Sources iRefIndex 3.0
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.
| 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... |
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 | 08/09/18 |
| 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) |
