Ontology meeting 2015-05-07

Attendees:

Minutes:

Follow-up: cellular component is_a anatomical structure?

Looking at http://wiki.geneontology.org/index.php/Ontology_meeting_2015-04-30#cellular_component_is_a_anatomical_structure.3F, could we please specify action items and point person(s).

GO-SO issues

Copying from last week:

There are various problems with our use of SO, some of which requires co-ordination with SO dev:

1. We need a bridge from SO transcript terms -> ChEBI:RNA. In the absence of this, lots of inference is mising. Will the long planned SO molecular save us, or do we need our own bridge axoims?
2. We use the SO terms nRNA, ncRNA and its children as if they refer to both mature and immature states of transcripts. In fact, according to SO they refer to the mature state. To align with SO properly we would need to review usage and use alternative SO terms where available. SO has an additional set of terms for primary transcripts, but no terms for immature. Primary transcript refers only to before splicing so no terms for intermediate state after splcing and before other modifications involved in maturation such as capping and polyadenylation for mRNA. Need to discuss possibilities of adding these with SO.

  DOS organising meeting with Karen Elibeck.  Details of this issue punted to future meeting.

part_of vs has_part in export from nucleus

dph-All of the named RNAs that are exported from the nucleus are exported as part of RNP complexes. In the ontology we had asserted that the RNA export has_part RNP export. This seemed backwards to me since the RNA is part of the RNP. I reversed these relations to make the RNA transport part_of the RNP transport.