Sources
From irefindex
Last edited: November 11th, 2008 Applies to iRefIndex release: 1.0, 1.1 and 2.0 Release date: November 11th, 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/ | 05/25/05 |
| BioGRID | PSI-MI 2.5 | http://www.thebiogrid.org/downloads.php BIOGRID-ORGANISM-2.0.38.psi25.zip | Version 2.0.38 |
| DIP | PSI-MI 2.5 | http://dip.doe-mbi.ucla.edu/dip/Download.cgi dip20080114.mif25.gz | 01/14/08 |
| HPRD, | PSI-MI 2.5 | http://www.hprd.org/download/ HPRD_SINGLE_PSIMI_090107.xml.tar.gz | Release 7. September 1, 2007 |
| IntAct, | PSI-MI 2.5 | ftp://ftp.ebi.ac.uk/pub/databases/intact/2008-03-14/psi25/ pmidMIF25.zip | 03/15/08 |
| MINT | PSI-MI 2.5 | ftp://mint.bio.uniroma2.it/pub/release/psi/2007-12-21/psi25/ full.psi25.zip | 12/21/07 |
| 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 | 07/24/07 |
| 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 13.1 (March 18, 2008) |
| UniProt, IsoForms | FASTA | http://beta.uniprot.org/downloads uniprot_sprot_varsplic.fasta.gz | 03/18/08 |
| 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: 55.1 (18-Mar-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: 55.1 (18-Mar-2008) |
| NCBI, RefSeq | GenPept | ftp://ftp.ncbi.nih.gov/refseq/release/complete see *.protein.gpff.gz files | Release 28 (March 9, 2008) |
| NCBI, MMDB/PDB | Tab-delimited text | ftp://ftp.ncbi.nih.gov/mmdb/pdbeast/table | 03/20/08 |
| NCBI, PDB sequences | FASTA | ftp://ftp.ncbi.nih.gov/blast/db/FASTA/pdbaa.gz | 03/20/08 |
| NCBI Gene2Refseq | Tab-delimited text | ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ gene2refseq.gz | 03/21/08 |
