Sources iRefIndex 6.0
Last edited:12th, September 2009
Applies to iRefIndex release: 6.0
Release date: <To_be_announced>
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:
- For statistics on the public dataset (distributed on the FTP site contains) please refer to:
| 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... |
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) | |
| 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) |
