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Sources iRefIndex 6.0

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Last edited:28th, December 2009

Applies to iRefIndex release: 6.0

Release date: 27th Oct 2009

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.

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

05/25/05
BioGRID PSI-MI 2.5 http://www.thebiogrid.org/downloads/datasets/BIOGRID-ALL-SINGLEFILE-2.0.53.psi25.xml.gz Version 2.0.53
DIP PSI-MI 2.5 http://dip.doe-mbi.ucla.edu/dip/Download.cgi (dip20090126.mif25) January 26, 2009
HPRD, PSI-MI 2.5 http://www.hprd.org/download/ (HPRD_SINGLE_PSIMI_070609.xml.tar.gz) Release 8. July 06, 2009
IntAct, PSI-MI 2.5 ftp://ftp.ebi.ac.uk/pub/databases/intact/2009-06-19/psi25/ (pmidMIF25.zip) July 19, 2009
MINT PSI-MI 2.5 ftp://mint.bio.uniroma2.it/pub/release/psi/2009-07-28/psi25/pmid/ July 28, 2009
MPACT PSI-MI 2.5 ftp://ftpmips.gsf.de/yeast/PPI/ (mpact-complete.psi25.xml.gz) January 10, 2008
MPPI PSI-MI 1.0 http://mips.gsf.de/proj/ppi/data/mppi.gz Not available
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/) 07/18/06
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) Not available (time stamp of file September 08 2008)
I2D PSI-MI 2.5 http://ophid.utoronto.ca/ophidv2.201/downloads.jsp (Not included in this release)

Sequence related resources

Source Format Location Version (date)
SEGUID Tab-delimited text ftp://bioinformatics.anl.gov/seguid/ seguidannotation September 23rd, 2008
UniProt Text http://www.uniprot.org/downloads
Download : 1.UniProtKB/Swiss-Prot (uniprot_sprot.dat.gz) 2.UniProtKB/TrEMBL (uniprot_trembl.dat.gz)
UniProt Release 15.3 (May 26th 2009)
UniProt, IsoForms FASTA http://www.uniprot.org/downloads uniprot_sprot_varsplic.fasta.gz Release 15.5 (July 07th 2009)
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 Release:57.3 (May 26th 2009)
UniProt, FLY Tab-delimited text file. http://www.expasy.org/cgi-bin/lists?fly.txt Drosophila: entries, gene names and cross-references to FlyBase. Release: 57.3 (May 26th 2009)
NCBI, RefSeq GenPept ftp://ftp.ncbi.nih.gov/refseq/release/complete see *.protein.gpff.gz files Release 35 (May 4th, 2009)
NCBI, MMDB/PDB Tab-delimited text ftp://ftp.ncbi.nih.gov/mmdb/pdbeast/table (Downloaded on May 14th, 2009)
NCBI, PDB sequences FASTA ftp://ftp.ncbi.nih.gov/blast/db/FASTA/pdbaa.gz (Downloaded on May 14th, 2009)
NCBI Gene2Refseq Tab-delimited text ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ gene2refseq.gz (Downloaded on May 14th, 2009)

All iRefIndex Pages

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