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Sources iRefIndex 11.0

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Last edited: 2013-05-27

Applies to iRefIndex release: 11.0

Release date: 2013-05-27

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.


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	2013-05-01 13:58:07
BIOGRID	RELEASE_URL	http://thebiogrid.org/downloads/archives/Release%20Archive/BIOGRID-3.2.100/
BIOGRID	DOWNLOAD_FILES	BIOGRID-ALL-3.2.100.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/2013/mif25/dip20130131.mif25.gz
DIP	FILENAME	dip20130131.mif25
DIP	DATE	01/31/2013
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	2013-05-02 11:34:00
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	
OPHID	RELEASE_URL	local copy
OPHID	DOWNLOAD_FILES	ophid*.xml

INNATEDB	DATE	2013-05-12 19:40:20
INNATEDB	RELEASE_URL	http://www.innatedb.com/download/interactions/
INNATEDB	DOWNLOAD_FILES	innatedb_all.mitab.gz

MPIDB	DATE	2013-05-16 19:06:17
MPIDB	RELEASE_URL	http://www.jcvi.org/mpidb/download.php?dbsource=
MPIDB	DOWNLOAD_FILES	MPI-IMEX MPI-LIT

Other data sources

PSI_MI	DATE	2013-05-16 19:06:23
PSI_MI	RELEASE_URL	http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/mi/rel25/data/
PSI_MI	DOWNLOAD_FILES	psi-mi25.obo

TAXONOMY	DATE	2013-05-16 16:20:00
TAXONOMY	RELEASE_URL	ftp://ftp.ncbi.nih.gov/pub/taxonomy/
TAXONOMY	DOWNLOAD_FILES	taxdump.tar.gz

DIG	DATE	2010-06-14
DIG	RELEASE_URL	local copy
DIG	DOWNLOAD_FILES	morbidmap14062010.txt

FLY	VERSION	2013_05
FLY	DATE	01-May-2013
FLY	RELEASE_URL	http://www.uniprot.org/docs/
FLY	DOWNLOAD_FILES	fly.txt

GENE	DATE	2013-05-16 01:13:00
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	2012-07-19 22:00:00
IPI	RELEASE_URL	ftp://ftp.ebi.ac.uk/pub/databases/IPI/last_release/current/
IPI	DOWNLOAD_FILES	*.fasta.gz

MMDB	DATE	2013-05-09 19:28:00
MMDB	RELEASE_URL	ftp://ftp.ncbi.nih.gov/mmdb/pdbeast/
MMDB	DOWNLOAD_FILES	table

PDB	DATE	2013-05-15 19:15:00
PDB	RELEASE_URL	ftp://ftp.ncbi.nih.gov/blast/db/FASTA/
PDB	DOWNLOAD_FILES	pdbaa.gz

REFSEQ	DATE	2013-05-01 14:23:00
REFSEQ	RELEASE_URL	ftp://ftp.ncbi.nih.gov/refseq/release//complete/
REFSEQ	DOWNLOAD_FILES	complete*.protein.gpff.gz

UNIPROT	VERSION	2013_05
UNIPROT	DATE	01-May-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_05
YEAST	DATE	01-May-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).