Ontology meeting 2020-02-03: Difference between revisions

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*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
*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'


*GO
===Follow-up from annotation call===
  [Typedef]
====Binding terms====
  id: results_in_division_of
*Curators asked for firm guidelines on when to request new 'binding' terms
  name: results_in_division_of
*Can we get back to them with a proposal?  For example:
  namespace: external
**Going forward, curators will annotate binding using an appropriately general genus term (TBD) and the 'has input' extension for the chemical entity
  comment: use occurs_in
**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
  xref: GOREL:0001019
**Things to consider:
  is_a: has_participant ! has participant
***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


*GOREL
[Typedef]
id: results_in_division_of
name: results_in_division_of
namespace: go/extensions/gorel
def: "The relationship linking a entity and its participation in a process that results in the division of the entity into two entities of the same type." [GOC:mtg_berkeley_2013]
comment: Example of use: an annotation of gene X to cell division with results_in_division_of CL:0000057 (fibroblast) means that at the end of the process a single fibroblast has divided into two fibroblasts.
subset: AE_cell_or_anatomical
subset: display_for_curators
subset: valid_for_annotation_extension
xref: GOREL:0001019
property_value: local_domain BFO:0000015 xsd:string
property_value: local_range "CL:0000000 WBbt:0004017" xsd:string
property_value: usage "The relationship linking a entity and its participation in a process that results in the division of the entity into two entities of the same type." xsd:string
domain: BFO:0000015
range: CL:0000000
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: has_participant ! has participant


*regulates_o_results_in_division_of
**Not used in the ontology
**For annotation, it looks like curators use 'regulates o has participant', 'regulates o results in division of' although there are very few of these annotations
[Typedef]
id: regulates_o_results_in_division_of
name: regulates division of
namespace: go/extensions/gorel
def: "This is the combination of the regulates relation with the results_in_division_of relation." [GOC:mtg_berkeley_2013]
subset: display_for_curators
subset: valid_for_annotation_extension
xref: GOREL:0001024
property_value: local_domain GO:0008150 xsd:string
property_value: local_range "CL:0000000 WBbt:0004017" xsd:string
property_value: usage "This is the combination of the regulates relation with the results_in_division_of relation." xsd:string
domain: BFO:0000015
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: regulates_o_has_participant ! regulates_o_has_participant
equivalent_to_chain: regulates results_in_division_of ! results_in_division_of
*PROPOSED ACTION: obsolete 'results in division of' and 'regulates o results in division of'
*Replacement:
**PROPOSAL 1: use 'occurs in' for logical definitions and to provide context in annotation for what cell is dividing and 'regulates o occurs in' for standard regulation annotations
**PROPOSAL 2: use 'has input' and 'has output' for logical definitions and to provide context in annotation for what cell is dividing and what cells that division produces and 'regulates o has input', 'regulates o has output' for standard regulation annotations
**PROPOSAL 3: some hybrid of the above 'occurs in' and 'has input' and 'has output'?
*PROPOSED ACTION: create a design pattern


==Other Business==
==Other Business==

Revision as of 15:53, 30 January 2020

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

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

Minutes should be recorded on individual tickets and in individual projects