Sources iRefIndex 19.0

Last edited: 2022-10-30

Applies to iRefIndex release: 19.0

Release date: 22-08-2022

Authors: Luc Ducazu

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_19.0

Data source information

Source	Release date	Release URL	Download files	Version
ATHALIANA	2022-02-23	http://ftp.ensemblgenomes.org/pub/plants/release-53/tsv/arabidopsis_thaliana/	Arabidopsis_thaliana.TAIR10.53.uniprot.tsv.gz
BAR	2022-08-07	http://bar.utoronto.ca:9090/psicquic/webservices/current/search/query/*	bar_psicquic.txt
BHF_UCL	2022-08-05	http://www.ebi.ac.uk/Tools/webservices/psicquic/bhf-ucl/webservices/current/search/query/*?format=tab27	bhfucl_psicquic.txt
BIND	2006-05-25		20060525*.txt
BIND_TRANSLATION	2014-05-20	http://download.baderlab.org/BINDTranslation/release1_0/	BINDTranslation_v1_xml_AllSpecies.tar.gz
BIOGRID	2022-08-05	https://downloads.thebiogrid.org/Download/BioGRID/Release-Archive/BIOGRID-4.4.209/	BIOGRID-ALL-4.4.209.psi25.zip
CORUM	2022-08-05	https://mips.helmholtz-muenchen.de/corum/download/	allComplexes.xml.zip
DIG	2010-06-14		morbidmap14062010.txt
DIP	2017-02-05	https://dip.doe-mbi.ucla.edu/	dip20170205.mif25.gz
FLY	2022-08-03	ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/docs/	fly.txt	2022_03
GENE	2022-08-05	http://ftp.ncbi.nlm.nih.gov/gene/DATA/	gene2refseq.gz gene_info.gz gene2go.gz gene_history.gz
GENPEPT	2022-06-17	ftp://ftp.ncbi.nih.gov/ncbi-asn1/protein_fasta/	gb*.fsa_aa.gz
HPIDB	2022-08-05	http://www.ebi.ac.uk/Tools/webservices/psicquic/hpidb/webservices/current/search/query/*?format=tab27	hpidb_psicquic.txt
HPRD	2010-04-13		HPRD_PSIMI_041310.tar.gz
HURI	2020-03-09	http://interactome-atlas.org/data/	HuRI.psi
IMEX	2022-08-06	http://www.ebi.ac.uk/Tools/webservices/psicquic/imex/webservices/current/search/query/*?format=tab27	imex_psicquic.txt
INNATEDB	2022-01-29	http://www.innatedb.com/download/interactions/	innatedb_all.mitab.gz
INTACT	2022-07-13	ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psi25/	pmidMIF25.zip
INTCOMPLEX	2022-07-13	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	2022-08-05	http://matrixdb.univ-lyon1.fr:8080/psicquic/webservices/current/search/query/*?format=tab27	matrixdb_psicquic.txt
MBINFO	2022-08-05	http://www.ebi.ac.uk/Tools/webservices/psicquic/mbinfo/webservices/current/search/query/*?format=tab27	mbinfo_psicquic.txt
MINT	2022-08-05	http://www.ebi.ac.uk/Tools/webservices/psicquic/mint/webservices/current/search/query/*?format=tab27	mint_psicquic.txt
MMDB	2014-05-29	ftp://ftp.ncbi.nih.gov/mmdb/pdbeast/	table
MPACT	2021-04-21		mpact-complete.psi25.xml.gz
MPIDB	2022-08-05	http://www.ebi.ac.uk/Tools/webservices/psicquic/mpidb/webservices/current/search/query/*?format=tab27	mpidb_psicquic.txt
MPPI	2021-04-19		mppi.gz
PDB	2022-07-30	ftp://ftp.ncbi.nih.gov/blast/db/FASTA/	pdbaa.gz
PSI_MI	2022-08-05	https://raw.githubusercontent.com//HUPO-PSI/psi-mi-CV/master/	psi-mi.obo
QUICKGO	2022-08-05	http://www.ebi.ac.uk/QuickGO/psicquic/webservices/current/search/query/*?format=tab27	quickgo_psicquic.txt
REACTOME	2022-08-05	http://www.ebi.ac.uk/Tools/webservices/psicquic/reactome/webservices/current/search/query/*	reactome_psicquic.txt
REFSEQ	2022-07-15	ftp://ftp.ncbi.nih.gov/refseq/release//complete/	complete*.protein.gpff.gz
TAXONOMY	2022-08-05	ftp://ftp.ncbi.nih.gov/pub/taxonomy/	taxdump.tar.gz
UNIPROT	2022-08-03	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	2022_03
UNIPROTPP	2022-08-05	http://www.ebi.ac.uk/Tools/webservices/psicquic/uniprot/webservices/current/search/query/*?format=tab27	uniprotpp_psicquic.txt
VIRUSHOST	2022-08-05	http://virhostnet.prabi.fr:9090/psicquic/webservices/current/search/query/*	virushost_psicquic.txt
YEAST	2022-08-03	ftp://ftp.uniprot.org//pub/databases/uniprot/current_release/knowledgebase/complete/docs/	yeast.txt	2022_03

All iRefIndex Pages

Follow this link for a listing of all iRefIndex related pages (archived and current).