Difference between revisions of "Sources iRefIndex 18.0"

From irefindex
(Created page with "Last edited: {{REVISIONYEAR}}-{{padleft:{{REVISIONMONTH}}|2}}-{{REVISIONDAY2}} Applies to iRefIndex release: 18.0 Release date: -06-2021 Authors: Joris Dekimpe Database: i...")
 
 
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Applies to iRefIndex release: 18.0
 
Applies to iRefIndex release: 18.0
  
−
Release date: -06-2021
+
Release date: 11-06-2021
  
−
Authors: Joris Dekimpe
+
Authors: Tom Nissens
  
 
Database: iRefIndex (http://irefindex.org)
 
Database: iRefIndex (http://irefindex.org)
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Description: This file lists interaction and protein sequence related resources used for the current build of the iRefIndex.
 
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.
 
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
+
*For statistics on the full dataset please refer to: https://irefindex.vib.be/wiki/index.php?title=Statistics_iRefIndex_18.0
  
  
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| align="center" style="background:#f0f0f0;"|'''Source''' ||align="center" style="background:#f0f0f0;"|'''Release date''' ||align="center" style="background:#f0f0f0;"|'''Release URL''' ||align="center" style="background:#f0f0f0;"|'''Download files''' ||align="center" style="background:#f0f0f0;"|'''Version'''
 
| align="center" style="background:#f0f0f0;"|'''Source''' ||align="center" style="background:#f0f0f0;"|'''Release date''' ||align="center" style="background:#f0f0f0;"|'''Release URL''' ||align="center" style="background:#f0f0f0;"|'''Download files''' ||align="center" style="background:#f0f0f0;"|'''Version'''
 
|-
 
|-
−
| BAR ||2020-05-24 ||http://bar.utoronto.ca:9090/psicquic/webservices/current/search/query/* ||bar_psicquic.txt ||
+
| ATHALIANA ||2019-11-20 ||ftp://ftp.ensemblgenomes.org/pub/plants/release-46/tsv/arabidopsis_thaliana/ ||Arabidopsis_thaliana.TAIR*.uniprot.tsv.gz ||
 
|-
 
|-
−
| BHF_UCL ||2020-04-29 ||http://www.ebi.ac.uk/Tools/webservices/psicquic/bhf-ucl/webservices/current/search/query/*?format=tab27 ||bhfucl_psicquic.txt ||
+
| BAR ||2021-04-27 ||http://bar.utoronto.ca:9090/psicquic/webservices/current/search/query/* ||bar_psicquic.txt ||
 
|-
 
|-
−
| BIND ||2020-04-27 ||  ||20060525*.txt ||
+
| BHF_UCL ||2021-04-22 ||http://www.ebi.ac.uk/Tools/webservices/psicquic/bhf-ucl/webservices/current/search/query/*?format=tab27 ||bhfucl_psicquic.txt ||
 +
|-
 +
| BIND ||2021-04-19 ||  ||20060525*.txt ||
 
|-
 
|-
 
| BIND_TRANSLATION ||2014-05-20 ||http://download.baderlab.org/BINDTranslation/release1_0/ ||BINDTranslation_v1_xml_AllSpecies.tar.gz ||
 
| 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 ||
+
| BIOGRID ||2021-04-19 ||https://downloads.thebiogrid.org/Download/BioGRID/Release-Archive/BIOGRID-3.5.187/ ||BIOGRID-ALL-3.5.187.psi25.zip ||
 
|-
 
|-
 
| CORUM ||2020-02-28 ||http://mips.helmholtz-muenchen.de/corum/download/ ||allComplexes.xml.zip ||
 
| CORUM ||2020-02-28 ||http://mips.helmholtz-muenchen.de/corum/download/ ||allComplexes.xml.zip ||
 
|-
 
|-
−
| DIG ||2020-04-23 ||  ||morbidmap14062010.txt ||
+
| DIG ||2021-04-19 ||  ||morbidmap14062010.txt ||
 
|-
 
|-
−
| DIP ||2020-04-26 ||https://dip.doe-mbi.ucla.edu/dip/Download.cgi?SM=3 ||dip20170205.mif25 ||
+
| DIP ||2021-04-29 ||https://imex.mbi.ucla.edu/xpsq-dip-all/service/rest/current/search/query/*?maxResults=104,965 ||dip_psicquic.txt ||
 
|-
 
|-
−
| FLY ||2020-02-26 ||http://www.uniprot.org/docs/ ||fly.txt ||2020_01
+
| FLY ||2021-04-07 ||http://www.uniprot.org/docs/ ||fly.txt ||2021_02
 
|-
 
|-
−
| GENE ||2020-04-22 ||ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ ||gene2refseq.gz gene_info.gz gene2go.gz gene_history.gz ||
+
| GENE ||2021-04-19 ||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 ||
+
| GENPEPT ||2021-02-17 ||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 ||
+
| HPIDB ||2021-04-22 ||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 ||
+
| HPRD ||2021-04-20 ||  ||HPRD_PSIMI_041310.tar.gz ||
 
|-
 
|-
−
| HURI ||2020-05-22 ||http://interactome-atlas.org/data/ ||HuRI.psi ||
+
| HURI ||2021-04-27 ||http://interactome-atlas.org/data/ ||HuRI.psi ||
 
|-
 
|-
−
| INNATEDB ||2018-07-05 ||http://www.innatedb.com/download/interactions/ ||innatedb_all.mitab.gz ||
+
| IMEX ||2021-04-22 ||http://www.ebi.ac.uk/Tools/webservices/psicquic/imex/webservices/current/search/query/*?format=tab27 ||imex_psicquic.txt ||
 
|-
 
|-
−
| INTACT ||2020-04-02 ||ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psi25/ ||pmidMIF25.zip ||
+
| INNATEDB ||2021-04-23 ||http://www.innatedb.com/download/interactions/ ||innatedb_psicquic.txt ||
 
|-
 
|-
−
| INTCOMPLEX ||2020-04-02 ||ftp://ftp.ebi.ac.uk/pub/databases/intact/complex/current/psi25/ ||complexesMIF25.zip ||
+
| INTACT ||2021-03-12 ||ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psi25/ ||pmidMIF25.zip ||
 
|-
 
|-
−
| IPI ||2012-07-20 ||ftp://ftp.ebi.ac.uk/pub/databases/IPI/last_release/current/ ||*.fasta.gz ||
+
| INTCOMPLEX ||2021-03-12 ||ftp://ftp.ebi.ac.uk/pub/databases/intact/complex/current/psi25/ ||complexesMIF25.zip ||
 
|-
 
|-
−
| MATRIXDB ||2020-05-22 ||http://matrixdb.univ-lyon1.fr/download/ ||matrixdb_FULL.tab ||
+
| MATRIXDB ||2021-04-26 ||http://matrixdb.univ-lyon1.fr:8080/psicquic/webservices/current/search/query/*?format=tab27 ||matrixdb_psicquic.txt ||
 
|-
 
|-
−
| MBINFO ||2020-04-29 ||http://www.ebi.ac.uk/Tools/webservices/psicquic/mbinfo/webservices/current/search/query/*?format=tab27 ||mbinfo_psicquic.txt ||
+
| MBINFO ||2021-04-23 ||http://www.ebi.ac.uk/Tools/webservices/psicquic/mbinfo/webservices/current/search/query/* ||mbinfo_psicquic.txt ||
 
|-
 
|-
−
| MINT ||2020-04-24 ||http://mint.bio.uniroma2.it/mitab/ ||MINT_MiTab.txt ||
+
| MINT ||2021-04-20 ||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 ||
 
| MMDB ||2014-05-29 ||ftp://ftp.ncbi.nih.gov/mmdb/pdbeast/ ||table ||
 
|-
 
|-
−
| MPACT ||2020-04-29 ||  ||mpact-complete.psi25.xml.gz ||
+
| MPACT ||2021-04-21 ||  ||mpact-complete.psi25.xml.gz ||
−
|-
 
−
| MPIDB ||2020-04-29 ||  ||mpidb_psicquic.txt ||
 
 
|-
 
|-
−
| MPPI ||2020-04-29 || ||mppi.gz ||
+
| MPIDB ||2021-04-23 ||http://www.ebi.ac.uk/Tools/webservices/psicquic/mpidb/webservices/current/search/query/*?format=tab27 ||mpidb_psicquic.txt ||
 
|-
 
|-
−
| PDB ||2020-04-18 ||ftp://ftp.ncbi.nih.gov/blast/db/FASTA/ ||pdbaa.gz ||
+
| MPPI ||2021-04-19 || ||mppi.gz ||
 
|-
 
|-
−
| PSI_MI ||2020-05-22 ||https://raw.githubusercontent.com//HUPO-PSI/psi-mi-CV/master/ ||psi-mi.obo ||
+
| PDB ||2021-04-10 ||ftp://ftp.ncbi.nih.gov/blast/db/FASTA/ ||pdbaa.gz ||
 
|-
 
|-
−
| QUICKGO ||2020-04-24 ||http://www.ebi.ac.uk/QuickGO/psicquic/webservices/current/search/query/* ||quickgo_psicquic.txt ||
+
| PSI_MI ||2021-04-19 ||https://raw.githubusercontent.com//HUPO-PSI/psi-mi-CV/master/ ||psi-mi.obo ||
 
|-
 
|-
−
| REACTOME ||2020-04-29 ||http://www.ebi.ac.uk/Tools/webservices/psicquic/reactome/webservices/current/search/query/* ||reactome_psicquic.txt ||
+
| QUICKGO ||2021-04-23 ||http://www.ebi.ac.uk/QuickGO/psicquic/webservices/current/search/query/*?format=tab27 ||quickgo_psicquic.txt ||
 
|-
 
|-
−
| REFSEQ ||2020-03-06 ||ftp://ftp.ncbi.nih.gov/refseq/release//complete/ ||complete*.protein.gpff.gz ||
+
| REACTOME ||2021-04-19 ||http://www.ebi.ac.uk/Tools/webservices/psicquic/reactome/webservices/current/search/query/*?format=tab27 ||reactome_psicquic.txt ||
 
|-
 
|-
−
| SPIKE ||2020-05-22 ||http://spike.cs.tau.ac.il/psicquic-ws/webservices/current/search/query/* ||spike_psicquic.txt ||
+
| SPIKE ||2021-04-19 ||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 ||
+
| TAXONOMY ||2021-04-19 ||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
+
| UNIPROT ||2021-04-07 ||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 ||2021_02
 
|-
 
|-
−
| UNIPROTPP ||2020-04-29 ||http://www.ebi.ac.uk/Tools/webservices/psicquic/uniprot/webservices/current/search/query/*?format=tab27 ||uniprotpp_psicquic.txt ||
+
| UNIPROTPP ||2021-04-23 ||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 ||
+
| VIRUSHOST ||2021-04-21 ||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
+
| YEAST ||2021-04-07 ||http://www.uniprot.org/docs/ ||yeast.txt ||2021_02
 
|}
 
|}
  

Latest revision as of 10:19, 20 August 2021

Last edited: 2021-08-20

Applies to iRefIndex release: 18.0

Release date: 11-06-2021

Authors: Tom Nissens

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 2019-11-20 ftp://ftp.ensemblgenomes.org/pub/plants/release-46/tsv/arabidopsis_thaliana/ Arabidopsis_thaliana.TAIR*.uniprot.tsv.gz
BAR 2021-04-27 http://bar.utoronto.ca:9090/psicquic/webservices/current/search/query/* bar_psicquic.txt
BHF_UCL 2021-04-22 http://www.ebi.ac.uk/Tools/webservices/psicquic/bhf-ucl/webservices/current/search/query/*?format=tab27 bhfucl_psicquic.txt
BIND 2021-04-19 20060525*.txt
BIND_TRANSLATION 2014-05-20 http://download.baderlab.org/BINDTranslation/release1_0/ BINDTranslation_v1_xml_AllSpecies.tar.gz
BIOGRID 2021-04-19 https://downloads.thebiogrid.org/Download/BioGRID/Release-Archive/BIOGRID-3.5.187/ BIOGRID-ALL-3.5.187.psi25.zip
CORUM 2020-02-28 http://mips.helmholtz-muenchen.de/corum/download/ allComplexes.xml.zip
DIG 2021-04-19 morbidmap14062010.txt
DIP 2021-04-29 https://imex.mbi.ucla.edu/xpsq-dip-all/service/rest/current/search/query/*?maxResults=104,965 dip_psicquic.txt
FLY 2021-04-07 http://www.uniprot.org/docs/ fly.txt 2021_02
GENE 2021-04-19 ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ gene2refseq.gz gene_info.gz gene2go.gz gene_history.gz
GENPEPT 2021-02-17 ftp://ftp.ncbi.nih.gov/ncbi-asn1/protein_fasta/ gb*.fsa_aa.gz
HPIDB 2021-04-22 http://www.ebi.ac.uk/Tools/webservices/psicquic/hpidb/webservices/current/search/query/*?format=tab27 hpidb_psicquic.txt
HPRD 2021-04-20 HPRD_PSIMI_041310.tar.gz
HURI 2021-04-27 http://interactome-atlas.org/data/ HuRI.psi
IMEX 2021-04-22 http://www.ebi.ac.uk/Tools/webservices/psicquic/imex/webservices/current/search/query/*?format=tab27 imex_psicquic.txt
INNATEDB 2021-04-23 http://www.innatedb.com/download/interactions/ innatedb_psicquic.txt
INTACT 2021-03-12 ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psi25/ pmidMIF25.zip
INTCOMPLEX 2021-03-12 ftp://ftp.ebi.ac.uk/pub/databases/intact/complex/current/psi25/ complexesMIF25.zip
MATRIXDB 2021-04-26 http://matrixdb.univ-lyon1.fr:8080/psicquic/webservices/current/search/query/*?format=tab27 matrixdb_psicquic.txt
MBINFO 2021-04-23 http://www.ebi.ac.uk/Tools/webservices/psicquic/mbinfo/webservices/current/search/query/* mbinfo_psicquic.txt
MINT 2021-04-20 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 2021-04-23 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 2021-04-10 ftp://ftp.ncbi.nih.gov/blast/db/FASTA/ pdbaa.gz
PSI_MI 2021-04-19 https://raw.githubusercontent.com//HUPO-PSI/psi-mi-CV/master/ psi-mi.obo
QUICKGO 2021-04-23 http://www.ebi.ac.uk/QuickGO/psicquic/webservices/current/search/query/*?format=tab27 quickgo_psicquic.txt
REACTOME 2021-04-19 http://www.ebi.ac.uk/Tools/webservices/psicquic/reactome/webservices/current/search/query/*?format=tab27 reactome_psicquic.txt
SPIKE 2021-04-19 http://spike.cs.tau.ac.il/psicquic-ws/webservices/current/search/query/* spike_psicquic.txt
TAXONOMY 2021-04-19 ftp://ftp.ncbi.nih.gov/pub/taxonomy/ taxdump.tar.gz
UNIPROT 2021-04-07 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 2021_02
UNIPROTPP 2021-04-23 http://www.ebi.ac.uk/Tools/webservices/psicquic/uniprot/webservices/current/search/query/*?format=tab27 uniprotpp_psicquic.txt
VIRUSHOST 2021-04-21 http://virhostnet.prabi.fr:9090/psicquic/webservices/current/search/query/* virushost_psicquic.txt
YEAST 2021-04-07 http://www.uniprot.org/docs/ yeast.txt 2021_02

All iRefIndex Pages

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

Retrieved from "http://irefindex.vib.be/wiki/index.php?title=Sources_iRefIndex_18.0&oldid=4417"