Sources iRefIndex 17.0

Last edited: 2020-06-30

Applies to iRefIndex release: 17.0

Release date: 29-06-2020

Authors: Joris Dekimpe

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.

• For statistics on the full dataset please refer to: https://irefindex.vib.be/wiki/index.php?title=Statistics_iRefIndex_16.0

Data source information

Source	Release date	Release URL	Download files	Version
BAR	2020-05-24	http://bar.utoronto.ca:9090/psicquic/webservices/current/search/query/*	bar_psicquic.txt
BHF_UCL	2020-04-29	http://www.ebi.ac.uk/Tools/webservices/psicquic/bhf-ucl/webservices/current/search/query/*?format=tab27	bhfucl_psicquic.txt
BIND	2020-04-27		20060525*.txt
BIND_TRANSLATION	2014-05-20	http://download.baderlab.org/BINDTranslation/release1_0/	BINDTranslation_v1_xml_AllSpecies.tar.gz
BIOGRID	2020-04-24	https://downloads.thebiogrid.org/Download/BioGRID/Release-Archive/BIOGRID-3.5.184/	BIOGRID-ALL-3.5.184.psi25.zip
CORUM	2020-02-28	http://mips.helmholtz-muenchen.de/corum/download/	allComplexes.xml.zip
DIG	2020-04-23		morbidmap14062010.txt
DIP	2020-04-26	https://dip.doe-mbi.ucla.edu/dip/Download.cgi?SM=3	dip20170205.mif25
FLY	2020-02-26	http://www.uniprot.org/docs/	fly.txt	2020_01
GENE	2020-04-22	ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/	gene2refseq.gz gene_info.gz gene2go.gz gene_history.gz
GENPEPT	2020-04-21	ftp://ftp.ncbi.nih.gov/ncbi-asn1/protein_fasta/	gb*.fsa_aa.gz
HPIDB	2020-05-08	http://www.ebi.ac.uk/Tools/webservices/psicquic/hpidb/webservices/current/search/query/*?format=tab27	hpidb_psicquic.txt
HPRD	2020-04-23		HPRD_PSIMI_041310.tar.gz
HURI	2020-05-22	http://interactome-atlas.org/data/	HuRI.psi
INNATEDB	2018-07-05	http://www.innatedb.com/download/interactions/	innatedb_all.mitab.gz
INTACT	2020-04-02	ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psi25/	pmidMIF25.zip
INTCOMPLEX	2020-04-02	ftp://ftp.ebi.ac.uk/pub/databases/intact/complex/current/psi25/	complexesMIF25.zip
IPI	2012-07-20	ftp://ftp.ebi.ac.uk/pub/databases/IPI/last_release/current/	*.fasta.gz
MATRIXDB	2020-05-22	http://matrixdb.univ-lyon1.fr/download/	matrixdb_FULL.tab
MBINFO	2020-04-29	http://www.ebi.ac.uk/Tools/webservices/psicquic/mbinfo/webservices/current/search/query/*?format=tab27	mbinfo_psicquic.txt
MINT	2020-04-24	http://mint.bio.uniroma2.it/mitab/	MINT_MiTab.txt
MMDB	2014-05-29	ftp://ftp.ncbi.nih.gov/mmdb/pdbeast/	table
MPACT	2020-04-29		mpact-complete.psi25.xml.gz
MPIDB	2020-04-29		mpidb_psicquic.txt
MPPI	2020-04-29		mppi.gz
PDB	2020-04-18	ftp://ftp.ncbi.nih.gov/blast/db/FASTA/	pdbaa.gz
PSI_MI	2020-05-22	https://raw.githubusercontent.com//HUPO-PSI/psi-mi-CV/master/	psi-mi.obo
QUICKGO	2020-04-24	http://www.ebi.ac.uk/QuickGO/psicquic/webservices/current/search/query/*	quickgo_psicquic.txt
REACTOME	2020-04-29	http://www.ebi.ac.uk/Tools/webservices/psicquic/reactome/webservices/current/search/query/*	reactome_psicquic.txt
REFSEQ	2020-03-06	ftp://ftp.ncbi.nih.gov/refseq/release//complete/	complete*.protein.gpff.gz
SPIKE	2020-05-22	http://spike.cs.tau.ac.il/psicquic-ws/webservices/current/search/query/*	spike_psicquic.txt
TAXONOMY	2020-04-22	ftp://ftp.ncbi.nih.gov/pub/taxonomy/	taxdump.tar.gz
UNIPROT	2020-04-22	ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/	uniprot_sprot.dat.gz uniprot_trembl.dat.gz uniprot_sprot_varsplic.fasta.gz reldate.txt	2020_02
UNIPROTPP	2020-04-29	http://www.ebi.ac.uk/Tools/webservices/psicquic/uniprot/webservices/current/search/query/*?format=tab27	uniprotpp_psicquic.txt
VIRUSHOST	2020-04-29	http://virhostnet.prabi.fr:9090/psicquic/webservices/current/search/query/*	virushost_psicquic.txt
YEAST	2020-04-22	http://www.uniprot.org/docs/	yeast.txt	2020_02

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