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Sources iRefIndex 15.0

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Last edited: 2018-03-10

Applies to iRefIndex release: 15.0

Release date: 22-01-2018

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

BIND_TRANSLATION        DATE    2014-05-20 20:32:00
BIND_TRANSLATION        RELEASE_URL     http://download.baderlab.org/BINDTranslation/release1_0/
BIND_TRANSLATION        DOWNLOAD_FILES  BINDTranslation_v1_xml_AllSpecies.tar.gz

BIOGRID DATE    2017-09-30 15:36:22
BIOGRID RELEASE_URL     https://thebiogrid.org/downloads/archives/Release%20Archive/BIOGRID-3.4.153/
BIOGRID DOWNLOAD_FILES  BIOGRID-ALL-3.4.153.psi25.zip

CORUM   DATE    2017-07-13 23:22:20
CORUM   RELEASE_URL     http://mips.helmholtz-muenchen.de/corum/download/
CORUM   DOWNLOAD_FILES  allComplexes.xml.zip  

DIP     DOWNLOAD        ftp://albot:9eBCcKmL@dip.doe-mbi.ucla.edu/2017/mif25/dip20170205.mif25.gz
DIP     FILENAME        dip20170205.mif25
DIP     DATE    02/05/2017
DIP     RELEASE_URL     http://dip.doe-mbi.ucla.edu/dip/Download.cgi?SM=3  

HPRD    DATE    2017-10-25 19:43:21
HPRD    RELEASE_URL     file:///data/alex/
HPRD    DOWNLOAD_FILES  HPRD_PSIMI_041310.tar.gz  

INTACT  DATE    2017-09-03 00:26:00
INTACT  RELEASE_URL     ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psi25/
INTACT  DOWNLOAD_FILES  pmidMIF25.zip  

INTCOMPLEX      DATE    2017-09-03 00:26:00
INTCOMPLEX      RELEASE_URL     ftp://ftp.ebi.ac.uk/pub/databases/intact/complex/current/psi25/
INTCOMPLEX      DOWNLOAD_FILES  complexesMIF25.zip  

I2D_IMEX        DATE    2017-10-25 19:44:20
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    2017-10-22 18:58:16
INNATEDB        RELEASE_URL     http://www.innatedb.com/download/interactions/
INNATEDB        DOWNLOAD_FILES  innatedb_all.mitab.gz  

MATRIXDB        DATE    2016-06-17 14:43:31
MATRIXDB        RELEASE_URL     http://matrixdb.univ-lyon1.fr/download/
MATRIXDB        DOWNLOAD_FILES  matrixdb_FULL.tab.gz


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    2017-10-25 19:44:42
REACTOME        RELEASE_URL     http://www.ebi.ac.uk/Tools/webservices/psicquic/reactome/webservices/current/search/query/*
REACTOME        DOWNLOAD_FILES  reactome_psicquic.txt

VIRUSHOST       DATE    2017-10-25 19:44:55
VIRUSHOST       RELEASE_URL     http://virhostnet.prabi.fr:9090/psicquic/webservices/current/search/query/*
VIRUSHOST       DOWNLOAD_FILES  virushost_psicquic.txt  

UNIPROTPP       DATE    2017-10-25 19:45:08
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    2017-10-25 19:45:12
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 DATE    2017-10-25 19:45:27
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    2017-10-25 19:45:28
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    2017-10-25 19:45:29
MOLCON  RELEASE_URL     http://www.ebi.ac.uk/Tools/webservices/psicquic/molcon/webservices/current/search/query/*?format=tab27
MOLCON  DOWNLOAD_FILES  molcon_psicquic.txt  

QUICKGO DATE    2017-11-24 07:41:34
QUICKGO RELEASE_URL     http://www.ebi.ac.uk/QuickGO/psicquic/webservices/current/search/query/*
QUICKGO DOWNLOAD_FILES  quickgo_psicquic.txt  



Supporting data sets

PSI_MI  DATE    2017-10-25 19:45:31
PSI_MI  RELEASE_URL     http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/mi/rel25/data/
PSI_MI  DOWNLOAD_FILES  psi-mi25.obo  

TAXONOMY        DATE    2017-10-25 17:20:00
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 2017_10
FLY     DATE    25-Oct-2017
FLY     RELEASE_URL     http://www.uniprot.org/docs/
FLY     DOWNLOAD_FILES  fly.txt  

GENE    DATE    2017-10-25 01:26:00
GENE    RELEASE_URL     ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
GENE    DOWNLOAD_FILES  gene2refseq.gz gene_info.gz gene2go.gz gene_history.gz  

GENPEPT DATE    2017-10-17 20:53:00
GENPEPT RELEASE_URL     ftp://ftp.ncbi.nih.gov/ncbi-asn1/protein_fasta/
GENPEPT DOWNLOAD_FILES  gb*.fsa_aa.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    2017-10-25 02:00:00
PDB     RELEASE_URL     ftp://ftp.ncbi.nih.gov/blast/db/FASTA/
PDB     DOWNLOAD_FILES  pdbaa.gz  

REFSEQ  DATE    2017-09-15 05:49:00
REFSEQ  RELEASE_URL     ftp://ftp.ncbi.nih.gov/refseq/release//complete/
REFSEQ  DOWNLOAD_FILES  complete*.protein.gpff.gz  

UNIPROT VERSION 2017_10
UNIPROT DATE    25-Oct-2017
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 2017_10
YEAST   DATE    25-Oct-2017
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).