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Sources iRefIndex 14.0

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Last edited: 2015-04-21

Applies to iRefIndex release: 14.0

Release date: 07-04-2013

Authors: 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 sets

BIND	DATE	2005-05-25
BIND	RELEASE_URL	http://bond.unleashedinformatics.com/downloads/data/BIND/data/bindflatfiles/bindindex/
BIND	DOWNLOAD_FILES	20060525*.txt

BIOGRID	DATE	2015-02-28 20:41:14
BIOGRID	RELEASE_URL	http://thebiogrid.org/downloads/archives/Release%20Archive/BIOGRID-3.3.122/
BIOGRID	DOWNLOAD_FILES	BIOGRID-ALL-3.3.122.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://sabry:z6RHVXe7@dip.doe-mbi.ucla.edu/2015/mif25/dip20150101.mif25.gz
DIP	FILENAME	dip20150101.mif25
DIP	DATE	01/01/2015
DIP	RELEASE_URL	http://dip.doe-mbi.ucla.edu/dip/Download.cgi?SM=3

HPRD	RELEASE_URL	http://hprd.org
HPRD	DOWNLOAD_FILES	HPRD_PSIMI_041310.tar.gz

I2D_IMEX	RELEASE_URL	http://www.ebi.ac.uk/Tools/webservices/psicquic/i2d/webservices/current/search/query/*?format=tab27
I2D_IMEX	DOWNLOAD_FILES	i2dimex_psicquic.txt

INNATEDB	DATE	2015-03-08 22:46:08
INNATEDB	RELEASE_URL	http://www.innatedb.com/download/interactions/
INNATEDB	DOWNLOAD_FILES	innatedb_ppi.mitab.gz

INTACT	DATE	2015-02-24 19:48:00
INTACT	RELEASE_URL	ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psi25/
INTACT	DOWNLOAD_FILES	pmidMIF25.zip

INTCOMPLEX	DATE	2015-02-24 19:49:00
INTCOMPLEX	RELEASE_URL	ftp://ftp.ebi.ac.uk/pub/databases/intact/complex/current/psi25/
INTCOMPLEX	DOWNLOAD_FILES	complexesMIF25.zip

MATRIXDB	DATE	2015-03-16 13:04:00
MATRIXDB	RELEASE_URL	http://matrixdb.ibcp.fr:8080/psicquic/webservices/current/search/query/*?format=tab27
MATRIXDB	DOWNLOAD_FILES	matrixdb_psicquic.txt

MPACT	DATE	2008-09-30 22:00:00
MPACT	RELEASE_URL	local copy
MPACT	DOWNLOAD_FILES	mpact-complete.psi25.xml.gz

MPPI	DATE	2004-06-01 15:37:37
MPPI	RELEASE_URL	local copy
MPPI	DOWNLOAD_FILES	mppi.gz

MPIDB	DATE	2015-03-16 11:56:28
MPIDB	RELEASE_URL	http://www.ebi.ac.uk/Tools/webservices/psicquic/mpidb/webservices/current/search/query/*?format=tab27
MPIDB	DOWNLOAD_FILES	mpidb_psicquic.txt

REACTOME	DATE	2015-03-13 20:11:32
REACTOME	RELEASE_URL	http://www.ebi.ac.uk/Tools/webservices/psicquic/reactome/webservices/current/search/query/*
REACTOME	DOWNLOAD_FILES	reactome_psicquic.txt

SPIKE	DATE	2015-03-13 10:08:02
SPIKE	RELEASE_URL	http://spike.cs.tau.ac.il/psicquic-ws/webservices/current/search/query/*
SPIKE	DOWNLOAD_FILES	spike_psicquic.txt

VIRUSHOST	DATE	2015-03-13 10:08:08
VIRUSHOST	RELEASE_URL	http://virhostnet.prabi.fr:9090/psicquic/webservices/current/search/query/*
VIRUSHOST	DOWNLOAD_FILES	virushost_psicquic.txt

UNIPROTPP	DATE	2015-03-16 12:21:57
UNIPROTPP	RELEASE_URL	http://www.ebi.ac.uk/Tools/webservices/psicquic/uniprot/webservices/current/search/query/*?format=tab27
UNIPROTPP	DOWNLOAD_FILES	uniprotpp_psicquic.txt

HPIDB	DATE	2015-03-14 01:19:30
HPIDB	RELEASE_URL	http://www.ebi.ac.uk/Tools/webservices/psicquic/hpidb/webservices/current/search/query/*?format=tab27
HPIDB	DOWNLOAD_FILES	hpidb_psicquic.txt

BHF_UCL	RELEASE_URL	http://www.ebi.ac.uk/Tools/webservices/psicquic/bhf-ucl/webservices/current/search/query/*?format=tab27
BHF_UCL	DOWNLOAD_FILES	bhfucl_psicquic.txt

MBINFO	DATE	2015-03-14 01:19:31
MBINFO	RELEASE_URL	http://www.ebi.ac.uk/Tools/webservices/psicquic/mbinfo/webservices/current/search/query/*?format=tab27
MBINFO	DOWNLOAD_FILES	mbinfo_psicquic.txt

MOLCON	DATE	2015-03-16 12:36:21
MOLCON	RELEASE_URL	http://www.ebi.ac.uk/Tools/webservices/psicquic/molcon/webservices/current/search/query/*?format=tab27
MOLCON	DOWNLOAD_FILES	molcon_psicquic.txt



Supporting data sets

PSI_MI	DATE	2015-03-13 10:08:11
PSI_MI	RELEASE_URL	http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/mi/rel25/data/
PSI_MI	DOWNLOAD_FILES	psi-mi25.obo

TAXONOMY	DATE	2015-03-13 08:20:00
TAXONOMY	RELEASE_URL	ftp://ftp.ncbi.nih.gov/pub/taxonomy/
TAXONOMY	DOWNLOAD_FILES	taxdump.tar.gz

DIG	DATE	2015-03-13 10:08:25
DIG	RELEASE_URL	file:///storage/localdata/dig/
DIG	DOWNLOAD_FILES	morbidmap14062010.txt

FLY	VERSION	2015_03
FLY	DATE	04-Mar-2015
FLY	RELEASE_URL	http://www.uniprot.org/docs/
FLY	DOWNLOAD_FILES	fly.txt

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	2015-03-13 10:13:26
IPI	RELEASE_URL	file:///storage/localdata/ipi/
IPI	DOWNLOAD_FILES	*.fasta.gz

MMDB	DATE	2014-05-28 22:00:00
MMDB	RELEASE_URL	ftp://ftp.ncbi.nih.gov/mmdb/pdbeast/
MMDB	DOWNLOAD_FILES	table

PDB	DATE	2015-03-11 03:00:00
PDB	RELEASE_URL	ftp://ftp.ncbi.nih.gov/blast/db/FASTA/
PDB	DOWNLOAD_FILES	pdbaa.gz

REFSEQ	DATE	2015-01-05 22:08:00
REFSEQ	RELEASE_URL	ftp://ftp.ncbi.nih.gov/refseq/release//complete/
REFSEQ	DOWNLOAD_FILES	complete*.protein.gpff.gz

UNIPROT	VERSION	2015_03
UNIPROT	DATE	04-Mar-2015
UNIPROT	RELEASE_URL	ftp://ftp.ebi.ac.uk/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	2015_03
YEAST	DATE	04-Mar-2015
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).