 Important | As of March 15th, 2013, this site is maintained at http://irefindex.org
This site is for archival purposes and may eventually be deleted. |
Sources iRefIndex 7.0
From Donaldson Group
Last edited: 2010-09-20
Applies to iRefIndex release: 7.0
Release date: 18th May 2010
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_7.0
- For statistics on the public dataset (distributed on the FTP site contains) please refer to: http://irefindex.uio.no/wiki/Statistics_iRefIndex_free_7.0
Interaction related resources
| Source | Format | Location | Version (date) | |
| BIND, | Tab-delimited text file. | ftp://ftp.bind.ca/pub/BIND/data/bindflatfiles/bindindex/ (This link is not available any more)
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... | 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 | |
| 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 | |
| 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) | |
| BIND_TRANSLATION | PSI-MI 2.5 | **January 8th, 2010(**see note below) | (from archive) |
** The BIND Translation files in this iRefIndex version were an incomplete, pre-release version of BIND Translate that was kindly provided by Gary Bader for the purpose of statistical examination; they are not available for download from either the Bader group or iRefIndex. In future releases of iRefIndex, BIND Translate data available at http://download.baderlab.org/BIND/ (http://baderlab.org/BINDTranslation) will be integrated and made available.
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).
