 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 8.0
From Donaldson Group
Last edited: 2011-01-20
Applies to iRefIndex release: 8.0
Release date: 2011-01-19
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_8.0
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... | 25th May, 2005 |
| BIND Translation | PSI-MI 2.5 | http://download.baderlab.org/BINDTranslation/release1_0/BINDTranslation_v1_xml_AllSpecies.tar.gz | release1_0, December 16th, 2010 (timestamp) |
| BioGRID | PSI-MI 2.5 | http://http://thebiogrid.org/downloads/archives/Release%20Archive/BIOGRID-3.1.71/BIOGRID-ALL-3.1.71.psi25.zip | Version 3.1.71 (November 25th 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 dip20101010.mif25.gz | October 10th, 2010 |
| HPRD | PSI-MI 2.5 | http://www.hprd.org/download HPRD_SINGLE_PSIMI_041310.xml.tar.gz | Release 9. April 13th, 2010 |
| IntAct | PSI-MI 2.5 | ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psi25/pmidMIF25.zip | December 16th, 2010 (timestamp) |
| MINT | PSI-MI 2.5 | /biotek/cnkeeper/storage/databases/donmysql/Sabry/data/MINT/2010-12-21/ | December 21st, 2010 |
| 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) |
| 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/) | July 07th, 2006 |
Sequence related resources
| Source | Format | Location | Version (date) |
| SEGUID | Tab-delimited text | ftp://bioinformatics.anl.gov/seguid/ seguidannotation | July 24th, 2007 (timestamp) |
| UniProt | Text | http://www.uniprot.org/downloads UniProtKB/Swiss-Prot (uniprot_sprot.dat.gz) | UniProt Knowledgebase Release 2010_12(Downloaded 21-December-2010): UniProtKB/Swiss-Prot UniProtKB/TrEMBL (from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/reldate.txt) |
| 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 44 (Downloaded on December 21st, 2010) (from http://www.ncbi.nlm.nih.gov/refseq/) |
| NCBI, MMDB/PDB | Tab-delimited text | ftp://ftp.ncbi.nih.gov/mmdb/pdbeast/table | (Downloaded on December 21st, 2010) |
| NCBI, PDB sequences | FASTA | ftp://ftp.ncbi.nih.gov/blast/db/FASTA/pdbaa.gz | (Downloaded on December 21st, 2010) |
| NCBI Gene2Refseq | Tab-delimited text | ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ gene2refseq.gz | (Downloaded on December 21st, 2010) |
All iRefIndex Pages
Follow this link for a listing of all iRefIndex related pages (archived and current).
