wiki:OntologiesInUse

Version 9 (modified by gomidori, 9 years ago) (diff)

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Ontologies used for extensions

ontologyabbrtracker URL
Cell OntologyCLhttp://sourceforge.net/tracker/?group_id=76834&atid=925065
CHEBICHEBIhttp://sourceforge.net/tracker/?group_id=125463&atid=703818
Gene OntologyGOhttps://sourceforge.net/tracker/?atid=440764&group_id=36855
PATOPATOhttp://sourceforge.net/tracker/?group_id=76834&atid=595654
PfamPfamN/A, but contact helpdesk - pfam-help at sanger.ac.uk
Protein OntologyPRhttp://sourceforge.net/tracker/?group_id=266825&atid=1135711
PSI-MODMODhttps://sourceforge.net/tracker/?group_id=65472&atid=776607
Sequence OntologySOhttp://sourceforge.net/tracker/?group_id=72703&atid=810408

An example of each relation used should be added here:

https://sourceforge.net/apps/trac/pombase/wiki/ListOfRelations

For some ontologies, terms used should be added to the collection of ontology subsets that we plan to maintain (proposed 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.