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 datasts maintained by GOA, as of Nov 1, 2019.
 
Up to date data is here: ftp://ftp.ebi.ac.uk/pub/contrib/goa/P2GO_SOURCES.dat


==GOA internal sources==
==GOA internal sources==
Line 51: Line 53:
* EcoliWiki**
* EcoliWiki**
* GeneDB P. falciparum**
* GeneDB P. falciparum**
* GO Reference Genomes -> OK has its own file location
* GO Reference Genomes -> separately loaded by the GO pipeline
* Human Protein Atlas
* Human Protein Atlas (obtained from https://www.proteinatlas.org/download/subcellular_location.tsv.zip)
* MGI -> OK has its own file location
* MGI -> separately loaded by the GO pipeline
* PomBase -> OK has its own file location
* PomBase -> separately loaded by the GO pipeline
* PseudoCAP -> OK has its own file location
* PseudoCAP -> separately loaded by the GO pipeline
* RGD -> OK has its own file location
* RGD -> separately loaded by the GO pipeline
* SGN**  
* SGN**  
* SynGO (via Noctua) -> OK has its own file location
* SynGO (via Noctua) -> OK has its own file location
* ZFIN -> OK has its own file location
* ZFIN -> separately loaded by the GO pipeline


** Need to have a location of the GAF file compliant with the guidelines (ie, not on the GO SVN).  
  ** Need to have a location of the GAF file compliant with the guidelines (ie, not on the GO SVN).


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

Revision as of 17:59, 8 January 2020

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 datasts maintained by GOA, as of Nov 1, 2019.

Up to date data is here: ftp://ftp.ebi.ac.uk/pub/contrib/goa/P2GO_SOURCES.dat

GOA internal sources

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

  • AgBase
  • Alzheimers Project at University of Toronto
  • AlzheimersResearchUK-UCL
  • Automated Function Prediction SIG CAFA Experiment (BHF-UCL Curators)
  • Automated Function Prediction SIG CAFA Experiment (UniProt Curators)
  • BHF-UCL
  • CACAO
  • CBI Computational Genomics Group
  • Complex Portal (via Protein2GO)
  • DFLAT
  • DictyBase (specific GAF file generated)
  • Evelyn's spkw2go file
  • FlyBase (specific GAF file generated)
  • GDB
  • GO_Central
  • Gramene
  • HGNC
  • HGNC-UCL
  • J. Craig Venter Institute
  • LIFEdb
  • Microbial ENergy processes Gene Ontology Project
  • MTBBASE
  • NTNU
  • PAMGO M. grisea
  • ParkinsonsUK-UCL
  • Proteome Inc
  • Roslin Institute
  • SGD (specific GAF file generated)
  • Structure-Function Linkage Database
  • SynGO
  • SynGO-UCL (UCL Curators)
  • SYSCILIA_CCNET
  • TAIR (via CCC)
  • TIGR
  • UniProt (EBI Curators)
  • UniProt (PIR Curators)
  • UniProt (SIB Curators)
  • WormBase (specific GAF file generated)
  • YuBioLab

GOA external sources: Integrated in GOA for viewing; reloaded daily

  • D.Hill's spkw2go file
  • EcoCyc**
  • EcoliWiki**
  • GeneDB P. falciparum**
  • GO Reference Genomes -> separately loaded by the GO pipeline
  • Human Protein Atlas (obtained from https://www.proteinatlas.org/download/subcellular_location.tsv.zip)
  • MGI -> separately loaded by the GO pipeline
  • PomBase -> separately loaded by the GO pipeline
  • PseudoCAP -> separately loaded by the GO pipeline
  • RGD -> separately loaded by the GO pipeline
  • SGN**
  • SynGO (via Noctua) -> OK has its own file location
  • ZFIN -> separately loaded by the GO pipeline
 ** Need to have a location of the GAF file compliant with the guidelines (ie, not on the GO SVN).

Review Status

Last reviewed: November 1, 2019

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