and the corresponding interactions. This does not return interactions between the neighbours of the query. This operation is the same as performing an iteration=0 search using iRefScape for all the nodes.<br />
This action has no effect for networks for which this operation has already been performed using the option presented at the end of the search.<br />
<br />
===Clear load history (Reload everything next time)===<br />
This will clear the iRefScape cache memory containing currently loaded nodes and edges. IRefScape keeps track of what is loaded to avoid reloading and thus increase efficiency. Therefore, if a search is performed twice,the network will not be re-loaded unless the user has requested that results be shown in a new view or they have selected this menu option. If the user wishes to reload the network then this option has to be used. When using other methods of expanding the network like “Expand one level” iRefScape handles the cache clearing automatically.<br />
<br />
===Reset node degree===<br />
This option resets the i.alive_degree of nodes. i.alive_degree provides how many nodes with a certain attribute type is connected to each node (set using filters). <br />
<br />
==Loading user variables (this section is being edited)==<br />
User variables can be attached to nodes and be browsed using the attribute browser. This file can not be used as a searchable index (can not be used as a search type). please see section XXX for details on searchable indices. <br />
<br />
There are three ways to load own variables for the user. <br />
#Use the Cytoscape attribute loading feature ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual'''])<br />
#Use a use attribute file with iRefScape (described in this section)<br />
#Include the attribute with the batch search file.(described in XXX).<br />
<br />
The iRefScape user attribute loader is provided as a complementing feature to the Cytoscape node attribute loading ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual''']). For most of the attribute loading operations the Cytoscape node attribute loader is sufficient and easier to use. However, when the iRefScape node attribute file is used, this can be used by just using the menu entry XXX. In addition the file will be available for subsequent operations.<br />
<br />
===iRefScape user variable file format===<br />
The first line of the file provides instructions and this line is compulsory.<br />
Example. <br />
#i.rog New_attribute<br />
<br />
<br />
The first line always starts with a hash ("#") and immediately followed by the iReFscape variable name. This iRefScape variable name is used to locate the nodes via the new attribute will be attached. Then a tab is used as a column separator, followed by the name of the user attribute name.This user attribute name should be unique( not already used). In the above example the user attribute to use is the i.rog and the user attribute name is "New_attribute".<br />
<br />
From the second line onwards, the attributes with the mapping attribute are provided.<br />
Example <br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
<br />
The first column provides the iRefScape attribute to use and the second column provides the user attribute. Multiple attributes should be separated with a pipe ("|"). The example line shown would locate the node with i.rog=4399398 and attach the "TENC1|UniProtKB:Q63HR2|" value to it with the attribute name "New_attribute"<br />
<br />
*Each column is separated by a TAB.<br />
*Each line ends with a new line character ("\n")<br />
*The file should be constructed using a plain text editor (e.g. Kate, notepad) and word processing software like Microsoft word should not be used to construct this file.<br />
* The file extension is ".txt"<br />
* Sample file "ONE__EXT__ROG_#Name_5_.iruv" can be found in the iRefScape installation directory (iRefIndex directory)<br />
*The file name should have the format _rog_'''USER_VARIABLE_NAME'''.iruv (The text in bold is supplied by the user. e.g., _rog_myAttribute.iruv ).<br />
<br />
Sample file<br />
#i.rog New_name<br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
452957 GFI1B|UniProtKB:Q5VTD9|<br />
561552 TENC1|UniProtKB:Q63HR2-4|<br />
534065 GFI1B_MOUSE|UniProtKB:O70237|<br />
<br />
==iRefScape search with batch file==<br />
When there are many search queries, it is convenient to construct a batch file and load this to iRefScape. There are 3 type of batch files;<br />
#Simple batch file (recommended for users just wanting to search for a list of things)<br />
#Attribute batch file (Attach additional attributes) <br />
#User index batch file (please refer XXX)<br />
<br />
=== Simple batch file ===<br />
<br />
Example file content:<br />
#geneID:3702<br />
814707<br />
814714<br />
814714<br />
817659<br />
818662<br />
<br />
*The first line starts with a hash ("#") and this line is compulsory.<br />
*Immediately after the hash (no space in between) the iRefScape attribute name should be provided. Please see below for accepted list of identifier with the corresponding label.<br />
<br />
{| {{table}}<br />
| align="center" style="background:#f0f0f0;"|'''Label to use in the batch file'''<br />
| align="center" style="background:#f0f0f0;"|'''Description'''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
|-<br />
| rog||iROGID, the integer reference redundant object group identifier([http://irefindex.uio.no/wiki/Protein_identifier_mapping \'\'\'details of mapper files to locate the iRGOID can be found here)\'\'\']||||||<br />
|-<br />
| geneID||NCBI Gene ID, this is always an integer||||||<br />
|-<br />
| UniProt_Ac||UniProt/KB accession||||||<br />
|-<br />
| RefSeq_Ac||RefSeq Accession||||||<br />
|-<br />
| UniProt_ID||UniProt identifier||||||<br />
|-<br />
| geneSymbol||NCBI Gene symbol||||||<br />
|-<br />
| PMID||PubMed identifier ||||||<br />
|-<br />
| src_intxn_id||Interaction identifiers used by source databases||||||<br />
|-<br />
| omim||OMIM identifier ([http://www.ncbi.nlm.nih.gov/omim \'\'\'OMIM home page\'\'\'])||||||<br />
|-<br />
| digid||diseases group identifier ([http://irefindex.uio.no/wiki/DiG:_Disease_groups \'\'\'DiG home page\'\'\'])||||||<br />
|-<br />
| <br />
|}<br />
<br />
<!--<br />
==Only variables==<br />
Users can load there own variables for proteins which are mapped to a ROGID. The file should follow the format given below;<br />
#Should be a plain text file with exactly two columns and each line ending with a new line character (pressing enter).<br />
#First column should contain the ROGID<br />
#Second column should contain the user attribute/variable. <br />
#The file name should have the format _rog_'''USER_VARIABLE_NAME'''.iruv (The text in bold is supplied by the user. e.g., _rog_myAttribute.iruv ).<br />
<br />
<pre><br />
e.g<br />
#rog USER_VARIABLE<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
q6/pRFyay7gQ6bb2rzvKYgfkeaE9606 2<br />
8sODZSppCsuEgRmhSHp3UjwOf2M9606 3<br />
obze7v7i2yTIIcJjd7laIriNFg89606 4<br />
Ty0OLkmhoUPjUuLQQv5ykN057oM9606 5<br />
4bhW4sEt1YhYwHnHCyDNV3vvThs9606 6<br />
Al8M+JdB4H+QnwITh8KcicdI2x49606 6<br />
rkL/SGL1Enj6KoFkPbbcoJ5vKJE9606 6<br />
<br />
</pre><br />
--><br />
<br />
== iRefINdex user searchable index ==<br />
<br />
==View tools==<br />
<br />
===Toggle selected multi-edges===<br />
iRefScape creates multiple edges between nodes to represent multiple evidences. If an interaction between two proteins has evidence from both MINT and IntAct, there will be 2 edges; one for MINT and one for IntAct. Although this provides more information for the user, sometime the user may prefer to collapse these edges to a single edge to facilitate viewing. When this action is performed on a network, all but a randomly selected edge between each node is hidden. The edges which are hidden has the i.flag=1 and the one remaining has i.flag=0. Therefore, while this process is random by default, the user can control which edges to keep and which to hide by editing the i.flag edge attribute before using the '''toggle multi-edge''' option.<br />
<br />
===Zoom to selected===<br />
This action brings the '''selected node(s)''' to the centre of the screen and makes the nodes as large as possible given that all selected nodes are visible. This action can also be performed manually using Cytoscape's zoom tool.<br />
<br />
===Select last iRefScape selection===<br />
This action shows the last selection '''performed by an iRefScape operation'''. This features does not record user selections or selections made by using Cytoscape tools (e.g filters).<br />
<br />
===Select nodes with different taxid than query node===<br />
Some interactions may involve proteins from multiple species. An interaction may truly occur between proteins from two species (e.g. an interaction between a Human protein and a virus protein). In other cases, this may be an artefact of how data was entered by the source database.<br />
<br />
===Select between nodes===<br />
This option highlights (selects) nodes interacting with at least two nodes that have been pre-selected by the user. The node attribute '''i.alive_degree''' will be recalculated to reflect the degree of each node with respect to this pre-selection.<br />
<br />
===Show spoke-represented complexes===<br />
Some complexes are represented as a set of binary interactions by some sources. This action attempts to highlight such complexes as a single unit by attaching them all to a single pseudonode. <br />
<br />
<br />
==Hide/Un-hide==<br />
<br />
===Hide selected nodes===<br />
This action hides the selected nodes. This operation is performed in a independent thread and more efficient than hiding using Cytoscape's 'hide node' utility for large networks.<br />
<br />
===Hide nodes (except pseudonodes)===<br />
This action hides all select nodes which represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Hide nodes not selected===<br />
Hides all nodes which are not currently selected<br />
<br />
===Hide nodes not selected (except pseudonodes)===<br />
Hides all nodes which are not currently selected and that represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Un-hide all===<br />
Un-hides all nodes which are hidden by the user.<br />
<br />
==Safe mode==<br />
This option is only available when using JAVA 1.5 and will not appear for Java 1.6 or newer. Selecting this will un-dock the iRefScape window and handles errors and exceptions thrown due to bugs in JAVA 1.5. When this mode is activated not all graphic features will be available.<br />
<br />
<br />
<br />
<br />
<br />
== All iRefIndex Pages ==<br />
<br />
Follow this link for a listing of all iRefIndex related pages (archived and current).<br />
[[Category:iRefIndex]]</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefScape_plugin_menu&diff=3456iRefScape plugin menu2011-06-08T14:01:31Z<p>Sabry: /* iRefScape user variable file format */</p>
<hr />
<div>==Search tools==<br />
<br />
===Retrieve interactions for the selected nodes===<br />
To load all protein-protein interactions and complexes involving one or more '''selected nodes'''. This action is the same as performing a iteration=1 search using iRefScape for the selected nodes.<br />
<br />
===Expand one level===<br />
To load all protein-protein interactions and complexes involving at least one of the nodes in the current network. The behaviour is same as performing iteration=1 search using iRefScape for all the nodes. <br />
<br />
===Load interactions between neighbours===<br />
To complete the interactions between the currently loaded nodes. When a search & load operation is performed in iRefScape, the network returned contains all the proteins interacting with the query and the corresponding interactions. This does not return interactions between the neighbours of the query. This operation is the same as performing an iteration=0 search using iRefScape for all the nodes.<br />
This action has no effect for networks for which this operation has already been performed using the option presented at the end of the search.<br />
<br />
===Clear load history (Reload everything next time)===<br />
This will clear the iRefScape cache memory containing currently loaded nodes and edges. IRefScape keeps track of what is loaded to avoid reloading and thus increase efficiency. Therefore, if a search is performed twice,the network will not be re-loaded unless the user has requested that results be shown in a new view or they have selected this menu option. If the user wishes to reload the network then this option has to be used. When using other methods of expanding the network like “Expand one level” iRefScape handles the cache clearing automatically.<br />
<br />
===Reset node degree===<br />
This option resets the i.alive_degree of nodes. i.alive_degree provides how many nodes with a certain attribute type is connected to each node (set using filters). <br />
<br />
==Loading user variables (this section is being edited)==<br />
User variables can be attached to nodes and be browsed using the attribute browser. This file can not be used as a searchable index (can not be used as a search type). please see section XXX for details on searchable indices. <br />
<br />
There are three ways to load own variables for the user. <br />
#Use the Cytoscape attribute loading feature ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual'''])<br />
#Use a use attribute file with iRefScape (described in this section)<br />
#Include the attribute with the batch search file.(described in XXX).<br />
<br />
The iRefScape user attribute loader is provided as a complementing feature to the Cytoscape node attribute loading ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual''']). For most of the attribute loading operations the Cytoscape node attribute loader is sufficient and easier to use. However, when the iRefScape node attribute file is used, this can be used by just using the menu entry XXX. In addition the file will be available for subsequent operations.<br />
<br />
===iRefScape user variable file format===<br />
The first line of the file provides instructions and this line is compulsory.<br />
Example. <br />
#i.rog New_attribute<br />
<br />
<br />
The first line always starts with a hash ("#") and immediately followed by the iReFscape variable name. This iRefScape variable name is used to locate the nodes via the new attribute will be attached. Then a tab is used as a column separator, followed by the name of the user attribute name.This user attribute name should be unique( not already used). In the above example the user attribute to use is the i.rog and the user attribute name is "New_attribute".<br />
<br />
From the second line onwards, the attributes with the mapping attribute are provided.<br />
Example <br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
<br />
The first column provides the iRefScape attribute to use and the second column provides the user attribute. Multiple attributes should be separated with a pipe ("|"). The example line shown would locate the node with i.rog=4399398 and attach the "TENC1|UniProtKB:Q63HR2|" value to it with the attribute name "New_attribute"<br />
<br />
*Each column is separated by a TAB.<br />
*Each line ends with a new line character ("\n")<br />
*The file should be constructed using a plain text editor (e.g. Kate, notepad) and word processing software like Microsoft word should not be used to construct this file.<br />
* The file extension is ".txt"<br />
* Sample file "ONE__EXT__ROG_#Name_5_.iruv" can be found in the iRefScape installation directory (iRefIndex directory)<br />
*The file name should have the format _rog_'''USER_VARIABLE_NAME'''.iruv (The text in bold is supplied by the user. e.g., _rog_myAttribute.iruv ).<br />
<br />
Sample file<br />
#i.rog New_name<br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
452957 GFI1B|UniProtKB:Q5VTD9|<br />
561552 TENC1|UniProtKB:Q63HR2-4|<br />
534065 GFI1B_MOUSE|UniProtKB:O70237|<br />
<br />
==iRefScape search with batch file==<br />
When there are many search queries, it is convenient to construct a batch file and load this to iRefScape. There are 3 type of batch files;<br />
#Simple batch file (recommended for users just wanting to search for a list of things)<br />
#Attribute batch file (Attach additional attributes) <br />
#User index batch file (please refer XXX)<br />
<br />
=== Simple batch file ===<br />
<br />
Example file content:<br />
#geneID:3702<br />
814707<br />
814714<br />
814714<br />
817659<br />
818662<br />
<br />
*The first line starts with a hash ("#") and this line is compulsory.<br />
*Immediately after the hash (no space in between) the iRefScape attribute name should be provided. Please see below for accepted list of identifier with the corresponding label.<br />
<br />
{| {{table}}<br />
| align="center" style="background:#f0f0f0;"|'''Label to use in the batch file'''<br />
| align="center" style="background:#f0f0f0;"|'''Description'''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
|-<br />
| rog||iROGID, the integer reference redundant object group identifier([http://irefindex.uio.no/wiki/Protein_identifier_mapping \'\'\'details of mapper files to locate the iRGOID can be found here)\'\'\']||||||<br />
|-<br />
| geneID||NCBI Gene ID, this is always an integer||||||<br />
|-<br />
| UniProt_Ac||UniProt/KB accession||||||<br />
|-<br />
| RefSeq_Ac||RefSeq Accession||||||<br />
|-<br />
| UniProt_ID||UniProt identifier||||||<br />
|-<br />
| geneSymbol||NCBI Gene symbol||||||<br />
|-<br />
| PMID||PubMed identifier ||||||<br />
|-<br />
| src_intxn_id||Interaction identifiers used by source databases||||||<br />
|-<br />
| omim||OMIM identifier ([http://www.ncbi.nlm.nih.gov/omim \'\'\'OMIM home page\'\'\'])||||||<br />
|-<br />
| digid||diseases group identifier ([http://irefindex.uio.no/wiki/DiG:_Disease_groups \'\'\'DiG home page\'\'\'])||||||<br />
|-<br />
| <br />
|}<br />
<br />
<!--<br />
==Only variables==<br />
Users can load there own variables for proteins which are mapped to a ROGID. The file should follow the format given below;<br />
#Should be a plain text file with exactly two columns and each line ending with a new line character (pressing enter).<br />
#First column should contain the ROGID<br />
#Second column should contain the user attribute/variable. <br />
#The file name should have the format _rog_'''USER_VARIABLE_NAME'''.iruv (The text in bold is supplied by the user. e.g., _rog_myAttribute.iruv ).<br />
<br />
<pre><br />
e.g<br />
#rog USER_VARIABLE<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
q6/pRFyay7gQ6bb2rzvKYgfkeaE9606 2<br />
8sODZSppCsuEgRmhSHp3UjwOf2M9606 3<br />
obze7v7i2yTIIcJjd7laIriNFg89606 4<br />
Ty0OLkmhoUPjUuLQQv5ykN057oM9606 5<br />
4bhW4sEt1YhYwHnHCyDNV3vvThs9606 6<br />
Al8M+JdB4H+QnwITh8KcicdI2x49606 6<br />
rkL/SGL1Enj6KoFkPbbcoJ5vKJE9606 6<br />
<br />
</pre><br />
--><br />
<br />
==View tools==<br />
<br />
===Toggle selected multi-edges===<br />
iRefScape creates multiple edges between nodes to represent multiple evidences. If an interaction between two proteins has evidence from both MINT and IntAct, there will be 2 edges; one for MINT and one for IntAct. Although this provides more information for the user, sometime the user may prefer to collapse these edges to a single edge to facilitate viewing. When this action is performed on a network, all but a randomly selected edge between each node is hidden. The edges which are hidden has the i.flag=1 and the one remaining has i.flag=0. Therefore, while this process is random by default, the user can control which edges to keep and which to hide by editing the i.flag edge attribute before using the '''toggle multi-edge''' option.<br />
<br />
===Zoom to selected===<br />
This action brings the '''selected node(s)''' to the centre of the screen and makes the nodes as large as possible given that all selected nodes are visible. This action can also be performed manually using Cytoscape's zoom tool.<br />
<br />
===Select last iRefScape selection===<br />
This action shows the last selection '''performed by an iRefScape operation'''. This features does not record user selections or selections made by using Cytoscape tools (e.g filters).<br />
<br />
===Select nodes with different taxid than query node===<br />
Some interactions may involve proteins from multiple species. An interaction may truly occur between proteins from two species (e.g. an interaction between a Human protein and a virus protein). In other cases, this may be an artefact of how data was entered by the source database.<br />
<br />
===Select between nodes===<br />
This option highlights (selects) nodes interacting with at least two nodes that have been pre-selected by the user. The node attribute '''i.alive_degree''' will be recalculated to reflect the degree of each node with respect to this pre-selection.<br />
<br />
===Show spoke-represented complexes===<br />
Some complexes are represented as a set of binary interactions by some sources. This action attempts to highlight such complexes as a single unit by attaching them all to a single pseudonode. <br />
<br />
<br />
==Hide/Un-hide==<br />
<br />
===Hide selected nodes===<br />
This action hides the selected nodes. This operation is performed in a independent thread and more efficient than hiding using Cytoscape's 'hide node' utility for large networks.<br />
<br />
===Hide nodes (except pseudonodes)===<br />
This action hides all select nodes which represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Hide nodes not selected===<br />
Hides all nodes which are not currently selected<br />
<br />
===Hide nodes not selected (except pseudonodes)===<br />
Hides all nodes which are not currently selected and that represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Un-hide all===<br />
Un-hides all nodes which are hidden by the user.<br />
<br />
==Safe mode==<br />
This option is only available when using JAVA 1.5 and will not appear for Java 1.6 or newer. Selecting this will un-dock the iRefScape window and handles errors and exceptions thrown due to bugs in JAVA 1.5. When this mode is activated not all graphic features will be available.<br />
<br />
<br />
<br />
<br />
<br />
== All iRefIndex Pages ==<br />
<br />
Follow this link for a listing of all iRefIndex related pages (archived and current).<br />
[[Category:iRefIndex]]</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefScape_plugin_menu&diff=3455iRefScape plugin menu2011-06-08T14:00:34Z<p>Sabry: /* Only variables */</p>
<hr />
<div>==Search tools==<br />
<br />
===Retrieve interactions for the selected nodes===<br />
To load all protein-protein interactions and complexes involving one or more '''selected nodes'''. This action is the same as performing a iteration=1 search using iRefScape for the selected nodes.<br />
<br />
===Expand one level===<br />
To load all protein-protein interactions and complexes involving at least one of the nodes in the current network. The behaviour is same as performing iteration=1 search using iRefScape for all the nodes. <br />
<br />
===Load interactions between neighbours===<br />
To complete the interactions between the currently loaded nodes. When a search & load operation is performed in iRefScape, the network returned contains all the proteins interacting with the query and the corresponding interactions. This does not return interactions between the neighbours of the query. This operation is the same as performing an iteration=0 search using iRefScape for all the nodes.<br />
This action has no effect for networks for which this operation has already been performed using the option presented at the end of the search.<br />
<br />
===Clear load history (Reload everything next time)===<br />
This will clear the iRefScape cache memory containing currently loaded nodes and edges. IRefScape keeps track of what is loaded to avoid reloading and thus increase efficiency. Therefore, if a search is performed twice,the network will not be re-loaded unless the user has requested that results be shown in a new view or they have selected this menu option. If the user wishes to reload the network then this option has to be used. When using other methods of expanding the network like “Expand one level” iRefScape handles the cache clearing automatically.<br />
<br />
===Reset node degree===<br />
This option resets the i.alive_degree of nodes. i.alive_degree provides how many nodes with a certain attribute type is connected to each node (set using filters). <br />
<br />
==Loading user variables (this section is being edited)==<br />
User variables can be attached to nodes and be browsed using the attribute browser. This file can not be used as a searchable index (can not be used as a search type). please see section XXX for details on searchable indices. <br />
<br />
There are three ways to load own variables for the user. <br />
#Use the Cytoscape attribute loading feature ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual'''])<br />
#Use a use attribute file with iRefScape (described in this section)<br />
#Include the attribute with the batch search file.(described in XXX).<br />
<br />
The iRefScape user attribute loader is provided as a complementing feature to the Cytoscape node attribute loading ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual''']). For most of the attribute loading operations the Cytoscape node attribute loader is sufficient and easier to use. However, when the iRefScape node attribute file is used, this can be used by just using the menu entry XXX. In addition the file will be available for subsequent operations.<br />
<br />
===iRefScape user variable file format===<br />
The first line of the file provides instructions and this line is compulsory.<br />
Example. <br />
#i.rog New_attribute<br />
<br />
<br />
The first line always starts with a hash ("#") and immediately followed by the iReFscape variable name. This iRefScape variable name is used to locate the nodes via the new attribute will be attached. Then a tab is used as a column separator, followed by the name of the user attribute name.This user attribute name should be unique( not already used). In the above example the user attribute to use is the i.rog and the user attribute name is "New_attribute".<br />
<br />
From the second line onwards, the attributes with the mapping attribute are provided.<br />
Example <br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
<br />
The first column provides the iRefScape attribute to use and the second column provides the user attribute. Multiple attributes should be separated with a pipe ("|"). The example line shown would locate the node with i.rog=4399398 and attach the "TENC1|UniProtKB:Q63HR2|" value to it with the attribute name "New_attribute"<br />
<br />
*Each column is separated by a TAB.<br />
*Each line ends with a new line character ("\n")<br />
*The file should be constructed using a plain text editor (e.g. Kate, notepad) and word processing software like Microsoft word should not be used to construct this file.<br />
* The file extension is ".txt"<br />
* Sample file "ONE__EXT__ROG_#Name_5_.iruv" can be found in the iRefScape installation directory (iRefIndex directory)<br />
<br />
<br />
Sample file<br />
#i.rog New_name<br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
452957 GFI1B|UniProtKB:Q5VTD9|<br />
561552 TENC1|UniProtKB:Q63HR2-4|<br />
534065 GFI1B_MOUSE|UniProtKB:O70237|<br />
<br />
==iRefScape search with batch file==<br />
When there are many search queries, it is convenient to construct a batch file and load this to iRefScape. There are 3 type of batch files;<br />
#Simple batch file (recommended for users just wanting to search for a list of things)<br />
#Attribute batch file (Attach additional attributes) <br />
#User index batch file (please refer XXX)<br />
<br />
=== Simple batch file ===<br />
<br />
Example file content:<br />
#geneID:3702<br />
814707<br />
814714<br />
814714<br />
817659<br />
818662<br />
<br />
*The first line starts with a hash ("#") and this line is compulsory.<br />
*Immediately after the hash (no space in between) the iRefScape attribute name should be provided. Please see below for accepted list of identifier with the corresponding label.<br />
<br />
{| {{table}}<br />
| align="center" style="background:#f0f0f0;"|'''Label to use in the batch file'''<br />
| align="center" style="background:#f0f0f0;"|'''Description'''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
|-<br />
| rog||iROGID, the integer reference redundant object group identifier([http://irefindex.uio.no/wiki/Protein_identifier_mapping \'\'\'details of mapper files to locate the iRGOID can be found here)\'\'\']||||||<br />
|-<br />
| geneID||NCBI Gene ID, this is always an integer||||||<br />
|-<br />
| UniProt_Ac||UniProt/KB accession||||||<br />
|-<br />
| RefSeq_Ac||RefSeq Accession||||||<br />
|-<br />
| UniProt_ID||UniProt identifier||||||<br />
|-<br />
| geneSymbol||NCBI Gene symbol||||||<br />
|-<br />
| PMID||PubMed identifier ||||||<br />
|-<br />
| src_intxn_id||Interaction identifiers used by source databases||||||<br />
|-<br />
| omim||OMIM identifier ([http://www.ncbi.nlm.nih.gov/omim \'\'\'OMIM home page\'\'\'])||||||<br />
|-<br />
| digid||diseases group identifier ([http://irefindex.uio.no/wiki/DiG:_Disease_groups \'\'\'DiG home page\'\'\'])||||||<br />
|-<br />
| <br />
|}<br />
<br />
<!--<br />
==Only variables==<br />
Users can load there own variables for proteins which are mapped to a ROGID. The file should follow the format given below;<br />
#Should be a plain text file with exactly two columns and each line ending with a new line character (pressing enter).<br />
#First column should contain the ROGID<br />
#Second column should contain the user attribute/variable. <br />
#The file name should have the format _rog_'''USER_VARIABLE_NAME'''.iruv (The text in bold is supplied by the user. e.g., _rog_myAttribute.iruv ).<br />
<br />
<pre><br />
e.g<br />
#rog USER_VARIABLE<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
q6/pRFyay7gQ6bb2rzvKYgfkeaE9606 2<br />
8sODZSppCsuEgRmhSHp3UjwOf2M9606 3<br />
obze7v7i2yTIIcJjd7laIriNFg89606 4<br />
Ty0OLkmhoUPjUuLQQv5ykN057oM9606 5<br />
4bhW4sEt1YhYwHnHCyDNV3vvThs9606 6<br />
Al8M+JdB4H+QnwITh8KcicdI2x49606 6<br />
rkL/SGL1Enj6KoFkPbbcoJ5vKJE9606 6<br />
<br />
</pre><br />
--><br />
<br />
==View tools==<br />
<br />
===Toggle selected multi-edges===<br />
iRefScape creates multiple edges between nodes to represent multiple evidences. If an interaction between two proteins has evidence from both MINT and IntAct, there will be 2 edges; one for MINT and one for IntAct. Although this provides more information for the user, sometime the user may prefer to collapse these edges to a single edge to facilitate viewing. When this action is performed on a network, all but a randomly selected edge between each node is hidden. The edges which are hidden has the i.flag=1 and the one remaining has i.flag=0. Therefore, while this process is random by default, the user can control which edges to keep and which to hide by editing the i.flag edge attribute before using the '''toggle multi-edge''' option.<br />
<br />
===Zoom to selected===<br />
This action brings the '''selected node(s)''' to the centre of the screen and makes the nodes as large as possible given that all selected nodes are visible. This action can also be performed manually using Cytoscape's zoom tool.<br />
<br />
===Select last iRefScape selection===<br />
This action shows the last selection '''performed by an iRefScape operation'''. This features does not record user selections or selections made by using Cytoscape tools (e.g filters).<br />
<br />
===Select nodes with different taxid than query node===<br />
Some interactions may involve proteins from multiple species. An interaction may truly occur between proteins from two species (e.g. an interaction between a Human protein and a virus protein). In other cases, this may be an artefact of how data was entered by the source database.<br />
<br />
===Select between nodes===<br />
This option highlights (selects) nodes interacting with at least two nodes that have been pre-selected by the user. The node attribute '''i.alive_degree''' will be recalculated to reflect the degree of each node with respect to this pre-selection.<br />
<br />
===Show spoke-represented complexes===<br />
Some complexes are represented as a set of binary interactions by some sources. This action attempts to highlight such complexes as a single unit by attaching them all to a single pseudonode. <br />
<br />
<br />
==Hide/Un-hide==<br />
<br />
===Hide selected nodes===<br />
This action hides the selected nodes. This operation is performed in a independent thread and more efficient than hiding using Cytoscape's 'hide node' utility for large networks.<br />
<br />
===Hide nodes (except pseudonodes)===<br />
This action hides all select nodes which represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Hide nodes not selected===<br />
Hides all nodes which are not currently selected<br />
<br />
===Hide nodes not selected (except pseudonodes)===<br />
Hides all nodes which are not currently selected and that represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Un-hide all===<br />
Un-hides all nodes which are hidden by the user.<br />
<br />
==Safe mode==<br />
This option is only available when using JAVA 1.5 and will not appear for Java 1.6 or newer. Selecting this will un-dock the iRefScape window and handles errors and exceptions thrown due to bugs in JAVA 1.5. When this mode is activated not all graphic features will be available.<br />
<br />
<br />
<br />
<br />
<br />
== All iRefIndex Pages ==<br />
<br />
Follow this link for a listing of all iRefIndex related pages (archived and current).<br />
[[Category:iRefIndex]]</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefScape_plugin_menu&diff=3454iRefScape plugin menu2011-06-08T13:58:44Z<p>Sabry: /* iRefScape search with batch file */</p>
<hr />
<div>==Search tools==<br />
<br />
===Retrieve interactions for the selected nodes===<br />
To load all protein-protein interactions and complexes involving one or more '''selected nodes'''. This action is the same as performing a iteration=1 search using iRefScape for the selected nodes.<br />
<br />
===Expand one level===<br />
To load all protein-protein interactions and complexes involving at least one of the nodes in the current network. The behaviour is same as performing iteration=1 search using iRefScape for all the nodes. <br />
<br />
===Load interactions between neighbours===<br />
To complete the interactions between the currently loaded nodes. When a search & load operation is performed in iRefScape, the network returned contains all the proteins interacting with the query and the corresponding interactions. This does not return interactions between the neighbours of the query. This operation is the same as performing an iteration=0 search using iRefScape for all the nodes.<br />
This action has no effect for networks for which this operation has already been performed using the option presented at the end of the search.<br />
<br />
===Clear load history (Reload everything next time)===<br />
This will clear the iRefScape cache memory containing currently loaded nodes and edges. IRefScape keeps track of what is loaded to avoid reloading and thus increase efficiency. Therefore, if a search is performed twice,the network will not be re-loaded unless the user has requested that results be shown in a new view or they have selected this menu option. If the user wishes to reload the network then this option has to be used. When using other methods of expanding the network like “Expand one level” iRefScape handles the cache clearing automatically.<br />
<br />
===Reset node degree===<br />
This option resets the i.alive_degree of nodes. i.alive_degree provides how many nodes with a certain attribute type is connected to each node (set using filters). <br />
<br />
==Loading user variables (this section is being edited)==<br />
User variables can be attached to nodes and be browsed using the attribute browser. This file can not be used as a searchable index (can not be used as a search type). please see section XXX for details on searchable indices. <br />
<br />
There are three ways to load own variables for the user. <br />
#Use the Cytoscape attribute loading feature ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual'''])<br />
#Use a use attribute file with iRefScape (described in this section)<br />
#Include the attribute with the batch search file.(described in XXX).<br />
<br />
The iRefScape user attribute loader is provided as a complementing feature to the Cytoscape node attribute loading ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual''']). For most of the attribute loading operations the Cytoscape node attribute loader is sufficient and easier to use. However, when the iRefScape node attribute file is used, this can be used by just using the menu entry XXX. In addition the file will be available for subsequent operations.<br />
<br />
===iRefScape user variable file format===<br />
The first line of the file provides instructions and this line is compulsory.<br />
Example. <br />
#i.rog New_attribute<br />
<br />
<br />
The first line always starts with a hash ("#") and immediately followed by the iReFscape variable name. This iRefScape variable name is used to locate the nodes via the new attribute will be attached. Then a tab is used as a column separator, followed by the name of the user attribute name.This user attribute name should be unique( not already used). In the above example the user attribute to use is the i.rog and the user attribute name is "New_attribute".<br />
<br />
From the second line onwards, the attributes with the mapping attribute are provided.<br />
Example <br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
<br />
The first column provides the iRefScape attribute to use and the second column provides the user attribute. Multiple attributes should be separated with a pipe ("|"). The example line shown would locate the node with i.rog=4399398 and attach the "TENC1|UniProtKB:Q63HR2|" value to it with the attribute name "New_attribute"<br />
<br />
*Each column is separated by a TAB.<br />
*Each line ends with a new line character ("\n")<br />
*The file should be constructed using a plain text editor (e.g. Kate, notepad) and word processing software like Microsoft word should not be used to construct this file.<br />
* The file extension is ".txt"<br />
* Sample file "ONE__EXT__ROG_#Name_5_.iruv" can be found in the iRefScape installation directory (iRefIndex directory)<br />
<br />
<br />
Sample file<br />
#i.rog New_name<br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
452957 GFI1B|UniProtKB:Q5VTD9|<br />
561552 TENC1|UniProtKB:Q63HR2-4|<br />
534065 GFI1B_MOUSE|UniProtKB:O70237|<br />
<br />
==iRefScape search with batch file==<br />
When there are many search queries, it is convenient to construct a batch file and load this to iRefScape. There are 3 type of batch files;<br />
#Simple batch file (recommended for users just wanting to search for a list of things)<br />
#Attribute batch file (Attach additional attributes) <br />
#User index batch file (please refer XXX)<br />
<br />
=== Simple batch file ===<br />
<br />
Example file content:<br />
#geneID:3702<br />
814707<br />
814714<br />
814714<br />
817659<br />
818662<br />
<br />
*The first line starts with a hash ("#") and this line is compulsory.<br />
*Immediately after the hash (no space in between) the iRefScape attribute name should be provided. Please see below for accepted list of identifier with the corresponding label.<br />
<br />
{| {{table}}<br />
| align="center" style="background:#f0f0f0;"|'''Label to use in the batch file'''<br />
| align="center" style="background:#f0f0f0;"|'''Description'''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
| align="center" style="background:#f0f0f0;"|''''''<br />
|-<br />
| rog||iROGID, the integer reference redundant object group identifier([http://irefindex.uio.no/wiki/Protein_identifier_mapping \'\'\'details of mapper files to locate the iRGOID can be found here)\'\'\']||||||<br />
|-<br />
| geneID||NCBI Gene ID, this is always an integer||||||<br />
|-<br />
| UniProt_Ac||UniProt/KB accession||||||<br />
|-<br />
| RefSeq_Ac||RefSeq Accession||||||<br />
|-<br />
| UniProt_ID||UniProt identifier||||||<br />
|-<br />
| geneSymbol||NCBI Gene symbol||||||<br />
|-<br />
| PMID||PubMed identifier ||||||<br />
|-<br />
| src_intxn_id||Interaction identifiers used by source databases||||||<br />
|-<br />
| omim||OMIM identifier ([http://www.ncbi.nlm.nih.gov/omim \'\'\'OMIM home page\'\'\'])||||||<br />
|-<br />
| digid||diseases group identifier ([http://irefindex.uio.no/wiki/DiG:_Disease_groups \'\'\'DiG home page\'\'\'])||||||<br />
|-<br />
| <br />
|}<br />
<br />
==Only variables==<br />
Users can load there own variables for proteins which are mapped to a ROGID. The file should follow the format given below;<br />
#Should be a plain text file with exactly two columns and each line ending with a new line character (pressing enter).<br />
#First column should contain the ROGID<br />
#Second column should contain the user attribute/variable. <br />
#The file name should have the format _rog_'''USER_VARIABLE_NAME'''.iruv (The text in bold is supplied by the user. e.g., _rog_myAttribute.iruv ).<br />
<br />
<pre><br />
e.g<br />
#rog USER_VARIABLE<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
q6/pRFyay7gQ6bb2rzvKYgfkeaE9606 2<br />
8sODZSppCsuEgRmhSHp3UjwOf2M9606 3<br />
obze7v7i2yTIIcJjd7laIriNFg89606 4<br />
Ty0OLkmhoUPjUuLQQv5ykN057oM9606 5<br />
4bhW4sEt1YhYwHnHCyDNV3vvThs9606 6<br />
Al8M+JdB4H+QnwITh8KcicdI2x49606 6<br />
rkL/SGL1Enj6KoFkPbbcoJ5vKJE9606 6<br />
<br />
</pre><br />
<br />
==View tools==<br />
<br />
===Toggle selected multi-edges===<br />
iRefScape creates multiple edges between nodes to represent multiple evidences. If an interaction between two proteins has evidence from both MINT and IntAct, there will be 2 edges; one for MINT and one for IntAct. Although this provides more information for the user, sometime the user may prefer to collapse these edges to a single edge to facilitate viewing. When this action is performed on a network, all but a randomly selected edge between each node is hidden. The edges which are hidden has the i.flag=1 and the one remaining has i.flag=0. Therefore, while this process is random by default, the user can control which edges to keep and which to hide by editing the i.flag edge attribute before using the '''toggle multi-edge''' option.<br />
<br />
===Zoom to selected===<br />
This action brings the '''selected node(s)''' to the centre of the screen and makes the nodes as large as possible given that all selected nodes are visible. This action can also be performed manually using Cytoscape's zoom tool.<br />
<br />
===Select last iRefScape selection===<br />
This action shows the last selection '''performed by an iRefScape operation'''. This features does not record user selections or selections made by using Cytoscape tools (e.g filters).<br />
<br />
===Select nodes with different taxid than query node===<br />
Some interactions may involve proteins from multiple species. An interaction may truly occur between proteins from two species (e.g. an interaction between a Human protein and a virus protein). In other cases, this may be an artefact of how data was entered by the source database.<br />
<br />
===Select between nodes===<br />
This option highlights (selects) nodes interacting with at least two nodes that have been pre-selected by the user. The node attribute '''i.alive_degree''' will be recalculated to reflect the degree of each node with respect to this pre-selection.<br />
<br />
===Show spoke-represented complexes===<br />
Some complexes are represented as a set of binary interactions by some sources. This action attempts to highlight such complexes as a single unit by attaching them all to a single pseudonode. <br />
<br />
<br />
==Hide/Un-hide==<br />
<br />
===Hide selected nodes===<br />
This action hides the selected nodes. This operation is performed in a independent thread and more efficient than hiding using Cytoscape's 'hide node' utility for large networks.<br />
<br />
===Hide nodes (except pseudonodes)===<br />
This action hides all select nodes which represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Hide nodes not selected===<br />
Hides all nodes which are not currently selected<br />
<br />
===Hide nodes not selected (except pseudonodes)===<br />
Hides all nodes which are not currently selected and that represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Un-hide all===<br />
Un-hides all nodes which are hidden by the user.<br />
<br />
==Safe mode==<br />
This option is only available when using JAVA 1.5 and will not appear for Java 1.6 or newer. Selecting this will un-dock the iRefScape window and handles errors and exceptions thrown due to bugs in JAVA 1.5. When this mode is activated not all graphic features will be available.<br />
<br />
<br />
<br />
<br />
<br />
== All iRefIndex Pages ==<br />
<br />
Follow this link for a listing of all iRefIndex related pages (archived and current).<br />
[[Category:iRefIndex]]</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefScape_plugin_menu&diff=3453iRefScape plugin menu2011-06-08T12:27:02Z<p>Sabry: /* iRefScape user variable file format */</p>
<hr />
<div>==Search tools==<br />
<br />
===Retrieve interactions for the selected nodes===<br />
To load all protein-protein interactions and complexes involving one or more '''selected nodes'''. This action is the same as performing a iteration=1 search using iRefScape for the selected nodes.<br />
<br />
===Expand one level===<br />
To load all protein-protein interactions and complexes involving at least one of the nodes in the current network. The behaviour is same as performing iteration=1 search using iRefScape for all the nodes. <br />
<br />
===Load interactions between neighbours===<br />
To complete the interactions between the currently loaded nodes. When a search & load operation is performed in iRefScape, the network returned contains all the proteins interacting with the query and the corresponding interactions. This does not return interactions between the neighbours of the query. This operation is the same as performing an iteration=0 search using iRefScape for all the nodes.<br />
This action has no effect for networks for which this operation has already been performed using the option presented at the end of the search.<br />
<br />
===Clear load history (Reload everything next time)===<br />
This will clear the iRefScape cache memory containing currently loaded nodes and edges. IRefScape keeps track of what is loaded to avoid reloading and thus increase efficiency. Therefore, if a search is performed twice,the network will not be re-loaded unless the user has requested that results be shown in a new view or they have selected this menu option. If the user wishes to reload the network then this option has to be used. When using other methods of expanding the network like “Expand one level” iRefScape handles the cache clearing automatically.<br />
<br />
===Reset node degree===<br />
This option resets the i.alive_degree of nodes. i.alive_degree provides how many nodes with a certain attribute type is connected to each node (set using filters). <br />
<br />
==Loading user variables (this section is being edited)==<br />
User variables can be attached to nodes and be browsed using the attribute browser. This file can not be used as a searchable index (can not be used as a search type). please see section XXX for details on searchable indices. <br />
<br />
There are three ways to load own variables for the user. <br />
#Use the Cytoscape attribute loading feature ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual'''])<br />
#Use a use attribute file with iRefScape (described in this section)<br />
#Include the attribute with the batch search file.(described in XXX).<br />
<br />
The iRefScape user attribute loader is provided as a complementing feature to the Cytoscape node attribute loading ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual''']). For most of the attribute loading operations the Cytoscape node attribute loader is sufficient and easier to use. However, when the iRefScape node attribute file is used, this can be used by just using the menu entry XXX. In addition the file will be available for subsequent operations.<br />
<br />
===iRefScape user variable file format===<br />
The first line of the file provides instructions and this line is compulsory.<br />
Example. <br />
#i.rog New_attribute<br />
<br />
<br />
The first line always starts with a hash ("#") and immediately followed by the iReFscape variable name. This iRefScape variable name is used to locate the nodes via the new attribute will be attached. Then a tab is used as a column separator, followed by the name of the user attribute name.This user attribute name should be unique( not already used). In the above example the user attribute to use is the i.rog and the user attribute name is "New_attribute".<br />
<br />
From the second line onwards, the attributes with the mapping attribute are provided.<br />
Example <br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
<br />
The first column provides the iRefScape attribute to use and the second column provides the user attribute. Multiple attributes should be separated with a pipe ("|"). The example line shown would locate the node with i.rog=4399398 and attach the "TENC1|UniProtKB:Q63HR2|" value to it with the attribute name "New_attribute"<br />
<br />
*Each column is separated by a TAB.<br />
*Each line ends with a new line character ("\n")<br />
*The file should be constructed using a plain text editor (e.g. Kate, notepad) and word processing software like Microsoft word should not be used to construct this file.<br />
* The file extension is ".txt"<br />
* Sample file "ONE__EXT__ROG_#Name_5_.iruv" can be found in the iRefScape installation directory (iRefIndex directory)<br />
<br />
<br />
Sample file<br />
#i.rog New_name<br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
452957 GFI1B|UniProtKB:Q5VTD9|<br />
561552 TENC1|UniProtKB:Q63HR2-4|<br />
534065 GFI1B_MOUSE|UniProtKB:O70237|<br />
<br />
==iRefScape search with batch file==<br />
<br />
==Only variables==<br />
Users can load there own variables for proteins which are mapped to a ROGID. The file should follow the format given below;<br />
#Should be a plain text file with exactly two columns and each line ending with a new line character (pressing enter).<br />
#First column should contain the ROGID<br />
#Second column should contain the user attribute/variable. <br />
#The file name should have the format _rog_'''USER_VARIABLE_NAME'''.iruv (The text in bold is supplied by the user. e.g., _rog_myAttribute.iruv ).<br />
<br />
<pre><br />
e.g<br />
#rog USER_VARIABLE<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
q6/pRFyay7gQ6bb2rzvKYgfkeaE9606 2<br />
8sODZSppCsuEgRmhSHp3UjwOf2M9606 3<br />
obze7v7i2yTIIcJjd7laIriNFg89606 4<br />
Ty0OLkmhoUPjUuLQQv5ykN057oM9606 5<br />
4bhW4sEt1YhYwHnHCyDNV3vvThs9606 6<br />
Al8M+JdB4H+QnwITh8KcicdI2x49606 6<br />
rkL/SGL1Enj6KoFkPbbcoJ5vKJE9606 6<br />
<br />
</pre><br />
<br />
==View tools==<br />
<br />
===Toggle selected multi-edges===<br />
iRefScape creates multiple edges between nodes to represent multiple evidences. If an interaction between two proteins has evidence from both MINT and IntAct, there will be 2 edges; one for MINT and one for IntAct. Although this provides more information for the user, sometime the user may prefer to collapse these edges to a single edge to facilitate viewing. When this action is performed on a network, all but a randomly selected edge between each node is hidden. The edges which are hidden has the i.flag=1 and the one remaining has i.flag=0. Therefore, while this process is random by default, the user can control which edges to keep and which to hide by editing the i.flag edge attribute before using the '''toggle multi-edge''' option.<br />
<br />
===Zoom to selected===<br />
This action brings the '''selected node(s)''' to the centre of the screen and makes the nodes as large as possible given that all selected nodes are visible. This action can also be performed manually using Cytoscape's zoom tool.<br />
<br />
===Select last iRefScape selection===<br />
This action shows the last selection '''performed by an iRefScape operation'''. This features does not record user selections or selections made by using Cytoscape tools (e.g filters).<br />
<br />
===Select nodes with different taxid than query node===<br />
Some interactions may involve proteins from multiple species. An interaction may truly occur between proteins from two species (e.g. an interaction between a Human protein and a virus protein). In other cases, this may be an artefact of how data was entered by the source database.<br />
<br />
===Select between nodes===<br />
This option highlights (selects) nodes interacting with at least two nodes that have been pre-selected by the user. The node attribute '''i.alive_degree''' will be recalculated to reflect the degree of each node with respect to this pre-selection.<br />
<br />
===Show spoke-represented complexes===<br />
Some complexes are represented as a set of binary interactions by some sources. This action attempts to highlight such complexes as a single unit by attaching them all to a single pseudonode. <br />
<br />
<br />
==Hide/Un-hide==<br />
<br />
===Hide selected nodes===<br />
This action hides the selected nodes. This operation is performed in a independent thread and more efficient than hiding using Cytoscape's 'hide node' utility for large networks.<br />
<br />
===Hide nodes (except pseudonodes)===<br />
This action hides all select nodes which represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Hide nodes not selected===<br />
Hides all nodes which are not currently selected<br />
<br />
===Hide nodes not selected (except pseudonodes)===<br />
Hides all nodes which are not currently selected and that represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
<br />
===Un-hide all===<br />
Un-hides all nodes which are hidden by the user.<br />
<br />
==Safe mode==<br />
This option is only available when using JAVA 1.5 and will not appear for Java 1.6 or newer. Selecting this will un-dock the iRefScape window and handles errors and exceptions thrown due to bugs in JAVA 1.5. When this mode is activated not all graphic features will be available.<br />
<br />
<br />
<br />
<br />
<br />
== All iRefIndex Pages ==<br />
<br />
Follow this link for a listing of all iRefIndex related pages (archived and current).<br />
[[Category:iRefIndex]]</div>Sabryhttp://irefindex.vib.be/wiki/index.php?title=iRefScape_plugin_menu&diff=3452iRefScape plugin menu2011-06-08T12:25:24Z<p>Sabry: /* Loading user variables (this section is being edited) */</p>
<hr />
<div>==Search tools==<br />
<br />
===Retrieve interactions for the selected nodes===<br />
To load all protein-protein interactions and complexes involving one or more '''selected nodes'''. This action is the same as performing a iteration=1 search using iRefScape for the selected nodes.<br />
<br />
===Expand one level===<br />
To load all protein-protein interactions and complexes involving at least one of the nodes in the current network. The behaviour is same as performing iteration=1 search using iRefScape for all the nodes. <br />
<br />
===Load interactions between neighbours===<br />
To complete the interactions between the currently loaded nodes. When a search & load operation is performed in iRefScape, the network returned contains all the proteins interacting with the query and the corresponding interactions. This does not return interactions between the neighbours of the query. This operation is the same as performing an iteration=0 search using iRefScape for all the nodes.<br />
This action has no effect for networks for which this operation has already been performed using the option presented at the end of the search.<br />
<br />
===Clear load history (Reload everything next time)===<br />
This will clear the iRefScape cache memory containing currently loaded nodes and edges. IRefScape keeps track of what is loaded to avoid reloading and thus increase efficiency. Therefore, if a search is performed twice,the network will not be re-loaded unless the user has requested that results be shown in a new view or they have selected this menu option. If the user wishes to reload the network then this option has to be used. When using other methods of expanding the network like “Expand one level” iRefScape handles the cache clearing automatically.<br />
<br />
===Reset node degree===<br />
This option resets the i.alive_degree of nodes. i.alive_degree provides how many nodes with a certain attribute type is connected to each node (set using filters). <br />
<br />
==Loading user variables (this section is being edited)==<br />
User variables can be attached to nodes and be browsed using the attribute browser. This file can not be used as a searchable index (can not be used as a search type). please see section XXX for details on searchable indices. <br />
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There are three ways to load own variables for the user. <br />
#Use the Cytoscape attribute loading feature ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual'''])<br />
#Use a use attribute file with iRefScape (described in this section)<br />
#Include the attribute with the batch search file.(described in XXX).<br />
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The iRefScape user attribute loader is provided as a complementing feature to the Cytoscape node attribute loading ([http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node%20and%20Edge%20Attributes '''Cytoscape manual''']). For most of the attribute loading operations the Cytoscape node attribute loader is sufficient and easier to use. However, when the iRefScape node attribute file is used, this can be used by just using the menu entry XXX. In addition the file will be available for subsequent operations.<br />
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===iRefScape user variable file format===<br />
The first line of the file provides instructions and this line is compulsory.<br />
Example. <br />
#i.rog New_attribute<br />
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The first line always starts with a hash ("#") and immediately followed by the iReFscape variable name. This iRefScape variable name is used to locate the nodes via the new attribute will be attached. Then a tab is used as a column separator, followed by the name of the user attribute name.This user attribute name should be unique( not already used). In the above example the user attribute to use is the i.rog and the user attribute name is "New_attribute".<br />
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From the second line onwards, the attributes with the mapping attribute are provided.<br />
Example <br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
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The first column provides the iRefScape attribute to use and the second column provides the user attribute. Multiple attributes should be separated with a pipe ("|"). The example line shown would locate the node with i.rog=4399398 and attach the "TENC1|UniProtKB:Q63HR2|" value to it with the attribute name "New_attribute"<br />
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*Each column is separated by a TAB.<br />
*Each line ends with a new line character ("\n")<br />
*The file should be constructed using a plain text editor (e.g. Kate, notepad) and word processing software like Microsoft word should not be used to construct this file.<br />
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Sample file<br />
#i.rog New_name<br />
4399398 TENC1|UniProtKB:Q63HR2|<br />
452957 GFI1B|UniProtKB:Q5VTD9|<br />
561552 TENC1|UniProtKB:Q63HR2-4|<br />
534065 GFI1B_MOUSE|UniProtKB:O70237|<br />
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==iRefScape search with batch file==<br />
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==Only variables==<br />
Users can load there own variables for proteins which are mapped to a ROGID. The file should follow the format given below;<br />
#Should be a plain text file with exactly two columns and each line ending with a new line character (pressing enter).<br />
#First column should contain the ROGID<br />
#Second column should contain the user attribute/variable. <br />
#The file name should have the format _rog_'''USER_VARIABLE_NAME'''.iruv (The text in bold is supplied by the user. e.g., _rog_myAttribute.iruv ).<br />
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<pre><br />
e.g<br />
#rog USER_VARIABLE<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
j4H4IZH/ecTvEDjCel+eLTCmFyE9606 1<br />
q6/pRFyay7gQ6bb2rzvKYgfkeaE9606 2<br />
8sODZSppCsuEgRmhSHp3UjwOf2M9606 3<br />
obze7v7i2yTIIcJjd7laIriNFg89606 4<br />
Ty0OLkmhoUPjUuLQQv5ykN057oM9606 5<br />
4bhW4sEt1YhYwHnHCyDNV3vvThs9606 6<br />
Al8M+JdB4H+QnwITh8KcicdI2x49606 6<br />
rkL/SGL1Enj6KoFkPbbcoJ5vKJE9606 6<br />
<br />
</pre><br />
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==View tools==<br />
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===Toggle selected multi-edges===<br />
iRefScape creates multiple edges between nodes to represent multiple evidences. If an interaction between two proteins has evidence from both MINT and IntAct, there will be 2 edges; one for MINT and one for IntAct. Although this provides more information for the user, sometime the user may prefer to collapse these edges to a single edge to facilitate viewing. When this action is performed on a network, all but a randomly selected edge between each node is hidden. The edges which are hidden has the i.flag=1 and the one remaining has i.flag=0. Therefore, while this process is random by default, the user can control which edges to keep and which to hide by editing the i.flag edge attribute before using the '''toggle multi-edge''' option.<br />
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===Zoom to selected===<br />
This action brings the '''selected node(s)''' to the centre of the screen and makes the nodes as large as possible given that all selected nodes are visible. This action can also be performed manually using Cytoscape's zoom tool.<br />
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===Select last iRefScape selection===<br />
This action shows the last selection '''performed by an iRefScape operation'''. This features does not record user selections or selections made by using Cytoscape tools (e.g filters).<br />
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===Select nodes with different taxid than query node===<br />
Some interactions may involve proteins from multiple species. An interaction may truly occur between proteins from two species (e.g. an interaction between a Human protein and a virus protein). In other cases, this may be an artefact of how data was entered by the source database.<br />
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===Select between nodes===<br />
This option highlights (selects) nodes interacting with at least two nodes that have been pre-selected by the user. The node attribute '''i.alive_degree''' will be recalculated to reflect the degree of each node with respect to this pre-selection.<br />
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===Show spoke-represented complexes===<br />
Some complexes are represented as a set of binary interactions by some sources. This action attempts to highlight such complexes as a single unit by attaching them all to a single pseudonode. <br />
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==Hide/Un-hide==<br />
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===Hide selected nodes===<br />
This action hides the selected nodes. This operation is performed in a independent thread and more efficient than hiding using Cytoscape's 'hide node' utility for large networks.<br />
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===Hide nodes (except pseudonodes)===<br />
This action hides all select nodes which represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
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===Hide nodes not selected===<br />
Hides all nodes which are not currently selected<br />
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===Hide nodes not selected (except pseudonodes)===<br />
Hides all nodes which are not currently selected and that represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.<br />
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===Un-hide all===<br />
Un-hides all nodes which are hidden by the user.<br />
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==Safe mode==<br />
This option is only available when using JAVA 1.5 and will not appear for Java 1.6 or newer. Selecting this will un-dock the iRefScape window and handles errors and exceptions thrown due to bugs in JAVA 1.5. When this mode is activated not all graphic features will be available.<br />
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== All iRefIndex Pages ==<br />
<br />
Follow this link for a listing of all iRefIndex related pages (archived and current).<br />
[[Category:iRefIndex]]</div>Sabry