wiki:OntologiesInUse

Version 12 (modified by mah79, 6 years ago) (diff)

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Ontologies used for extensions

ontologyabbrtracker URL
Cell OntologyCLhttp://code.google.com/p/cell-ontology/issues/list
CHEBICHEBIhttps://sourceforge.net/p/chebi/curator-requests/
Gene OntologyGOhttps://sourceforge.net/p/geneontology/ontology-requests/
PATOPATOhttps://github.com/gkoutos/pato/issues/
PfamPfamN/A, but contact helpdesk - pfam-help at sanger.ac.uk
Protein OntologyPRhttp://sourceforge.net/p/pro-obo/term-requests/
PSI-MODMODhttp://sourceforge.net/p/psidev/mod-controlled-vocab-changes/
Sequence OntologySOhttps://sourceforge.net/p/song/term-tracker/

An example of each relation used should be added here:

ListOfRelationsForGO

For some ontologies, terms used should be added to the collection of ontology subsets that we maintain (as a /mini-ontologies/ sub-directory of the pombe-embl svn repository)

  • chebi.obo
  • pato.obo
  • cl.obo

For these ontologies please edit the is_a parent to point to PATO:0000001 ("quality"), CL:0000000 ("cell"), or CHEBI:24431 ("chemical entity") as appropriate.