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Difference between revisions of "Sources and Issues Next Release"

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=== DIP interaction types ===
 
=== DIP interaction types ===
Not all interaction types are properly extracted from DIP XML records because some are stored in an unexpected filed.
+
 
 +
Not all interaction types are properly extracted from DIP XML records because some are stored in an unexpected field.
  
 
See [[Bugzilla:251]].
 
See [[Bugzilla:251]].
  
 +
=== Review interaction detection type mappings===
  
 
 
=== Review interaction detection type mappings===
 
 
Some InnateDB detection types have been reported to be mapped to a parent term.
 
Some InnateDB detection types have been reported to be mapped to a parent term.
 
  
 
See [[Bugzilla:252]].
 
See [[Bugzilla:252]].
  
=== Check that BIND small-molecules are not mis-ampped to proteins===
+
=== Check that BIND small-molecules are not mis-mapped to proteins===
 
+
  
 
See [[Bugzilla:253]].
 
See [[Bugzilla:253]].
  
=== Estimate accurate time to build irefindex===
+
=== Estimate accurate time to build iRefIndex===
 
+
  
 
See [[Bugzilla:254]].
 
See [[Bugzilla:254]].
  
=== BioGrid interaction record ids (pre-build issue) ===
+
=== BioGRID interaction record ids (pre-build issue) ===
  
Capture Biogrid interaction record ids so iRefWeb can link out to BioGrid.
+
Capture BioGRID interaction record ids so iRefWeb can link out to BioGRID.
  
The only interaction id available from the BioGrid files are already being used and also there in the iRefWeb, such as...
+
The only interaction id available from the BioGRID files are already being used and also there in the iRefWeb, such as...
  
 
  <primaryRef db="grid" id="103" refType="identity" refTypeAc="MI:0356" dbAc="MI:0463" />
 
  <primaryRef db="grid" id="103" refType="identity" refTypeAc="MI:0356" dbAc="MI:0463" />
  
 
See [[Bugzilla:250]].
 
See [[Bugzilla:250]].
 
 
  
 
=== MITAB/iRefScape canonicalization ===
 
=== MITAB/iRefScape canonicalization ===

Revision as of 06:08, 13 February 2012

NoteNote

This is a planning template for the next release. It does not correspond to a released product. See http://irefindex.uio.no/ for the most recent release and related documentation. This page can be used to create the sources page. Check for xxx before copying and pasting to the appropriate sources page for the new release. Do not edit xxx in this page. Leave this page as a template. After making a new release page, update the general Sources for iRefIndex redirect page.

Last edited: 2012-02-13

Applies to iRefIndex release: xxx

Release date: xxx

Authors: Ian Donaldson, Sabry Razick and Paul Boddie

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

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

Description: This file lists interaction and protein sequence related resources used for the current build of the iRefIndex. Statistics for the iRefIndex are available and include a breakdown of interactors and interactions from each data source.

Contents

Issues

DIP interaction types

Not all interaction types are properly extracted from DIP XML records because some are stored in an unexpected field.

See Bugzilla:251.

Review interaction detection type mappings

Some InnateDB detection types have been reported to be mapped to a parent term.

See Bugzilla:252.

Check that BIND small-molecules are not mis-mapped to proteins

See Bugzilla:253.

Estimate accurate time to build iRefIndex

See Bugzilla:254.

BioGRID interaction record ids (pre-build issue)

Capture BioGRID interaction record ids so iRefWeb can link out to BioGRID.

The only interaction id available from the BioGRID files are already being used and also there in the iRefWeb, such as...

<primaryRef db="grid" id="103" refType="identity" refTypeAc="MI:0356" dbAc="MI:0463" />

See Bugzilla:250.

MITAB/iRefScape canonicalization

Change this to choose canonical sequence rather than longest sequence (mapping score L). Examples GeneID 84148 and 512564 unnecessarily separates Grid interaction data from interaction data from other databases.

See Bugzilla:255.

Build issues

Interaction related resources

Source Format Location Version (date)
BIND Tab-delimited text file. ftp://ftp.bind.ca/pub/BIND/data/bindflatfiles/bindindex/ (no longer available - see below).

20050525.complex2refs.txt

20050525.ints.txt

20050525.refs.txt

20050525.complexes.txt

20050525.labels.txt

20050525.complex2subunits.txt

These file are no longer available via ftp but are available from the authors. BIND archival content is now managed by Thomson Scientific. See http://bond.unleashedinformatics.com/ and http://bond.unleashedinformatics.com/downloads/data/BIND/

For historical purposes, a snapshot of the the Blueprint web-site may be viewed at...

http://web.archive.org/web/20050204013426/www.blueprint.org/index.html

...via the internet archive at...

http://web.archive.org/web/*/http://www.blueprint.org

2005-05-25
BIND Translation PSI-MI 2.5 http://download.baderlab.org/BINDTranslation/release1_0/BINDTranslation_v1_xml_AllSpecies.tar.gz Version 1.0 (2010-12-15)
BioGRID PSI-MI 2.5 http://thebiogrid.org/downloads/archives/Release%20Archive/BIOGRID-3.1.81/BIOGRID-ALL-3.1.81.psi25.zip Version 3.1.81 (2011-10-01)
CORUM PSI-MI 2.5 http://mips.gsf.de/genre/proj/corum/index.html
http://mips.gsf.de/genre/export/sites/default/corum/allComplexes.psimi.zip
2009-12-02
DIP PSI-MI 2.5 http://dip.doe-mbi.ucla.edu/dip/Download.cgi


dip20101010.mif25
Note: date on last IMEx release file is from 2008

2010-10-10
HPRD PSI-MI 2.5 http://www.hprd.org/download
HPRD_PSIMI_041310.tar.gz
Release 9 (2010-04-13)
IntAct PSI-MI 2.5 ftp://ftp.ebi.ac.uk/pub/databases/intact/2011-09-29/psi25/pmidMIF25.zip 2011-09-29
MINT PSI-MI 2.5 ftp://mint.bio.uniroma2.it/pub/release/psi/current/psi25/pmid/ 2010-12-21
MPACT PSI-MI 2.5 ftp://ftpmips.gsf.de/yeast/PPI/mpact-complete.psi25.xml.gz 2008-01-10
MPPI PSI-MI 1.0 http://mips.gsf.de/proj/ppi/data/mppi.gz 2004-06-01 (from archive)
OPHID PSI-MI 1.0 http://ophid.utoronto.ca/ophid/downloads.html (This service no longer available, please refer to http://ophid.utoronto.ca/ophidv2.201/) 2006-07-07
New for this release
InnateDB PSI-MI 2.5 http://www.innatedb.com/download.jsp
Curated InnateDB Data
2011-03-06
MPIDB MITAB format file http://www.jcvi.org/mpidb (information)

http://www.jcvi.org/mpidb/download.php (general downloads)
http://www.jcvi.org/mpidb/interaction.php?dbsource=MPI-LIT (specific download for MPI-LIT)
http://www.jcvi.org/mpidb/interaction.php?dbsource=MPI-IMEX (specific download for MPI-IMEX)

Downloaded on 2011-10-03
MatrixDB PSI-MI 2.5 http://matrixdb.ibcp.fr/
MatrixDB_20100826.xml.zip
2010-08-26 (timestamp)

Sequence related resources (not updated yet)

Source Format Location Version (date)
SEGUID Tab-delimited text ftp://bioinformatics.anl.gov/seguid/
seguidannotation
2007-07-24 (timestamp)
UniProt Text http://www.uniprot.org/downloads
UniProtKB/Swiss-Prot (uniprot_sprot.dat.gz)
UniProt Knowledgebase Release 2011_09 (2011-09-21) (Downloaded on 2011-10-04):
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL
(from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/reldate.txt)
UniProt Text http://www.uniprot.org/downloads
UniProtKB/TrEMBL (uniprot_trembl.dat.gz)
UniProt, IsoForms FASTA http://www.uniprot.org/downloads uniprot_sprot_varsplic.fasta.gz
UniProt, SGD Tab-delimited text file. http://www.expasy.org/cgi-bin/lists?yeast.txt
Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
UniProt, FLY Tab-delimited text file. http://www.expasy.org/cgi-bin/lists?fly.txt
Drosophila: entries, gene names and cross-references to FlyBase.
NCBI, RefSeq GenPept ftp://ftp.ncbi.nih.gov/refseq/release/complete
see *.protein.gpff.gz files
Release 49 (2011-09-09) (Downloaded on 2011-10-04)
(from http://www.ncbi.nlm.nih.gov/refseq/)
NCBI, MMDB/PDB Tab-delimited text ftp://ftp.ncbi.nih.gov/mmdb/pdbeast/table (Downloaded on 2011-10-04)
NCBI, PDB sequences FASTA ftp://ftp.ncbi.nih.gov/blast/db/FASTA/pdbaa.gz (Downloaded on 2011-10-03)
NCBI Gene2Refseq Tab-delimited text ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
gene2refseq.gz
(Downloaded on 2011-10-04)

All iRefIndex Pages

Follow this link for a listing of all iRefIndex related pages (archived and current).