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Sources iRefIndex 10.0

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Last edited: 2013-03-14

Applies to iRefIndex release: 10.0

Release date: 2013-03-02

Authors: Paul Boddie and Ian Donaldson

Database: iRefIndex (http://irefindex.org)


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.


Interaction data sources

BIND	DATE	2005-05-25
BIND	RELEASE_URL
http://bond.unleashedinformatics.com/downloads/data/BIND/data/bindflatfiles/bindindex/
BIND	DOWNLOAD_FILES	20060525*.txt
BIND_TRANSLATION	DATE	2010-12-15 15:54:01
BIND_TRANSLATION	RELEASE_URL	http://download.baderlab.org/BINDTranslation/release1_0/
BIND_TRANSLATION	DOWNLOAD_FILES	BINDTranslation_v1_xml_AllSpecies.tar.gz
BIOGRID	DATE	2012-08-31 19:24:08
BIOGRID	RELEASE_URL	http://thebiogrid.org/downloads/archives/Release%20Archive/BIOGRID-3.1.92/
BIOGRID	DOWNLOAD_FILES	BIOGRID-ALL-3.1.92.psi25.zip
CORUM	DATE	2009-12-02 18:24:15
CORUM	RELEASE_URL	http://mips.gsf.de/genre/export/sites/default/corum/
CORUM	DOWNLOAD_FILES	allComplexes.psimi.zip
DIP	DOWNLOAD	ftp://dip.doe-mbi.ucla.edu/2012/mif25/dip20120818.mif25.gz
DIP	FILENAME	dip20120818.mif25
DIP	DATE	08/18/2012
DIP	RELEASE_URL	http://dip.doe-mbi.ucla.edu/dip/Download.cgi?SM=3
HPRD	FILENAME	HPRD_PSIMI_041310.tar.gz
HPRD	VERSION	Release 9
HPRD	DATE	04-13-10
HPRD	RELEASE_URL	http://www.hprd.org/RELEASE9/
HPRD	DOWNLOAD_FILES	HPRD_PSIMI_041310.tar.gz
INTACT	DATE	2012-12-14 20:04:00
INTACT	RELEASE_URL	ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psi25/
INTACT	DOWNLOAD_FILES	pmidMIF25.zip
MATRIXDB	DATE	2012-08-03 11:26:01
MATRIXDB	RELEASE_URL	http://matrixdb.ibcp.fr/cgi-bin/download%3C../../
MATRIXDB	DOWNLOAD_FILES	MatrixDB_20120801.xml.zip
MINT	DATE	2011-12-04 23:00:00
MINT	RELEASE_URL	ftp://mint.bio.uniroma2.it/pub/release/psi/current/psi25/pmids/
MINT	DOWNLOAD_FILES	*.psi25.zip
MPACT	DATE	2008-09-30 22:00:00
MPACT	RELEASE_URL	ftp://ftpmips.gsf.de/yeast/PPI/
MPACT	DOWNLOAD_FILES	mpact-complete.psi25.xml.gz
MPPI	DATE	2004-06-01 15:37:37
MPPI	RELEASE_URL	http://mips.gsf.de/proj/ppi/data/
MPPI	DOWNLOAD_FILES	mppi.gz
OPHID	DATE	2013-01-14 10:33:18
OPHID	RELEASE_URL	local archive of last release
OPHID	DOWNLOAD_FILES	ophid*.xml
INNATEDB	DATE	2013-01-13 14:14:49
INNATEDB	RELEASE_URL	http://www.innatedb.com/download/interactions/
INNATEDB	DOWNLOAD_FILES	innatedb_all.mitab.gz
MPIDB	DATE	2013-01-14 04:24:36
MPIDB	RELEASE_URL	http://www.jcvi.org/mpidb/download.php?dbsource=
MPIDB	DOWNLOAD_FILES	MPI-IMEX MPI-LIT

Other data sources

PSI_MI	DATE	2013-01-14 04:24:42
PSI_MI	RELEASE_URL	http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/mi/rel25/data/
PSI_MI	DOWNLOAD_FILES	psi-mi25.obo
TAXONOMY	DATE	2013-01-14 03:20:00
TAXONOMY	RELEASE_URL	ftp://ftp.ncbi.nih.gov/pub/taxonomy/
TAXONOMY	DOWNLOAD_FILES	taxdump.tar.gz
DIG	DATE	2013-01-14 10:34:17
DIG	RELEASE_URL	file:///storage/localdata/DIG/
DIG	DOWNLOAD_FILES	morbidmap14062010.txt
FLY	VERSION	2013_01
FLY	DATE	09-Jan-2013
FLY	RELEASE_URL	http://www.uniprot.org/docs/
FLY	DOWNLOAD_FILES	fly.txt
GENE	DATE	2013-01-13 04:10:00
GENE	RELEASE_URL	ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
GENE	DOWNLOAD_FILES	gene2refseq.gz gene_info.gz gene2go.gz gene_history.gz
IPI	DATE	2012-07-20 15:07:00
IPI	RELEASE_URL	ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/
IPI	DOWNLOAD_FILES	*.fasta.gz
MMDB	DATE	2013-01-10 14:03:00
MMDB	RELEASE_URL	ftp://ftp.ncbi.nih.gov/mmdb/pdbeast/
MMDB	DOWNLOAD_FILES	table
PDB	DATE	2013-01-13 20:45:00
PDB	RELEASE_URL	ftp://ftp.ncbi.nih.gov/blast/db/FASTA/
PDB	DOWNLOAD_FILES	pdbaa.gz
REFSEQ	DATE	2012-11-09 22:31:00
REFSEQ	RELEASE_URL	ftp://ftp.ncbi.nih.gov/refseq/release//complete/
REFSEQ	DOWNLOAD_FILES	complete*.protein.gpff.gz
UNIPROT	VERSION	2013_01
UNIPROT	DATE	09-Jan-2013
UNIPROT	RELEASE_URL	ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/
UNIPROT	DOWNLOAD_FILES	uniprot_sprot.dat.gz uniprot_trembl.dat.gz uniprot_sprot_varsplic.fasta.gz reldate.txt
YEAST	VERSION	2013_01
YEAST	DATE	09-Jan-2013
YEAST	RELEASE_URL	http://www.uniprot.org/docs/
YEAST	DOWNLOAD_FILES	yeast.txt


All iRefIndex Pages

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