Sources iRefIndex 8.0

This is a planning template for the next release 8.0.  It does not correspond to a released product.
See http://irefindex.uio.no/ for the most recent release and related documentation.
This page will be updated as release 8.0 id built.  
Check for xxx before  release. 

Last edited: 2010-09-14

Applies to iRefIndex release: 8.0

Release date: xxx

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_xxx
• For statistics on the public dataset (distributed on the FTP site contains) please refer to:http://irefindex.uio.no/wiki/Statistics_iRefIndex_free_xxx

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... http://web.archive.org/web/*/http://www.blueprint.org	25th May, 2005
BIND Translation	PSI-MI 2.5	http://download.baderlab.org/BIND/PSIMI25_AllInclusive_AllSpecies.zip	March 26th, 2010 (timestamp)
BioGRID	PSI-MI 2.5	http://www.thebiogrid.org/downloads.php /Current Release/BIOGRID-ALL-3.0.68.psi.zip	Version 3.0.68 (August 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 dip20091230.mif25	December 30th, 2009
HPRD	PSI-MI 2.5	http://www.hprd.org/download/ HPRD_SINGLE_PSIMI_070609.xml.tar.gz	Release 8. July 6th, 2009
IntAct	PSI-MI 2.5	ftp://ftp.ebi.ac.uk/pub/databases/intact/2010-01-22/psi25/pmidMIF25.zip	January 22nd, 2010
MINT	PSI-MI 2.5	ftp://mint.bio.uniroma2.it/pub/release/psi/current/psi25/pmid/	November 11th, 2009
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
I2D	PSI-MI 2.5	http://ophid.utoronto.ca/ophidv2.201/downloads.jsp	Downloaded on February 8th, 2010
MatrixDB	?	http://matrixdb.ibcp.fr/ ?	?
MPIDB	?	http://www.jcvi.org/mpidb ?	?
InnateDB	?	www.innatedb.com ?	?

Sequence related resources

Source	Format	Location	Version (date)
SEGUID	Tab-delimited text	ftp://bioinformatics.anl.gov/seguid/ seguidannotation	August 7th, 2007 (server gives "08/07/107")
UniProt	Text	http://www.uniprot.org/downloads UniProtKB/Swiss-Prot (uniprot_sprot.dat.gz)	UniProt Knowledgebase Release 15.14: UniProtKB/Swiss-Prot Release 57.14 (09-Feb-2010) UniProtKB/TrEMBL Release 40.14 (09-Feb-2010)
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 39 (January 30th, 2010)
NCBI, MMDB/PDB	Tab-delimited text	ftp://ftp.ncbi.nih.gov/mmdb/pdbeast/table	(Downloaded on February 8th, 2010)
NCBI, PDB sequences	FASTA	ftp://ftp.ncbi.nih.gov/blast/db/FASTA/pdbaa.gz	(Downloaded on February 8th, 2010)
NCBI Gene2Refseq	Tab-delimited text	ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ gene2refseq.gz	(Downloaded on February 8th, 2010)

All iRefIndex Pages

Follow this link for a listing of all iRefIndex related pages (archived and current).