UniProt-GOA datasources: Difference between revisions

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UniProt-GOA maintains annotations from several sources. Not all these sources are in the [https://github.com/geneontology/go-site/blob/master/metadata/datasets/goa.yaml GOA.yaml file], only those for which GOA produces a separate GAF/GPAD file.  
UniProt-GOA maintains annotations from several sources. Not all these sources are in the [https://github.com/geneontology/go-site/blob/master/metadata/datasets/goa.yaml goa.yaml file], only those for which GOA produces a separate GAF/GPAD file.  


This is the full list of datasts maintained by GOA, as of Nov 1, 2019
This is the full list of data sources is here [https://ftp.ebi.ac.uk/pub/contrib/goa/GO.annotation_sources].


==GOA internal sources==
==GOA internal sources==
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* AgBase
* AgBase
* Alzheimers Project at University of Toronto
* Alzheimers_University_of_Toronto
* AlzheimersResearchUK-UCL
* Automated Function Prediction SIG CAFA Experiment (BHF-UCL Curators)
* Automated Function Prediction SIG CAFA Experiment (UniProt Curators)
* BHF-UCL
* BHF-UCL
** ARUK-UCL
** HGNC-UCL
** ParkinsonsUK-UCL
* CACAO
* CACAO
* CBI Computational Genomics Group
* CAFA
* Complex Portal (via Protein2GO)
* CBI Computational Genomics Group (CCG)
* DFLAT
* DFLAT
* DictyBase (specific GAF file generated)
* dictyBase
* Evelyn's spkw2go file
* FlyBase
* FlyBase (specific GAF file generated)
* Human Genome Database (GDB)
* GDB
* GO_Central
* GO_Central
* Gramene
* Gramene (GR)
* HGNC
* HGNC
* HGNC-UCL
* J. Craig Venter Institute (JCVI)
* J. Craig Venter Institute
* LIFEdb
* LIFEdb
* Microbial ENergy processes Gene Ontology Project
* Microbial ENergy processes Gene Ontology Project (MENGO)
* MTBBASE
* MTBBASE
* NTNU
* NTNU_SB
* PAMGO M. grisea
* PAMGO_MGG
* ParkinsonsUK-UCL
* PINC
* Proteome Inc
* Roslin_Institute
* Roslin Institute
* Structure-Function Linkage Database (SFLD)
* SGD (specific GAF file generated)
* SGD
* Structure-Function Linkage Database
* SYSCILIA_CCNET
* SynGO
* SynGO
* SynGO-UCL (UCL Curators)
* SynGO-UCL
* SYSCILIA_CCNET
* TAIR (via CCC)
* TIGR
* TIGR
* UniProt (EBI Curators)
* UniProt
* UniProt (PIR Curators)
* WormBase (WB)
* UniProt (SIB Curators)
* WormBase (specific GAF file generated)
* YuBioLab
* YuBioLab


==GOA external sources: Integrated in GOA for viewing; reloaded daily ==
* D.Hill's spkw2go file
* EcoCyc**
* EcoliWiki**
* GeneDB P. falciparum**
* GO Reference Genomes -> OK has its own file location
* Human Protein Atlas
* MGI -> OK has its own file location
* PomBase -> OK has its own file location
* PseudoCAP -> OK has its own file location
* RGD -> OK has its own file location
* SGN**
* SynGO (via Noctua) -> OK has its own file location
* ZFIN -> OK has its own file location


** Need to have a location of the GAF file compliant with the guidelines (ie, not on the GO SVN).
 
'''Automated pipelines'''
* EC2GO GO_REF:0000002
* Ensembl Compara GO_REF:0000107
* EnsemblFungi GO_REF:0000107
* EnsemblMetazoa GO_REF:0000107
* EnsemblPlants GO_REF:0000107
* EnsemblProtists GO_REF:0000107
* GOC GOC Gene Ontology Consortium GO_REF:0000108
* InterPro2GO GO_REF:0000002
* RNAcentral GO_REF:0000115
* UniPathway2GO GO_REF:0000041
* UniProt Keywords2GO GO_REF:0000004
* UniProt Subcellular Location2GO GO_REF:0000023
* UniRule2GO GO_REF:0000104
 
==GOCentral/ Noctua Internal sources==
* GO_Central (IBA) -> separately loaded by the GO pipeline - GOREF:0000033
* MGI
* XenBase
* ZFIN


== Review Status ==
== Review Status ==


Last reviewed: November 1, 2019
Last reviewed: November 30, 2023


[[Category:Release Pipeline]]
[[Category:Release Pipeline]]

Latest revision as of 15:40, 18 December 2023

UniProt-GOA maintains annotations from several sources. Not all these sources are in the goa.yaml file, only those for which GOA produces a separate GAF/GPAD file.

This is the full list of data sources is here [1].

GOA internal sources

Those are fully integrated into Protein2GO and in the GOA database, and are edited via Protein2GO

  • AgBase
  • Alzheimers_University_of_Toronto
  • BHF-UCL
    • ARUK-UCL
    • HGNC-UCL
    • ParkinsonsUK-UCL
  • CACAO
  • CAFA
  • CBI Computational Genomics Group (CCG)
  • DFLAT
  • dictyBase
  • FlyBase
  • Human Genome Database (GDB)
  • GO_Central
  • Gramene (GR)
  • HGNC
  • J. Craig Venter Institute (JCVI)
  • LIFEdb
  • Microbial ENergy processes Gene Ontology Project (MENGO)
  • MTBBASE
  • NTNU_SB
  • PAMGO_MGG
  • PINC
  • Roslin_Institute
  • Structure-Function Linkage Database (SFLD)
  • SGD
  • SYSCILIA_CCNET
  • SynGO
  • SynGO-UCL
  • TIGR
  • UniProt
  • WormBase (WB)
  • YuBioLab


Automated pipelines

  • EC2GO GO_REF:0000002
  • Ensembl Compara GO_REF:0000107
  • EnsemblFungi GO_REF:0000107
  • EnsemblMetazoa GO_REF:0000107
  • EnsemblPlants GO_REF:0000107
  • EnsemblProtists GO_REF:0000107
  • GOC GOC Gene Ontology Consortium GO_REF:0000108
  • InterPro2GO GO_REF:0000002
  • RNAcentral GO_REF:0000115
  • UniPathway2GO GO_REF:0000041
  • UniProt Keywords2GO GO_REF:0000004
  • UniProt Subcellular Location2GO GO_REF:0000023
  • UniRule2GO GO_REF:0000104

GOCentral/ Noctua Internal sources

  • GO_Central (IBA) -> separately loaded by the GO pipeline - GOREF:0000033
  • MGI
  • XenBase
  • ZFIN

Review Status

Last reviewed: November 30, 2023

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