Sources iRefIndex 16.0

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Last edited: 2019-10-04

Applies to iRefIndex release: 16.0

Release date: 29-05-2019

Authors: Sam Dupont

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_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    2019-04-26 07:30:52
BIOGRID                 RELEASE_URL     https://thebiogrid.org/downloads/archives/Release%20Archive/BIOGRID-3.5.171/
BIOGRID                 DOWNLOAD_FILES  BIOGRID-ALL-3.5.171.psi25.zip
CORUM                   DATE    2019-03-27 18:59:49
CORUM                   RELEASE_URL     http://mips.helmholtz-muenchen.de/corum/download/
CORUM                   DOWNLOAD_FILES  allComplexes.xml.zip
DIP                     RELEASE_URL     http://dip.doe-mbi.ucla.edu/dip/Download.cgi?SM=3
HPRD                    DATE    2019-04-24 08:31:39
HPRD                    RELEASE_URL     file:///data/alex/
HPRD                    DOWNLOAD_FILES  HPRD_PSIMI_041310.tar.gz
INTACT                  DATE    2019-03-23 09:58:00
INTACT                  RELEASE_URL     ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psi25/
INTACT                  DOWNLOAD_FILES  pmidMIF25.zip
INTCOMPLEX              DATE    2019-03-23 09:58:00
INTCOMPLEX              RELEASE_URL     ftp://ftp.ebi.ac.uk/pub/databases/intact/complex/current/psi25/
INTCOMPLEX              DOWNLOAD_FILES  complexesMIF25.zip
MPACT                   DATE    2019-04-24 08:32:42
MPACT                   RELEASE_URL     file:///data/ian/mpact/
MPACT                   DOWNLOAD_FILES  mpact-complete.psi25.xml.gz
MPPI                    DATE    2019-04-24 08:33:00
MPPI                    RELEASE_URL     file:///data/ian/mppi/
MPPI                    DOWNLOAD_FILES  mppi.gz
SPIKE                   DATE    2012-01-25 14:49:34
SPIKE                   RELEASE_URL     http://www.cs.tau.ac.il//~spike/download/
SPIKE                   DOWNLOAD_FILES  LatestSpikeDB.xml.zip
MINT                    DATE    2019-04-25 08:18:34
MINT                    RELEASE_URL     http://mint.bio.uniroma2.it/mitab/
MINT                    DOWNLOAD_FILES  MINT_MiTab.txt
MPIDB                   DATE    2019-04-23 13:38:35
MPIDB                   RELEASE_URL     file:///data/irdata15A/MPIDB/
MPIDB                   DOWNLOAD_FILES  mpidb_psicquic.txt
I2D_IMEX                DATE    2019-04-23 13:38:35
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    2018-07-05 12:06:54
INNATEDB                RELEASE_URL     http://www.innatedb.com/download/interactions/
INNATEDB                DOWNLOAD_FILES  innatedb_all.mitab.gz
MATRIXDB                DATE    2019-01-14 10:22:50
MATRIXDB                RELEASE_URL     http://matrixdb.univ-lyon1.fr/download/
MATRIXDB                DOWNLOAD_FILES  matrixdb_FULL.tab.gz
REACTOME        DATE    2019-04-23 13:39:14
REACTOME        RELEASE_URL     http://www.ebi.ac.uk/Tools/webservices/psicquic/reactome/webservices/current/search/query/*
REACTOME        DOWNLOAD_FILES  reactome_psicquic.txt
VIRUSHOST       DATE    2019-04-23 13:39:16
VIRUSHOST       RELEASE_URL     http://virhostnet.prabi.fr:9090/psicquic/webservices/current/search/query/*
VIRUSHOST       DOWNLOAD_FILES  virushost_psicquic.txt
UNIPROTPP       DATE    2019-04-23 13:39:27
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    2019-04-23 13:39:30
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 DATE    2019-04-23 13:39:33
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    2019-04-23 13:39:36
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    2019-04-23 13:39:36
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    2019-04-26 08:19:35
QUICKGO RELEASE_URL     http://www.ebi.ac.uk/QuickGO/psicquic/webservices/current/search/query/*
QUICKGO DOWNLOAD_FILES  quickgo_psicquic.txt
PSI_MI  DATE    2019-04-23 13:39:36
PSI_MI  RELEASE_URL     http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/mi/rel25/data/
PSI_MI  DOWNLOAD_FILES  psi-mi25.obo
TAXONOMY        DATE    2019-04-23 11:23:00
TAXONOMY        RELEASE_URL     ftp://ftp.ncbi.nih.gov/pub/taxonomy/
TAXONOMY        DOWNLOAD_FILES  taxdump.tar.gz
BIND    DATE    2017-10-25 19:45:46
BIND    RELEASE_URL     file:///data/ian/bond.unleashedinformatics.com/downloads/data/BIND/data/bindflatfiles/bindindex/
BIND    DOWNLOAD_FILES  20060525*.txt
DIG     DATE    2019-04-24 08:29:11
DIG     RELEASE_URL     file:///data/ian/dig/
DIG     DOWNLOAD_FILES  morbidmap14062010.txt
FLY     VERSION 2019_03
FLY     DATE    10-Apr-2019
FLY     RELEASE_URL     http://www.uniprot.org/docs/
FLY     DOWNLOAD_FILES  fly.txt
GENE    DATE    2019-04-22 23:43:00
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    2019-04-22 17:03:00
GENPEPT RELEASE_URL     ftp://ftp.ncbi.nih.gov/ncbi-asn1/protein_fasta/
GENPEPT DOWNLOAD_FILES  gb*.fsa_aa.gz
IPI     DATE    2012-07-19 22:00:00
IPI     RELEASE_URL     ftp://ftp.ebi.ac.uk/pub/databases/IPI/last_release/current/
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    2019-04-09 02:00:00
PDB     RELEASE_URL     ftp://ftp.ncbi.nih.gov/blast/db/FASTA/
PDB     DOWNLOAD_FILES  pdbaa.gz
REFSEQ  DATE    2019-03-18 15:27:00
REFSEQ  RELEASE_URL     ftp://ftp.ncbi.nih.gov/refseq/release//complete/
REFSEQ  DOWNLOAD_FILES  complete*.protein.gpff.gz
UNIPROT VERSION 2019_03
UNIPROT DATE    10-Apr-2019
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 2019_03
YEAST   DATE    10-Apr-2019
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).

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