Sources iRefIndex 20.0

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Last edited: 2023-08-28

Applies to iRefIndex release: 20.0

Release date: 30-08-2023

Authors: Alexander Botzki

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.


Data source information

Source Release date Release URL Download files Version
ATHALIANA 2023-04-13 http://ftp.ensemblgenomes.org/pub/plants/release-57/tsv/arabidopsis_thaliana/ Arabidopsis_thaliana.TAIR10.57.uniprot.tsv.gz
BAR 0001-01-01 http://bar.utoronto.ca:9090/psicquic/webservices/current/search/query/* bar_psicquic.txt
BHF_UCL 2023-08-18 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 2023-08-18 https://downloads.thebiogrid.org/Download/BioGRID/Release-Archive/BIOGRID-4.4.224/ BIOGRID-ALL-4.4.224.psi25.zip
CORUM 0001-01-01 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 2023-06-28 ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/docs/ fly.txt 2023_03
GENE 2023-08-18 http://ftp.ncbi.nlm.nih.gov/gene/DATA/ gene2refseq.gz gene_info.gz gene2go.gz gene_history.gz
GENPEPT 2023-08-17 ftp://ftp.ncbi.nih.gov/ncbi-asn1/protein_fasta/ gb*.fsa_aa.gz
HPIDB 2023-08-18 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 2023-08-18 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 2023-06-06 ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psi25/ pmidMIF25.zip
INTCOMPLEX 2023-06-06 ftp://ftp.ebi.ac.uk/pub/databases/intact/complex/current/psi25/ complexesMIF25.zip
IPI 0001-01-01 ftp://ftp.ebi.ac.uk/pub/databases/IPI/last_release/current/ *.fasta.gz
MATRIXDB 2023-08-18 http://matrixdb.univ-lyon1.fr:8080/psicquic/webservices/current/search/query/*?format=tab27 matrixdb_psicquic.txt
MBINFO 2023-08-18 http://www.ebi.ac.uk/Tools/webservices/psicquic/mbinfo/webservices/current/search/query/*?format=tab27 mbinfo_psicquic.txt
MINT 2023-08-18 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 2023-08-18 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 2023-07-27 ftp://ftp.ncbi.nih.gov/blast/db/FASTA/ pdbaa.gz
PSI_MI 2023-08-18 https://raw.githubusercontent.com//HUPO-PSI/psi-mi-CV/master/ psi-mi.obo
QUICKGO 2023-08-18 http://www.ebi.ac.uk/QuickGO/psicquic/webservices/current/search/query/*?format=tab27 quickgo_psicquic.txt
REACTOME 2023-08-18 http://www.ebi.ac.uk/Tools/webservices/psicquic/reactome/webservices/current/search/query/* reactome_psicquic.txt
REFSEQ 2023-07-14 ftp://ftp.ncbi.nih.gov/refseq/release//complete/ complete*.protein.gpff.gz
TAXONOMY 2023-08-18 ftp://ftp.ncbi.nih.gov/pub/taxonomy/ taxdump.tar.gz
UNIPROTPP 2023-08-18 http://www.ebi.ac.uk/Tools/webservices/psicquic/uniprot/webservices/current/search/query/*?format=tab27 uniprotpp_psicquic.txt
UNIPROT 2023-08-18 ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/" uniprot_*.dat.gz release.txt
VIRUSHOST 2023-08-18 http://virhostnet.prabi.fr:9090/psicquic/webservices/current/search/query/* virushost_psicquic.txt

All iRefIndex Pages

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

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