Ontology meeting 2016-06-09

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Attendees: Chris, Heiko, Tanya, Dvid OS, David H, Melanie Regrets: Paola Minutes: Melanie


ETINEs update

Chris, Heiko and David OS to report.

Minutes

ETINES

Chris: pipeline will use Robot to split out inferences to separate file. Still some work required to update Robot to allow this. WIll be done by next Editor's meeting Heiko: Inferred axioms will show in TG but will not actually be part of the commit. They'll be added in by the regular inference job.

Relations

Some GO specific relations are potentially useful in LEGO, as are usage notes on relations available to curators doing annotation extension. But some shortcut relations will stay specific to annotation extension (not needed in LEGO or ontology). How do we achieve this?

Relations pipeline is still a bit of a mess:

  • gorel-edit.owl imports ro.owl
  • gene_ontology_write.obo imports a subset of ro.owl + ro_pending
  • GO specific relations (with GOREL identifiers) used in the GO editors file and annotation extensions are duplicated between gorel and ro-pending (audit needed). There is no import link between these two files.

GO rel should just be used for AE - no real pathway to keep relations in sync with RO_pending Chris: RO pending should go away, relations in the ontology should go into RO DOS: Agree but will have to be carefully co-ordinated.

=> RO should be primary space, with all axioms but for GO specific usage including local domain/range. May need to add an AP "GO usage" for some of those which could then live in RO

Decisions:

  • All relations with GOREL identifiers that are used outside of AEs should be in RO. This will make the available for LEGO and allow us to retire RO_pending.
  • RO can include GO usage statements (currently in gorel.(obo/owl) only, - making them available to LEGO users. To do this we need a new AP, GO_usage with an RO URI.
  • Other, AE specific annotations (e.g. local domain and range) will stay in gorel-edit.owl

Some careful co-ordination will be required to achieve this change.