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Sources iRefIndex 3.0

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Last edited: March 9th, 2009

Applies to iRefIndex release: 3.0

Release date: March 9th, 2009

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/)

Description: This file lists interaction and protein sequence related resources used for the current build of the iRefIndex.

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 at 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/BIOGRID-ORGANISM-2.0.49.psi25.zip Version 2.0.49
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_090107.xml.tar.gz Release 7. September 01, 2007
IntAct, PSI-MI 2.5 ftp://ftp.ebi.ac.uk/pub/databases/intact/2009-02-06/psi25/ pmidMIF25.zip August 22, 2008
MINT PSI-MI 2.5 ftp://ftp://mint.bio.uniroma2.it/pub/release/psi/2008-04-07/full.psi25.zip April 07, 2008
MPact PSI-MI 2.5 ftp://ftpmips.gsf.de/yeast/PPI/ mpact-complete.psi25.xml April 19, 2007
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) 08/09/18

Sequence related resources

Source Format Location Version (date)
SEGUID Tab-delimited text ftp://bioinformatics.anl.gov/seguid/ seguidannotation September 23rd, 2008
UniProt Text http://beta.uniprot.org/downloads
Download : 1.UniProtKB/Swiss-Prot (uniprot_sprot.dat.gz) 2.UniProtKB/TrEMBL (uniprot_trembl.dat.gz)
UniProt release 14.0 (September 02, 2008)
UniProt, IsoForms FASTA http://beta.uniprot.org/downloads uniprot_sprot_varsplic.fasta.gz September 25th, 2008
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: 56.2 (September 23rd, 2008)
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: 56.2 (September 25th, 2008)
NCBI, RefSeq GenPept ftp://ftp.ncbi.nih.gov/refseq/release/complete see *.protein.gpff.gz files Release 33 (January 20, 2009)
NCBI, MMDB/PDB Tab-delimited text ftp://ftp.ncbi.nih.gov/mmdb/pdbeast/table (Downloaded on February 19, 2009)
NCBI, PDB sequences FASTA ftp://ftp.ncbi.nih.gov/blast/db/FASTA/pdbaa.gz (Downloaded on February 19, 2009)
NCBI Gene2Refseq Tab-delimited text ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ gene2refseq.gz (Downloaded on February 19, 2009)