Sources iRefIndex 2.0
Last edited: November 11th, 2008
Applies to iRefIndex release: beta 2.0
Release date: October 17th, 2008
Authors: Ian Donaldson and Sabry Razick
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 snapshots 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 (http://web.archive.org/web/*/http://www.blueprint.org). |
05/25/05 |
| BioGRID | PSI-MI 2.5 | http://www.thebiogrid.org/BIOGRID-ORGANISM-2.0.45.psi25.zip | Version 2.0.45 |
| DIP | PSI-MI 2.5 | http://dip.doe-mbi.ucla.edu/dip/Download.cgi dip20080708.mif25 | 07/08/08 |
| 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/2008-08-22/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 |
| 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 31 (August 30, 2008) |
| NCBI, MMDB/PDB | Tab-delimited text | ftp://ftp.ncbi.nih.gov/mmdb/pdbeast/table | (Downloaded on October 08th,2008) |
| NCBI, PDB sequences | FASTA | ftp://ftp.ncbi.nih.gov/blast/db/FASTA/pdbaa.gz | (Downloaded on October 08th,2008) |
| NCBI Gene2Refseq | Tab-delimited text | ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ gene2refseq.gz | (Downloaded on October 08th,2008) |
