View source for README iRefIndex experiment MITAB 5.1

Last edited: 25th, August 2009

Applies to iRefIndex release: 5.1 

Release date: 21th, August 2009

Download location: Download available only via SFTP, please send request to  ian.donaldson at biotek.uio.no for details

Authors: Ian Donaldson and Sabry Razick (with changes from Paul Boddie)

Database: iRefIndex (http://irefindex.uio.no)

Organization: Biotechnology Centre of Oslo, University of Oslo 
(http://www.biotek.uio.no/) 

Note: this distribution includes only those data that may be freely 
distributed under the copyright license of the source database.
See Description below.

== <span style="color:#0f0086"> Description  </span> ==
 
This file describes the contents of the irefindex/current/data directory and the 
format of the tab-delimited text files contained within. Each index file 
follows the PSI-MITAB2.5 format with additional columns for annotating 
edges and nodes. <span style="color:#ff0086"> Each line in PSI-MITAB2.5 format represents a single 
interaction record from an experiment  </span>.  Assignment of source 
interaction records to these redundant groups is described at 
http://irefindex.uio.no.  The PSI-MI2.5 format plus additional columns 
are described at the end of the file.

Details on the build process are available from the publication PMID 18823568.

There are two sets of data free and proprietary.  Free version includes only those data that may be freely 
distributed under the copyright license of the source database. This includes data from 
BIND, BioGRID, IntAct, MINT, MPPI and OPHID.

iRefIndex also integrates data from CORUM, DIP, HPRD and MPact. These data are not distributed publicly.
These data may be made available to academic users under a collaborative agreement.

Contact ian.donaldson at biotek.uio.no if you are interested in using the 
iRefIndex database or would like your database included in the public release of the index.

== Directory contents ==

{|
|<tt>README</tt>                      ||pointer to this file at http://irefindex.uio.no/wiki/README_iRefIndex_experiment_MITAB_5.1
|-
|<tt>Sources</tt>                     ||pointer to data files for this release at http://irefindex.uio.no/wiki/Sources_iRefIndex_5.0
|-
|<tt>Statistics</tt>                  ||pointer to statisitics for this release at http://irefindex.uio.no/wiki/Statistics_iRefIndex_5.0
|-
|<tt>xxxx.mitab.mmddyyyy.txt.zip</tt> ||individual indices in PSI-MITAB2.5 format<br>
|}

iRefIndex data is distributed as a set of tab-delimited text files with names of the form <tt>xxxx.experiment.mitab.mmddyyyy.txt.zip</tt> where <tt>mmddyyyy</tt> represents the file's creation date.

The complete index is available as <tt>All.mitab.mmddyyyy.txt.zip</tt> .

Taxon specific data sets are also available for:

{|
|                         ||'''Taxon Id'''
|-
|Homo sapiens             ||9606 (human)
|-
|Mus musculus             ||10090 (mouse)
|-
|Rattus norvegicus        ||10116 (brown rat)
|-
|Caenorhabditis elegans   ||6239 (nematode)
|-
|Drosophila melanogaster  ||7227 (fruit fly)
|-
|Saccharomyces cerevisiae ||4932 (baker's yeast)
|-
|Escherichia coli.	  ||562  (E. Coli)
|-
|Other                    ||other
|-
|All			  ||all
|}

Taxon specific subsets of the data are named <tt>xxxx.mitab.mmddyyyy.txt.zip</tt> where <tt>xxxx</tt> is the taxonomy identifier of at least one of the interactors according to either the source interaction database or the sequence database record.  Each zip compressed file contains a single text file with the corresponding name <tt>xxxx.mitab.mmddyyyy.txt</tt>.

In some cases, other objects may belong to other taxons if a virus-host interaction is being represented or if a protein from another organism has been used to model a protein in the specified organism.  

Taxonomy identifiers are provided in the data sets allowing these exceptions to be identified.  The taxonomy identifiers listed are derived from the source protein sequence record.  In some cases, this taxonomy identifier will be a child of the taxon listed in the file's title; for example, Escherichia coli K12 (taxonomy identifier 83333) will appear in the Escherichia coli (taxonomy identifier 562) file.

A description of the NCBI taxon identifiers is available at the following location:

http://www.ncbi.nlm.nih.gov/sites/entrez?db=taxonomy 

The above data taxon division scheme leads to duplications; for instance, an interaction present in the mouse index could also appear in the human index if the interaction record lists protein sequence records from both human and mouse. The <tt>All.mitab.mmddyyyy</tt> file is a complete and non-redundant listing. 

The data format and divisions provided in this initial release were chosen in the hopes that they would be immediately useful to the largest 
possible set of users.  Other formats and divisions are possible and we welcome your input on future releases.

== Changes from last version ==
 <span style="color:red"> This is not a new release but error corrections for the distributed files for beta 5.0, We would like to thank Michel Dumontier
 for pointing out errors </span>
Mapping to MI (PSIMI CV identifier) improved. Colon in grid identifiers corrected (earlier MI:0463:(grid) now MI:0463(grid)).
When identifiers include reserver characters the whole identifier included in quotes.

== Known Issues ==

<ol>
To be edited

</ol>

== Understanding the iRefIndex MITAB format ==

iRefIndex is distributed in PSI-MITAB format.  This format was originally described in
a recent PSI-MI paper (PMID 17925023).

Since this PSI-MITAB format allows for only two interactors to be described on each line, it is best suited for describing binary interaction data (the original experiment, say yeast two hybrid, gives a binary readout).  However, other source PSI-MI XML source records will describe interactions involving only one interactor type (dimers or multimers) or they will contain associative interaction data (say from immunoprecipitation experiments where the exact interactions between any pair of interactors are unknown.  These cases are problematic for the PSI-MITAB format.  This README describes exactly how we use the MITAB format to describe these alternate (non-binary) interaction types.
  
Each row in the MITAB file represents a **group** of interaction records from primary sources.  Each member of this group describes an interaction involving the exact same set of proteins (as defined by their primary sequence and taxon ids).

The natural keys for each interaction record in this group (i.e. the record identifiers from the source database) are listed in column 14.  For example:

<pre>intact:EBI-761694|intact:EBI-762624|mint:MINT-15283</pre>
 
Our surrogate (primary) key for this group of redundant interaction records (RIG) is also listed in row 14, as the very first entry (see example below).  Keys in row 14 are bar (<tt>|</tt>) delimited.  The source db name and record id in each key are separated by a colon. 
 
The RIG identifier is a 27 character key that is derived from the ROGIDs of the interactors involved in the interaction record (see columns 1 and 2).  Our RIG identifier is also listed (by itself) in column 20 for convenience.  The ROGID is a SHA-1 digest of the protein interactor's primary amino acid sequence concatenated with the NCBI taxon id (see the paper for details).
 
Sometimes source interaction records in PSI-MI format only list one interactor.  These are cases where either 1) an intramolecular interaction is being represented or 2) a multimer (3 or more) of some protein is being represented.  These records are difficult to represent in the PSI-MITAB format because PSI-MITAB requires that each row (interaction) list two interactors.  The way we handle this is to list the ROG identifier for the single interactor twice (once in each of columns 1 and 2) of the MITAB.  The RIG identifier for these interactions will be the SHA-1 digest of the interactor’s ROG id (see column 20). These interactions are marked by a Y in column 21 (see the README).

Note that column 21 may also contain a C.  This indicates that the MITAB entry describes membership of a protein in some complex.  These entries correspond to PSI-MI records where more than two interactors are listed (associative interaction data).  In these cases, the first column holds the ROG identifier of the complex and the second column contains the ROG id of the protein.  We chose this method of representation so you can distinguish true binary interactions from complex membership.  Other people might take an interaction record with multiple interactors and make a list of binary interactions (based on the spoke or matrix model) and then list these binary interactions in the MITAB.  This would be wrong.  It implies interactions that may not exist and hides the fact that the entry is not a binary interaction but a binary representation of a complex-interaction.
 
As an example, let’s say that a source interaction record contained interactors A, B and C found by affinity purification and mass-spec.  We would calculate the RIG id as being X (a SHA-1 digest of A, B and C ROG ids concatenated together).
 
Then we would represent the complex in the MITAB file using three lines:
X-A, X-B, and X-C.  All three entries would have the same string in column 1 (the RIG id for the complex)
All three entries would have the same string in column 21 (again, the RIG id for the complex)
 
This allows you to reconstruct the members of the original interaction record that describes a complex of proteins (say from an affinity purification experiment).  From there, you can choose to make a spoke or matrix model by yourself if you want.

For binary interaction data, column 21 will contain an X.  Two protein interactor ROGIDs will be listed in columns 1 and 2.

== License ==
 
Data released on this public ftp site are released under the Creative 
Commons Attribution License http://creativecommons.org/licenses/by/2.5/.  
This means that you are free to use, modify and redistribute these data 
for personal or commercial use so long as you provide appropriate 
credit.  See next section.

iRefIndex data distributed on the FTP site includes only those data that 
may be freely distributed under the copyright license of the source database. 
This includes data from BIND, BioGRID, IntAct, MINT, MPPI and OPHID.

iRefIndex also integrates data from CORUM, DIP, HPRD and MPact. These data are 
not distributed publicly. These data may be made available to academic users 
under a collaborative agreement.

Contact ian.donaldson at biotek.uio.no if you are interested in using the 
iRefIndex database or would like your database included in the public release 
of the index.

Copyright © 2008, 2009 Ian Donaldson

== Citation ==

Credit should include citing the iRefIndex paper (PMID 18823568) and any of the 
source databases upon which this resource is based.  See 
http://irefindex.uio.no for appropriate citations.

== Disclaimer ==

Data is distributed in the hope that it will be useful, but WITHOUT ANY 
WARRANTY; without even the implied warranty of MERCHANTABILITY or 
FITNESS FOR A PARTICULAR PURPOSE.

== Description of PSI-MITAB2.5 file ==

Each line in this file represents either

# an interaction between two proteins (binary interaction) or
# the membership of a protein in some complex (complex membership) or
# an interaction that involves only one protein type (multimer or self-interaction).

See column 21 for more details.

=== Column number: 1  (uidA)===

{|
|Column name: ||uidA
|-
|Column type: ||String
|-
|Description: ||Unique identifier for interactor A
|-
|Example: ||<pre>irefindex:hhZYhMtr5JC1lGIKtR1wxHAd3JY83333</pre>
|}

'''Notes'''

If this line (entry) describes a binary interaction between two proteins, 
then the protein with the 'ascibetically' (ASCII value sort order) larger ROGID is listed first as 
uidA.  If this entry describes the membership of a protein in a complex, 
then the ROGID of the complex is always listed first as uidA and the 
protein's ROGID is listed as uidB (column 2).  If this entry describes a 
an interaction involving only one protein type, then the ROGID of that 
protein is listed both as uidA and uidB.

The ROGID (redundant object group identifier) for proteins, 
consists of the SEGUID for the protein concatenated with the taxon 
identifier for the protein.  For complex nodes, the ROGID
is calculated as the SHA-1 digest of the ROGID's of all the protein
participants (after first ordering them by ASCII-based lexicographical
sorting in ascending order and concatenating them) See the iRefIndex paper
for details. The SEGUID is always 27 characters long.  So the ROGID will be
composed of 27 characters concatenated with a taxon identifier for proteins.

=== Column number: 2  (uidB)===

{|
|Column name: ||uidB
|-
|Column type: ||String
|-
|Description: ||Unique identifier for interactor B
|-
|Example: ||<pre>irefindex:ImnYkXur2U4xVdz5PVvprq8Zgd483333</pre>
|}

'''Notes'''

See notes for column 1.

=== Column number: 3 (altA)===

{|
|Column name: ||altA
|-
|Column type: ||<nowiki>a|b</nowiki>: pipe-delimited set of strings
|-
|Description: ||Alternative identifiers for interactor A
|-
|Example: ||<pre>uniprotkb:P23367|refseq:NP_418591|entrezgene/locuslink:948691</pre>
|}

'''Notes'''

Each pipe-delimited entry is a database_name:accession pair delimited by 
a colon.  Database names are taken from the MI controlled vocabulary at 
http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI
Database references listed in this column may include the following:

;uniprotkb
:The accessions this protein is known by in UniProt(http://www.uniprot.org/). More information regarding this protein can be retrieved using this accession from UniProt. See the AC line in the flat file. http://au.expasy.org/sprot/userman.html#AC_line. Uniprot accessions are mapped to nodes using an exact match to the ROGID.  If the node's ROGID maps to a specific isoform of the protein, then the Uniprot accession for the isoform is given.
;refseq 
:If a protein accession exists in the RefSeq data base (http://www.ncbi.nlm.nih.gov/RefSeq/) that reference is indicated here. More information about this protein can be obtained from RefSeq using this accession.  Refseq accessions are mapped to nodes using an exact match between the node's ROGID and the ROGID for the most recent version of the RefSeq accession.
;entrezgene/locuslink  
:NCBI gene Identifiers for the gene encoding this protein. See ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2refseq column GeneID given protein's accession.version
;other
:If none of the three identifier types are available then other databasename:accession pairs will be listed. Thes database names may not follow the MI controlled vocabulary.

Example:

<pre>emb:CAA44868.1|gb:AAA23715.1|gb:AAB02995.1|emb:CAA56736.1|uniprot:P24991</pre>

;irefindex
:If the node represents a complex, then the rogid for the complex will be listed here, such as the following:

<pre>irefindex:xBr9cTXgzPLNxsaKiYyHcoEm/DM</pre>

Note that this column value may contain duplicate identifiers.

=== Column number: 4 (altB)===

{|
|Column name: ||altB
|-
|Column type: ||<nowiki>a|b</nowiki>: pipe-delimited set of strings
|-
|Description: ||Alternative identifiers for interactor B
|-
|Example: ||<pre>uniprotkb:P06722|refseq:NP_417308|entrezgene/locuslink:947299</pre>
|}

'''Notes'''

See notes for column 3.

=== Column number: 5 (aliasA) ===

{|
|Column name: ||aliasA
|-
|Column type: ||<nowiki>a|b</nowiki>: pipe-delimited set of strings
|-
|Description: ||Aliases for interactor A
|-
|Example: ||<pre>uniprotkb:MUTL_ECOLI|entrezgene/locuslink:mutL</pre>
|}

'''Notes'''

Each pipe-delimited entry is a databasename:alias pair delimited by a 
colon.  Database names are taken from the PSI-MI controlled vocabulary 
at http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI
Database names and sources listed in this column may include the 
following:

;<nowiki>uniprotkb:entry name</nowiki>
:the entry name given by UniProt. See Entry name in the ID line of the flat file. http://au.expasy.org/sprot/userman.html#ID_line
;<nowiki>entrezgene/locuslink:symbol</nowiki>
:the NCBI gene symbol for the gene encoding this protein. See ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info column Symbol given GeneID
;<nowiki>irefindex:complex</nowiki>
:If the node is a complex then <tt>irefindex:complex</tt> will be listed here.
;NA
:<tt>NA</tt> may be listed here if aliases are Not Available

=== Column number: 6 (aliasB) ===

{|
|Column name: ||aliasB
|-
|Column type: ||<nowiki>a|b</nowiki>: pipe-delimited set of strings
|-
|Description: ||Aliases for interactor B
|-
|Example: ||<pre>uniprotkb:MUTH_ECOLI|entrezgene/locuslink:mutH</pre>
|}

'''Notes'''

See notes for column 5.

=== Column number: 7 (Method) ===

{|
|Column name: ||Method
|-
|Column type: ||<nowiki>a|b</nowiki>: pipe-delimited set of strings
|-
|Description: ||Interaction detection methods
|-
|Example: ||<pre>MI:0000(2 hybrid|affinity chrom|adenylate cyclase|two hybrid)</pre>
|}

'''Notes'''

This is a non-redundant list of method short labels found in interaction records.
Detection method. Path for PSI-MI 2.5:

<pre>entrySet/entry/experimentList/experimentDescription/interactionDetectionMethod/names/shortLabel/</pre>

When available, the PSI-MI controlled vocabulary term for the method will be provided such as <tt>MI:0399(2h fragment pooling)</tt>. Otherwise, <tt>MI:0000</tt> will appear before the list of pipe-delimited shortLabels.

<tt>NA</tt> or <tt>-1</tt> may appear in place of a recognised shortLabel.

For example:

<pre>
MI:0000(-1)
MI:0000(NA)
</pre>

=== Column number: 8 (author) ===

{|
|Column name: ||author
|-
|Column type: ||<nowiki>a|b</nowiki>: pipe-delimited set of strings
|-
|Description: ||
|-
|Example: ||<pre>hall-1999-1|hall-1999-2|mansour-2001-1|mansour-2001-2|hall-1999</pre>
|}

'''Notes'''

According to MITAB2.5 format this column should contain a pipe-delimited list of author surnames in which the interaction has been shown.

Note that this column value may contain duplicate identifiers.

=== Column number: 9 (pmids) ===

{|
|Column name: ||pmids
|-
|Column type: ||<nowiki>a|b</nowiki>: pipe-delimited set of strings
|-
|Description: ||PubMed Identifiers
|-
|Example: ||<pre>pubmed:9880500|pubmed:11585365</pre>
|}

'''Notes'''

This is a non-redundant list of PubMed identifiers pointing to 
literature that supports the interaction. 
According to MITAB2.5 format, this column should contain a pipe 
delimited set of databaseName:identifier pairs such as <tt>pubmed:12345</tt>.
The source database name is always <tt>pubmed</tt>.

The special value <tt>-</tt> may appear in place of the identifiers.

=== Column number: 10 (taxa) ===

{|
|Column name: ||taxa
|-
|Column type: ||string
|-
|Description: ||Taxonomy identifier for interactor A
|-
|Example: ||<pre>taxid:83333</pre>
|}

'''Notes'''

The NCBI taxonomy identifier listed here is that of the sequence record for the interactor and may be different than what is listed in the interaction record.  See the methods section for more details. See the NCBI taxonomy database at http://www.ncbi.nlm.nih.gov/sites/entrez?db=taxonomy . According to MITAB2.5 format, this column should contain a pipe delimited set of databaseName:identifier pairs such as <tt>taxid:12345</tt>. The source database name has been listed as taxid since it is always NCBI's taxonomy database. The value in this column will be <tt>NA</tt> if the interactor is a complex. 

=== Column number: 11 (taxb) ===

{|
|Column name: ||taxb
|-
|Column type: ||string
|-
|Description: ||Taxonomy identifier for interactor B
|-
|Example: ||<pre>taxid:83333</pre>
|}

'''Notes'''

See notes for column 10.

=== Column number: 12  (interactionType) ===

{|
|Column name: ||interactionType
|-
|Column type: ||<nowiki>a|b</nowiki>: pipe-delimited set of strings
|-
|Description: ||Interaction Type from controlled vocabulary or short label
|-
|Example: ||<pre>MI:0218(physical interaction)</pre>
|}

'''Notes'''

Taken from the PSI-MI controlled vocabulary and represented as...

<pre>database:identifier(interaction type)</pre>

...(when available in the interaction record) or Path for PSI-MI 2.5:

<pre>entrySet/entry/interactionList/interaction/interactionType/names/shortLabel</pre>

If the MI controlled vocabulary identifier is unavailable then <tt>MI:0000</tt> is listed.

<tt>NA</tt> may be listed here if the interaction type in not available (meaning that we could not find the interaction type in the record provided by the source database).

=== Column number: 13 (sourcedb) ===

{|
|Column name: ||sourcedb
|-
|Column type: ||<nowiki>a|b</nowiki>: pipe-delimited set of strings
|-
|Description: ||Source databases containing this interaction 
|-
|Example: ||<pre>MI:0469(intact)|MI:0471(mint)</pre>
|}

'''Notes'''

Taken from the PSI-MI controlled vocabulary and represented as...

<pre>database:identifier(sourceName)</pre>

=== Column number: 14 (interactionIdentifiers) ===

{|
|Column name: ||interactionIdentifiers
|-
|Column type: ||<nowiki>a|b</nowiki>: pipe-delimited set of strings
|-
|Description: ||source interaction database and accession
|-
|Example: ||<pre>intact:EBI-761694|intact:EBI-762624|mint:MINT-15283</pre>
|}

'''Notes'''

Each reference is presented as a databaseName:identifier pair.  

The identifier given for irefindex is the RIGID.
The RIGID (for redundant interaction group identifier) consists of the two
node identifiers (see columns 1 and 2) concatenated and then digested with
the SHA-1 algorithm.  The two node identifiers are ordered in columns one
and two according to ASCII-based lexicographical sorting in ascending order.
See the iRefIndex paper for details.  The RIGID points to a set of redundant
protein-protein interactions that involve the same set of proteins with the
exact same primary sequences.
The source databaseNames that appear in this column are taken from the
PSI-MI controlled vocabulary at
http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI where possible

Interaction record identifiers are not available for mppi and ophid so 
these entries will appear as mppi:found and ophid:found

Sometimes, <tt>FOUND</tt> will appear as in:

<pre>intact:EBI-861910|intact:FOUND:1</pre>

=== Column number: 15 (confidence) ===

{|
|Column name: ||confidence
|-
|Column type: ||<nowiki>a|b</nowiki>: pipe-delimited set of strings
|-
|Description: ||Confidence scores
|-
|Example: ||<pre>lpr:0|hpr:12</pre>
|}

'''Notes'''

Each reference is presented as a scoreName:score pair.  Three confidence 
scores are provided: <tt>lpr</tt>, <tt>hpr</tt> and <tt>np</tt>.

PubMed Identifiers (PMIDs) point to literature references that support 
an interaction. A PMID may be used to support more than one interaction.  

The lpr score (lowest pmid re-use) is the lowest number of distinct 
interactions (RIGIDs: see column 14) that any one PMID (supporting the 
interaction in this row) is used to support.  A value of one indicates 
that at least one of the PMIDs supporting this interaction has never 
been used to support any other interaction.  This likely indicates that 
only one interaction was described by that reference and that the 
present interaction is not derived from high throughput methods.

The hpr score (highest pmid re-use) is the highest number of 
interactions (RIGIDs: see column 14) that any one PMID (supporting the 
interaction in this row) is used to support. A high value (e.g. greater 
than 50) indicates that one PMID describes at least 50 other 
interactions and it is more likely that high-throughput methods were 
used.

The np score (number pmids) is the total number of unique PMIDs used to 
support the interaction described in this row.

<tt>-</tt> may appear in the score field, indicating the absence of a score value.

----

COLUMNS PAST THIS POINT ARE NOT DEFINED BY THE PSI-MITAB2.5 STANDARD.  
THESE COLUMNS MAY CHANGE FROM ONE RELEASE TO ANOTHER

=== Column number: 16 (entrezGeneA) ===

{|
|Column name: ||entrezGeneA
|-
|Column type: ||pipe delimited list of integers or a string
|-
|Description: ||EntrezGene identifier(possibly a pipe-delimited list) for interactor A
|-
|Example: ||<pre>947299</pre>
|}

'''Notes'''

If an EntrezGene identifier is not found for the interactor, then a 
ROGID will appear in this column (see notes to column 1).  

If the interactor is a node representing a complex, then the ROGID for 
the complex will appear here.

=== Column number: 17 (entrezGeneB) ===

{|
|Column name: ||entrezGeneB
|-
|Column type: ||Integer
|-
|Description: ||EntrezGene identifier for interactor B
|-
|Example: ||<pre>948691</pre>
|}

'''Notes'''

See notes for column 16.

=== Column number: 18 (atype) ===

{|
|Column name: ||atype
|-
|Column type: ||string
|-
|Description: ||Is interactor A a protein or a complex?
|-
|Example: ||<pre>MI:0326(protein)</pre>
|}

'''Notes'''

This will always be one of...

<pre>
MI:0326(protein)
MI:0315(protein complex)
</pre>

=== Column number: 19 (btype) ===

{|
|Column name: ||btype
|-
|Column type: ||string
|-
|Description: ||Is interactor B a protein or a complex?
|-
|Example: ||<pre>MI:0326(protein)</pre>
|}

'''Notes'''

See column 18.

=== Column number: 20 (rigid) ===

{|
|Column name: ||rigid
|-
|Column type: ||string
|-
|Description: ||Redundant interaction group identifier
|-
|Example: ||<pre>3ERiFkUFsm7ZUHIRJTx8ZlHILRA</pre>
|}

'''Notes'''

The RIGID (for redundant interaction group identifier) consists of the
ROG identifiers for each of the protein participants (see notes above)
ordered by ASCII-based lexicographic sorting in ascending order,
concatenated and then digested with the SHA-1 algorithm.  See the iRefIndex
paper for details.  This identifier points to a set of redundant
protein-protein interactions that involve the same set of proteins with the
exact same primary sequences.

=== Column number: 21 (edgetype) ===

{|
|Column name: ||edgetype
|-
|Column type: ||Character
|-
|Description: ||Does the edge represent a binary interaction (X), complex membership (C), or a multimer (Y)?
|-
|Example: ||<pre>X</pre>
|}

'''Notes'''

Edges can be labelled as either X, C or Y:

;X
:a binary interaction with two protein participants
;C
:denotes that a protein is part of some complex of proteins.  One of the nodes is a protein.  The other node represents a complex of proteins (see columns 18-19).  The edge represents the idea that the protein is a member of the complex. 
;Y
:for dimers and polymers. In case of dimers and polymers when the number of subunits is not described in the original interaction record, the edge is labelled by a Y. Interactor A (column 1) will be identical to the Interactor B (column 2).  The graphical representation of this will appear as a single node connected to itself (loop).  The actual number of self-interacting subunits may be 2 (dimer) or more (say 5 for a pentamer). Refer to the original interaction record for more details and see column 22. 

Column 1, Column 21 and Column 2 are all concatenated into a single 
space-delimited identifier to create the interaction identifier when 
this file is imported into Cytoscape; for example:

<pre>qE03bpSsQiJouJbn6ISt8DnD/pA9606 (X) E4tMCoGbaqAfjU8QXbQzbAb8fGQ9606</pre>


=== Column number: 22 (experimental_roleA) ===
{|
|Column name: ||experimental_roleA
|-
|Column type: ||string
|-
|Description: ||Whether the interactor A is the bait or the pray, if this information is relevant and available.

|-
|Example: ||<pre>unspecified, bait , pray</pre>
|}


=== Column number: 23 (experimental_roleB) ===
{|
|Column name: ||experimental_roleB
|-
|Column type: ||string
|-
|Description: ||Whether the interactor B is the bait or the pray, if this information is relevant and available.

|-
|Example: ||<pre>unspecified, bait , pray</pre>
|}




=== Column number: 24 (numParticipants) ===

{|
|Column name: ||numParticipants
|-
|Column type: ||Integer
|-
|Description: ||Number of participants in the interaction
|-
|Example: ||<pre>2</pre>
|}

'''Notes'''

* For edges labelled <tt>X</tt> (see column 21) this value will be two.  
* For edges labelled <tt>C</tt>, this value will be equivalent to the number of protein subunits included in the complex(represented by the complex node).
* For interactions labelled <tt>Y</tt>, this value will either be the number of self-interacting subunits (if present in the original interaction record) or 1 where the exact number of subunits is unknown or unspecified.


=== Column number: 25 (ROGA) ===

{|
|Column name: ||ROGA
|-
|Column type: ||Integer
|-
|Description: ||Integer representation of uidA
|-
|Example: ||<pre>617653</pre>
|}

=== Column number: 26 (ROGB)===

{|
|Column name: ||ROGB
|-
|Column type: ||Integer
|-
|Description: ||Integer representation of uidB 
|-
|Example: ||<pre>4052696</pre>
|}

=== Column number: 27 (interaction_name)===

{|
|Column name: ||interaction_name
|-
|Column type: ||String
|-
|Description: ||The name of the interaction,
|-
|Example: ||<pre>MTA1-HDAC core complex</pre>
|}

'''Notes'''

* A name was selected from the original interaction data provided when available. 
* When no interaction name available a name was constructed using the names of the interactors (e.g.Interaction involving HCK_HUMAN and RASA1_HUMAN).

[[Category:iRefIndex]]