Ontology meeting 2020-02-03

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See calendar for details

On call: Harold, David, Peter, Barbara, Jim, Karen, Kimberly, Pascale, Chris, Tanya, Bill

Note David will not be here next week. We will need someone else to host this call.


Discussion topics

Issue tracker rota

Lately there have been a large number of tickets open in the areas of immunology and organism-interaction; so many that it has become a project in and of itself. Since Pascale is the only one comfortable editing this area of the ontology, it has effectively removed her from the rota. This means that there are only two editors working on tickets for all other request, David and Harold. Everyone else is off the rota and assigned to projects. In addition Harold and David have projects on which they are supposed to be working. What can we do about this?

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

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)
  • Entered a ticket in the CL tracker, for which David OS has made some updates https://github.com/obophenotype/cell-ontology/issues/617 pull request needs review
  • 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) although these are not of highest priority since they haven't been used in annotation

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: review and update annotations to use 'has input' (create go-annotation ticket - couldn't find one already)
    • Note that we will need to update the local range for 'has input' to allow for cells before doing this
  • PROPOSED ACTION: obsolete 'results in division of' see https://github.com/geneontology/go-ontology/issues/18804
  • PROPOSED ACTION: keep 'regulates o results in division of' for now
      • fate of the chained relations is still undecided
      • we have a model for importing them
      • we haven't decided on exporting them, but are leaning towards not doing that
  • PROPOSED ACTION: create a design pattern for cell division using 'has input'
localization and transporter activity shapes
  • Review proposed shape for localization
    • what about multi-organism localization (GO:1902579) defined as: localization AND ('bearer of' some 'multi-organismal process quality')
      • note that 'bearer of' is not in the ShEx

Follow-up from 2020-01-28 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

Compound functions and molecular function regulators

  • We need to decide on a design pattern for compound functions
  • For the estrogen nuclear receptor, the demo GO-CAM model had estrogen binding 'directly positively regulates' nuclear receptor activity
  • This results in an inferred molecular function regulator annotation on the estrogen binding node meaning that the estrogen receptor is a molecular function regulator of itself, which curators felt was not biologically correct/intuitive and they wouldn't want to show this to users
  • Can we model compound functions with 'has part' in the ontology rather than a regulatory relation between the separate functions?
  • Note that we will still get many inferred molecular function regulator MF annotations for models where we use the 'directly positively/negatively regulates' relation between two activities 'enabled by' different gene products
  • Do we still want molecular function regulator as an MF class in the ontology? Should we keep its logical definition?
  • Do we want to export inferred molecular function regulator annotations, even for upstreams gps who activity directly regulates that of downstream gps?

Inferred Protein Binding Annotations

  • We still get inferred protein binding annotations when connecting two MFs with a directly positively regulates relation and the second MF is enabled by a protein entity
  • Change SWRL rule?

BPs of type 'regulation of MF'

(Pascale): Are we still creating terms like 'regulation of poly(A)-specific ribonuclease activity' (see https://github.com/geneontology/go-ontology/issues/16793). I thought this was now captured as MF 'enzyme regulator activity'. Can we make a decision on that ?

Other Business


Minutes should be recorded on individual tickets and in individual projects