Annotation Conf. Call 2019-09-24: Difference between revisions
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** Some relations are in the Relations Ontology (RO), others have just been in gorel (relations only used in the Gene 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) | ** 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) | ||
* | *Relations Usage | ||
* | **Definitely in | ||
* | **In, but usage restricted to specific ontology terms and their children | ||
**Out for now (need further discussion) | |||
**Definitely out | |||
* [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 | |||
***others | |||
**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 | |||
***others | |||
* [https://docs.google.com/spreadsheets/d/1DuON03hEfEDDC7_6CCnnR3JcBA4ltQgGFP0otAeMZKs '''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 | |||
***[https://docs.google.com/spreadsheets/d/1DuON03hEfEDDC7_6CCnnR3JcBA4ltQgGFP0otAeMZKs See spreadsheet] | |||
* [https://docs.google.com/spreadsheets/d/17LcW5v4mX18jJjAXfXethJnnI0cTg--PZUGXtV7NWsY '''Cellular Component'''] | |||
**Definitely in: | |||
***part_of | |||
**In but usage restricted to specific component terms | |||
***adjacent_to | |||
****extracellular region | |||
***overlaps | |||
****cell junction-type terms | |||
**Out for now (need further discussion) | |||
***produced_by | |||
**Definitely out: | |||
***[https://docs.google.com/spreadsheets/d/17LcW5v4mX18jJjAXfXethJnnI0cTg--PZUGXtV7NWsY See spreadsheet] | |||
*'''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'? | |||
= Minutes = | = Minutes = | ||
*Present: | *Present: David H, Dustin, Edith, Harold, Justin, Kimberly, Laurent-Philippe, Li, Michele, Midori, Pascale, Patrick M, Petra, Rob, Sabrina, Seth, Stacia, Stan, Suzi A, Tanya | ||
[[Category:Annotation Working Group]] | [[Category:Annotation Working Group]] |
Latest revision as of 11:27, 24 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
- 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: David H, Dustin, Edith, Harold, Justin, Kimberly, Laurent-Philippe, Li, Michele, Midori, Pascale, Patrick M, Petra, Rob, Sabrina, Seth, Stacia, Stan, Suzi A, Tanya