Annotation Conf. Call 2019-09-24: Difference between revisions
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*Relations Usage | *Relations Usage | ||
**Definitely in | **Definitely in | ||
**In, but usage restricted to specific ontology terms and their children | **In, but usage restricted to specific ontology terms and their children | ||
**Out for now (need further discussion) | **Out for now (need further discussion) | ||
**Definitely out | |||
* [https://docs.google.com/spreadsheets/d/1okodOSG7mWgS8ZE8T95XjPr0-9G1vEIkAy2BkipEfRw Biological Process] | * [https://docs.google.com/spreadsheets/d/1okodOSG7mWgS8ZE8T95XjPr0-9G1vEIkAy2BkipEfRw 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 | |||
*Definitely out | |||
**chained relations, e.g. regulates_o_occurs_in | |||
***annotations using these relations will be [http://noctua.geneontology.org/editor/graph/gomodel:5c4605cc00000396 modeled in GO-CAM] but the relations won't be used in the GO-CAM models themselves | |||
* [https://docs.google.com/spreadsheets/d/1DuON03hEfEDDC7_6CCnnR3JcBA4ltQgGFP0otAeMZKs Molecular Function] | * [https://docs.google.com/spreadsheets/d/1DuON03hEfEDDC7_6CCnnR3JcBA4ltQgGFP0otAeMZKs Molecular Function] | ||
* [https://docs.google.com/spreadsheets/d/17LcW5v4mX18jJjAXfXethJnnI0cTg--PZUGXtV7NWsY Cellular Component] | * [https://docs.google.com/spreadsheets/d/17LcW5v4mX18jJjAXfXethJnnI0cTg--PZUGXtV7NWsY Cellular Component] |
Revision as of 15:53, 23 September 2019
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
- 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
- chained relations, e.g. regulates_o_occurs_in
Minutes
- Present: