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Last edited: 2011-03-25

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

Taxon specific MITAB files

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

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

Repeated lines There are multiple lines that are repeated many times. These appear to arise from BIND 3DBP division (see for example lines 6,14,118,126 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# . Could be handled as a post-processing step on MITAB to take the unique set of all MITAB lines.

Interaction related resources

Source	Format	Location	Version (date)
BIND,	Tab-delimited text file.	ftp://ftp.bind.ca/pub/BIND/data/bindflatfiles/bindindex/ 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
BioGRID	PSI-MI 2.5	http://www.thebiogrid.org/downloads.php /Current Release/BIOGRID-ALL-2.0.61.psi.zip	Version 2.0.61 (January 31st, 2010)
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 dip20091230.mif25	December 30th, 2009
HPRD,	PSI-MI 2.5	http://www.hprd.org/download/ HPRD_SINGLE_PSIMI_070609.xml.tar.gz	Release 8. July 6th, 2009
IntAct,	PSI-MI 2.5	ftp://ftp.ebi.ac.uk/pub/databases/intact/2010-01-22/psi25/pmidMIF25.zip	January 22nd, 2010
MINT	PSI-MI 2.5	ftp://mint.bio.uniroma2.it/pub/release/psi/current/psi25/pmid/	November 11th, 2009
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)
I2D	PSI-MI 2.5	http://ophid.utoronto.ca/ophidv2.201/downloads.jsp	Downloaded on February 8th, 2010

Sequence related resources

Source	Format	Location	Version (date)
SEGUID	Tab-delimited text	ftp://bioinformatics.anl.gov/seguid/ seguidannotation	August 7th, 2007 (server gives "08/07/107")
UniProt	Text	http://www.uniprot.org/downloads UniProtKB/Swiss-Prot (uniprot_sprot.dat.gz)	UniProt Knowledgebase Release 15.14: UniProtKB/Swiss-Prot Release 57.14 (09-Feb-2010) UniProtKB/TrEMBL Release 40.14 (09-Feb-2010)
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 39 (January 30th, 2010)
NCBI, MMDB/PDB	Tab-delimited text	ftp://ftp.ncbi.nih.gov/mmdb/pdbeast/table	(Downloaded on February 8th, 2010)
NCBI, PDB sequences	FASTA	ftp://ftp.ncbi.nih.gov/blast/db/FASTA/pdbaa.gz	(Downloaded on February 8th, 2010)
NCBI Gene2Refseq	Tab-delimited text	ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ gene2refseq.gz	(Downloaded on February 8th, 2010)

All iRefIndex Pages

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