Difference between revisions of "Sources iRefIndex 14.0"

From irefindex
(Created page with "Last edited: {{REVISIONYEAR}}-{{padleft:{{REVISIONMONTH}}|2}}-{{REVISIONDAY2}} Applies to iRefIndex release: 13.0 Release date: 09-12-2013 Authors: Ian Donaldson Database:...")
 
Line 1: Line 1:
 
Last edited: {{REVISIONYEAR}}-{{padleft:{{REVISIONMONTH}}|2}}-{{REVISIONDAY2}}
 
Last edited: {{REVISIONYEAR}}-{{padleft:{{REVISIONMONTH}}|2}}-{{REVISIONDAY2}}
  
−
Applies to iRefIndex release: 13.0
+
Applies to iRefIndex release: 14.0
  
−
Release date: 09-12-2013
+
Release date: 07-04-2013
  
 
Authors: Ian Donaldson
 
Authors: Ian Donaldson
Line 12: Line 12:
 
Description: This file lists interaction and protein sequence related resources used for the current build of the iRefIndex.
 
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.
 
Statistics for the iRefIndex are available and include a breakdown of interactors and interactions from each data source.
−
*For statistics on the full dataset please refer to: http://irefindex.org/wiki/index.php?title=Statistics_iRefIndex_13.0
+
*For statistics on the full dataset please refer to: http://irefindex.org/wiki/index.php?title=Statistics_iRefIndex_14.0
  
  
 
<pre>
 
<pre>
 +
'''Interaction data sets'''
 +
 
BIND DATE 2005-05-25
 
BIND DATE 2005-05-25
 
BIND RELEASE_URL http://bond.unleashedinformatics.com/downloads/data/BIND/data/bindflatfiles/bindindex/
 
BIND RELEASE_URL http://bond.unleashedinformatics.com/downloads/data/BIND/data/bindflatfiles/bindindex/
 
BIND DOWNLOAD_FILES 20060525*.txt
 
BIND DOWNLOAD_FILES 20060525*.txt
  
−
BIND_TRANSLATION DATE 2010-12-15 15:54:01
+
BIOGRID DATE 2015-02-28 20:41:14
−
BIND_TRANSLATION RELEASE_URL http://download.baderlab.org/BINDTranslation/release1_0/
+
BIOGRID RELEASE_URL http://thebiogrid.org/downloads/archives/Release%20Archive/BIOGRID-3.3.122/
−
BIND_TRANSLATION DOWNLOAD_FILES BINDTranslation_v1_xml_AllSpecies.tar.gz
+
BIOGRID DOWNLOAD_FILES BIOGRID-ALL-3.3.122.psi25.zip
−
 
 
−
BIOGRID DATE 2013-11-01 03:16:29
 
−
BIOGRID RELEASE_URL http://thebiogrid.org/downloads/archives/Release%20Archive/BIOGRID-3.2.106/
 
−
BIOGRID DOWNLOAD_FILES BIOGRID-ALL-3.2.106.psi25.zip
 
  
 
CORUM DATE 2009-12-02 18:24:15
 
CORUM DATE 2009-12-02 18:24:15
Line 32: Line 30:
 
CORUM DOWNLOAD_FILES allComplexes.psimi.zip
 
CORUM DOWNLOAD_FILES allComplexes.psimi.zip
  
−
DIP DOWNLOAD ftp://dip.doe-mbi.ucla.edu/2013/mif25/dip20131031.mif25.gz
+
DIP DOWNLOAD ftp://sabry:z6RHVXe7@dip.doe-mbi.ucla.edu/2015/mif25/dip20150101.mif25.gz
−
DIP FILENAME dip20131031.mif25
+
DIP FILENAME dip20150101.mif25
−
DIP DATE 10/31/2013
+
DIP DATE 01/01/2015
−
DIP RELEASE_URL http://dip.doe-mbi.ucla.edu/dip/
+
DIP RELEASE_URL http://dip.doe-mbi.ucla.edu/dip/Download.cgi?SM=3
  
 
HPRD RELEASE_URL http://hprd.org
 
HPRD RELEASE_URL http://hprd.org
 
HPRD DOWNLOAD_FILES HPRD_PSIMI_041310.tar.gz
 
HPRD DOWNLOAD_FILES HPRD_PSIMI_041310.tar.gz
  
−
INTACT DATE 2013-11-21 00:19:00
+
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 RELEASE_URL ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psi25/
 
INTACT DOWNLOAD_FILES pmidMIF25.zip
 
INTACT DOWNLOAD_FILES pmidMIF25.zip
  
−
MATRIXDB DATE 2012-08-03 11:26:01
+
INTCOMPLEX DATE 2015-02-24 19:49:00
−
MATRIXDB RELEASE_URL http://matrixdb.ibcp.fr/cgi-bin/download%3C../../
+
INTCOMPLEX RELEASE_URL ftp://ftp.ebi.ac.uk/pub/databases/intact/complex/current/psi25/
−
MATRIXDB DOWNLOAD_FILES MatrixDB_20120801.xml.zip
+
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 DATE 2008-09-30 22:00:00
Line 56: Line 65:
 
MPPI DOWNLOAD_FILES mppi.gz
 
MPPI DOWNLOAD_FILES mppi.gz
  
−
OPHID DATE 2006-07-07
+
MPIDB DATE 2015-03-16 11:56:28
−
OPHID RELEASE_URL local copy
+
MPIDB RELEASE_URL http://www.ebi.ac.uk/Tools/webservices/psicquic/mpidb/webservices/current/search/query/*?format=tab27
−
OPHID DOWNLOAD_FILES ophid*.xml
+
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
 +
 
  
−
MPIDB DATE 2011-10-03
 
−
MPIDB RELEASE_URL http://www.jcvi.org/mpidb/download.php?dbsource=
 
−
MPIDB DOWNLOAD_FILES MPI-IMEX MPI-LIT
 
  
−
INNATEDB DATE 2013-11-25 09:00:45
+
'''Supporting data sets'''
−
INNATEDB RELEASE_URL http://www.innatedb.com/download/interactions/
 
−
INNATEDB DOWNLOAD_FILES innatedb_all.mitab.gz
 
  
−
PSI_MI DATE 2013-11-28 11:24:01
+
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 RELEASE_URL http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/mi/rel25/data/
 
PSI_MI DOWNLOAD_FILES psi-mi25.obo
 
PSI_MI DOWNLOAD_FILES psi-mi25.obo
  
−
TAXONOMY DATE 2013-11-28 10:20:00
+
TAXONOMY DATE 2015-03-13 08:20:00
 
TAXONOMY RELEASE_URL ftp://ftp.ncbi.nih.gov/pub/taxonomy/
 
TAXONOMY RELEASE_URL ftp://ftp.ncbi.nih.gov/pub/taxonomy/
 
TAXONOMY DOWNLOAD_FILES taxdump.tar.gz
 
TAXONOMY DOWNLOAD_FILES taxdump.tar.gz
  
−
DIG DATE 2010-06-14
+
DIG DATE 2015-03-13 10:08:25
−
DIG RELEASE_URL file:///storage/localdata/DIG/
+
DIG RELEASE_URL file:///storage/localdata/dig/
 
DIG DOWNLOAD_FILES morbidmap14062010.txt
 
DIG DOWNLOAD_FILES morbidmap14062010.txt
  
−
FLY VERSION 2013_11
+
FLY VERSION 2015_03
−
FLY DATE 13-Nov-2013
+
FLY DATE 04-Mar-2015
 
FLY RELEASE_URL http://www.uniprot.org/docs/
 
FLY RELEASE_URL http://www.uniprot.org/docs/
 
FLY DOWNLOAD_FILES fly.txt
 
FLY DOWNLOAD_FILES fly.txt
  
−
GENE DATE 2013-11-28 01:28:00
 
 
GENE RELEASE_URL ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
 
GENE RELEASE_URL ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
 
GENE DOWNLOAD_FILES gene2refseq.gz gene_info.gz gene2go.gz gene_history.gz
 
GENE DOWNLOAD_FILES gene2refseq.gz gene_info.gz gene2go.gz gene_history.gz
  
−
IPI DATE 2013-11-28 11:27:31
+
IPI DATE 2015-03-13 10:13:26
−
IPI RELEASE_URL file:///storage/localdata/IPI/
+
IPI RELEASE_URL file:///storage/localdata/ipi/
 
IPI DOWNLOAD_FILES *.fasta.gz
 
IPI DOWNLOAD_FILES *.fasta.gz
  
−
MMDB DATE 2013-11-28 08:38:00
+
MMDB DATE 2014-05-28 22:00:00
 
MMDB RELEASE_URL ftp://ftp.ncbi.nih.gov/mmdb/pdbeast/
 
MMDB RELEASE_URL ftp://ftp.ncbi.nih.gov/mmdb/pdbeast/
 
MMDB DOWNLOAD_FILES table
 
MMDB DOWNLOAD_FILES table
  
−
PDB DATE 2013-11-27 21:24:00
+
PDB DATE 2015-03-11 03:00:00
 
PDB RELEASE_URL ftp://ftp.ncbi.nih.gov/blast/db/FASTA/
 
PDB RELEASE_URL ftp://ftp.ncbi.nih.gov/blast/db/FASTA/
 
PDB DOWNLOAD_FILES pdbaa.gz
 
PDB DOWNLOAD_FILES pdbaa.gz
  
−
REFSEQ DATE 2013-11-12 19:53:00
+
REFSEQ DATE 2015-01-05 22:08:00
 
REFSEQ RELEASE_URL ftp://ftp.ncbi.nih.gov/refseq/release//complete/
 
REFSEQ RELEASE_URL ftp://ftp.ncbi.nih.gov/refseq/release//complete/
 
REFSEQ DOWNLOAD_FILES complete*.protein.gpff.gz
 
REFSEQ DOWNLOAD_FILES complete*.protein.gpff.gz
  
−
UNIPROT VERSION 2013_11
+
UNIPROT VERSION 2015_03
−
UNIPROT DATE 13-Nov-2013
+
UNIPROT DATE 04-Mar-2015
−
UNIPROT RELEASE_URL ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/
+
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
 
UNIPROT DOWNLOAD_FILES uniprot_sprot.dat.gz uniprot_trembl.dat.gz uniprot_sprot_varsplic.fasta.gz reldate.txt
  
−
YEAST VERSION 2013_11
+
YEAST VERSION 2015_03
−
YEAST DATE 13-Nov-2013
+
YEAST DATE 04-Mar-2015
 
YEAST RELEASE_URL http://www.uniprot.org/docs/
 
YEAST RELEASE_URL http://www.uniprot.org/docs/
 
YEAST DOWNLOAD_FILES yeast.txt
 
YEAST DOWNLOAD_FILES yeast.txt

Revision as of 10:45, 21 April 2015

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).

Retrieved from "http://irefindex.vib.be/wiki/index.php?title=Sources_iRefIndex_14.0&oldid=4250"