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Last edited: 2011-06-06

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.

• For statistics on full public dataset please refer to: http://irefindex.uio.no/wiki/Statistics_iRefIndex_xxx
• For statistics on the public dataset (distributed on the FTP site contains) please refer to:http://irefindex.uio.no/wiki/Statistics_iRefIndex_free_xxx

Issues

Hard Release date: July 1st.

Yeast taxon id changes See http://www.uniprot.org/news/2011/05/03/release

New databases To Be Discussed

BioGrid interaction record ids (pre-build issue) To Be Done

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

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

RIGID recalculation (pre-build issue)

See bug 242. Modify existing RIGID table or loose continuity of iRIGIDs with last release.

Taxon specific MITAB files (post-processing issue)

Taxon specific files should contain interactions ONLY if one or both taxa, taxb have the appropriate taxon (regardless of what the source database said the interaction taxon was. Change README. Example see PMID http://wodaklab.org/iRefWeb/pubReport/detail?pubmed=12565857+ A "mouse" interaction from HPRD lists only human interactors (the paper is about mouse and they have made a transfer to human without noting what they have done.) As a result, this human interaction ends up in the mouse MITAB (because HPRD says it was mouse). BioGRID correctly curates the paper as about mouse.

CORUM methods (code change implemented)

Ensure that all CORUM methods (with MI terms) are parsed.

• This is now fixed (Sabry) - please get the latest mapper from CVS

Repeated lines (post-processing issue)

There are multiple lines that are repeated many times. These appear to arise from BIND 3DBP division (see for example lines 5,13,117,125 in Ecoli MITAB and others arising from BIND ID 92720 - 44 pieces of experimental evidence and 5 PMIDs) because the accessions for the different experimental forms are not present in MITAB. See Antonio and bug# 245. Could be handled as a post-processing step on MITAB to take the unique set of all MITAB lines.

MITAB/irefscape canonicalization (post-processing issue)

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.

Decided not to chnage L method...instead:

Resolve by distributing non-canonicalized data as before AND a canonicalized MITAB file with complete provenance info (this will become the main MITAB file we release and it will support PSICQUIC services and we will drop non-canonicalised version in future releases). Also, canonicalize irefscape data and include provenace data for interactors in edge attribute viewer.

Requires review of current MITAB file format by Ian.

Other issues

• Discuss the way to include I2D -- No I2D will not be included
• Parse all new datasets to a temporary database and test before homogenizing. -- not required, no new data sources
• Whether to use both BIND text and BIND_Translation OR only one of them

• The default output data will be the canonical form. The MITAB will have the canonical Accession as the UIDA and UIDB. There will be new columns beforeCanonicalizationReferenceA, beforeCanonicalizationReferenceB. The aliases and the alternative identifiers will be of the canonical group not of a specific protein. With the new columns and all the references, it has to be tested whether the row width will exceed any thresholds (e.g. MySQL maximum row with), (I assume this would not be a problem).

• For iRefScape, once the canonicalization is performed there will be no "uncanonicalize option" (currently there is a option to use canonical expansion).

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	25th May, 2005
BINDTranslate	PSI-MI 2.5	http://download.baderlab.org/BINDTranslation/release1_0/BINDTranslation_v1_xml_AllSpecies.tar.gz	Version 1.0 (December 15th, 2010)
BioGRID	PSI-MI 2.5	http://thebiogrid.org/downloads/archives/Release%20Archive/BIOGRID-3.1.77/BIOGRID-ALL-3.1.77.psi25.zip	Version 3.1.77 (June 1st, 2011)
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	December 2nd, 2009
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	October 10th, 2010
HPRD,	PSI-MI 2.5	http://www.hprd.org/download/ HPRD_PSIMI_041310.tar.gz	Release 9. April 13th, 2010
IntAct,	PSI-MI 2.5	ftp://ftp.ebi.ac.uk/pub/databases/intact/2011-05-23/psi25/pmidMIF25.zip	May 25th, 2011
MINT	PSI-MI 2.5	ftp://mint.bio.uniroma2.it/pub/release/psi/current/psi25/pmid/	December 21st, 2010
MPACT	PSI-MI 2.5	ftp://ftpmips.gsf.de/yeast/PPI/ mpact-complete.psi25.xml.gz	January 10th, 2008
MPPI	PSI-MI 1.0	http://mips.gsf.de/proj/ppi/data/mppi.gz	June 1st, 2004 (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/)	July 07th, 2006
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 http://www.jcvi.org/mpidb/download.php	Downloaded on ***?***
MatrixDB	PSI-MI 2.5	http://matrixdb.ibcp.fr/ MatrixDB_20100826.xml.zip	August 26th, 2010 (timestamp)

Sequence related resources

Source	Format	Location	Version (date)
SEGUID	Tab-delimited text	ftp://bioinformatics.anl.gov/seguid/ seguidannotation	July 24th, 2007 (timestamp)
UniProt	Text	http://www.uniprot.org/downloads UniProtKB/Swiss-Prot (uniprot_sprot.dat.gz)	UniProt Knowledgebase Release 2010_12(Downloaded 21-December-2010): 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 44 (Downloaded on December 21st, 2010) (from http://www.ncbi.nlm.nih.gov/refseq/)
NCBI, MMDB/PDB	Tab-delimited text	ftp://ftp.ncbi.nih.gov/mmdb/pdbeast/table	(Downloaded on December 21st, 2010)
NCBI, PDB sequences	FASTA	ftp://ftp.ncbi.nih.gov/blast/db/FASTA/pdbaa.gz	(Downloaded on December 21st, 2010)
NCBI Gene2Refseq	Tab-delimited text	ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ gene2refseq.gz	(Downloaded on December 21st, 2010)

All iRefIndex Pages

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