Annotation Conf. Call 2019-09-24
Agenda
October GOC Meeting - Berkeley
Pipeline
- There have been some glitches with the GOC pipeline.
- New ontology terms may not be available for use yet.
- Software team is aware of the issues and working on restoring the pipeline to its regular schedule.
- Any updates here?
GO-CAMs and Annotation Extensions
- Update on relations allowed for GO-CAM as specified in ShEx (Shape Expressions)
- Approach:
- Examine relations used in GO
- Annotations extensions
- Ontology
- Some relations are in the Relations Ontology (RO), others have just been in gorel (relations only used in the Gene Ontology)
- Trying to move towards using only RO relations, using a smaller set of relations to make curation easier (but still maintain accurate representation of the biology)
- Examine relations used in GO
- Relations Usage
- Definitely in
- In, but usage restricted to specific ontology terms and their children
- Out for now (need further discussion)
- Definitely out
- Biological Process
- Definitely in:
- part_of
- has_input
- has_output
- occurs_in
- transports_or_maintains_localization_of
- has_target_end_location (Reactome)
- has_target_start_location (Reactome)
- regulates
- negatively_regulates
- positively_regulates
- In but usage restricted to extending from 'activity regulating processes', e.g. transcription, translation:
- causally_upstream_of
- causally_upstream_of_negative_effect
- causally_upstream_of_positive_effect
- Out for now (need further discussion)
- results in.....
- curators would request appropriate terms for now
- others
- results in.....
- Definitely out
- chained relations, e.g. regulates_o_occurs_in
- annotations using these relations will be modeled in GO-CAM but the relations won't be used in the GO-CAM models themselves
- others
- chained relations, e.g. regulates_o_occurs_in
- Definitely in:
- Molecular Function
- Definitely in:
- enabled_by
- part_of
- occurs_in
- has_output
- has_input
- regulates
- negatively_regulates
- positively_regulates
- directly_regulates
- directly_negatively_regulates
- directly_positively_regulates
- causally_upstream_of_or_within
- causally_upstream_of_or_within_negative_effect
- causally_upstream_of_or_within_positive_effect
- causally_upstream_of
- causally_upstream_of_negative_effect
- causally_upstream_of_positive_effect
- happens_during
- In but usage restricted to specific function terms
- directly_provides_input_for
- Out for now (need further discussion)
- occurs_at
- compound function relations
- Definitely out
- Definitely in:
- Cellular Component
- Definitely in:
- part_of
- In but usage restricted to specific component terms
- adjacent_to
- extracellular region
- overlaps
- cell junction-type terms
- adjacent_to
- Out for now (need further discussion)
- produced_by
- Definitely out:
- Definitely in:
- GO-CAM GPAD outputs
- Still work to be done here
- Should we limit the AEs generated and if so, how?
- Should we try to get chained annotation extension relations back out of GO-CAM models?
- How do we want to propagate 'contributes to'?
- Still work to be done here
Minutes
- Present: Dustin, Edith, Harold, Justin, Kimberly, Li, Michele, Midori, Pascale, Patrick, Sabrina, Seth, Stan