Ontology meeting 2020-02-03

Conference Line

See calendar for details

On call:

Agenda

Discussion topics

Aligning Ontology, Annotation, ShEx

• We are creating ontology term-specific shapes in the ShEx schema
• The goal is to align what is used for annotation with the equivalent expression in logical definitions of the ontology
• We are also moving towards only using RO relations in GO, i.e. retiring, or incorporating into RO, GOREL relations or RO-pending relations

GOREL relations proposed to RO

• 'acts on population of'
• no comments or action on this ticket - who can help with this?

GOREL relations that could potentially be retired and replaced with existing RO relations

• ACTION: As a pilot, David and Kimberly replaced 'occurs in' in cell division logical definitions with 'has input' for specific cell types
• https://github.com/geneontology/go-ontology/pull/18690
• Also removed some asserted parents for cell division terms - this changed some parentage wrt neuroblasts and somatic stem cell parentage (but is now consistent with CL)
• Overall, this wasn't too difficult and we could continue along these lines for the other relations in question (results in fission of, results in fusion of, results in maintenance of, results in distribution of)

From 2020-01-27 call:

'results in division of' (GOREL:0001019)

• Not used in the ontology
  • In the ontology, logical definitions use:
    • 'occurs in', e.g. cystoblast division = cell division and 'occurs in' some cystoblast
    • 'has input', e.g. germ-line stem cell division = cell division and 'has input' some germ-line stem cell
    • loosely, but not exclusively, along somatic vs stem cell lines
  • No design pattern (that I could find)

• For annotation, it looks like curators use 'occurs in', 'has participant, 'results in division of' although there aren't many annotation extensions at all for 'cell division' and children

• PROPOSED ACTION: finish review of ontology diff
• PROPOSED ACTION: obsolete 'results in division of' and 'regulates o results in division of'
• PROPOSED ACTION: create a design pattern for cell division using 'has input'

Follow-up from annotation call

Binding terms

• Curators asked for firm guidelines on when to request new 'binding' terms
• Can we get back to them with a proposal? For example:
  • Going forward, curators will annotate binding using an appropriately general genus term (TBD) and the 'has input' extension for the chemical entity
  • We can generate monthly reports of annotation extension use to see if there are any highly (TBD) used extensions for which we should create ontology terms
  • Things to consider:
    • For chemical entities, what ontology terms should curators use?
    • What should we do with existing terms in the ontology?
    • We still need to convey what binding events we want to capture as MFs, and why, in GO

Other Business

https://github.com/geneontology/go-ontology/projects/1