Sources

From irefindex
Revision as of 10:00, 6 November 2008 by Sabry (talk | contribs)

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.


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/ 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


Sequence related resources

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