Annotation Conf. Call 2019-09-24: Difference between revisions
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**Definitely out | **Definitely out | ||
* [https://docs.google.com/spreadsheets/d/1okodOSG7mWgS8ZE8T95XjPr0-9G1vEIkAy2BkipEfRw Biological Process] | * [https://docs.google.com/spreadsheets/d/1okodOSG7mWgS8ZE8T95XjPr0-9G1vEIkAy2BkipEfRw Biological Process] | ||
*Definitely in: | **Definitely in: | ||
**part_of | ***part_of | ||
**has_input | ***has_input | ||
**has_output | ***has_output | ||
**occurs_in | ***occurs_in | ||
**transports_or_maintains_localization_of | ***transports_or_maintains_localization_of | ||
**has_target_end_location (Reactome) | ***has_target_end_location (Reactome) | ||
**has_target_start_location (Reactome) | ***has_target_start_location (Reactome) | ||
**regulates | ***regulates | ||
**negatively_regulates | ***negatively_regulates | ||
**positively_regulates | ***positively_regulates | ||
*In but usage restricted to extending from 'activity regulating processes', e.g. transcription, translation: | **In but usage restricted to extending from 'activity regulating processes', e.g. transcription, translation: | ||
**causally_upstream_of | ***causally_upstream_of | ||
**causally_upstream_of_negative_effect | ***causally_upstream_of_negative_effect | ||
**causally_upstream_of_positive_effect | ***causally_upstream_of_positive_effect | ||
*Out for now (need further discussion) | **Out for now (need further discussion) | ||
**results in..... | ***results in..... | ||
***curators would request appropriate terms for now | ****curators would request appropriate terms for now | ||
**others | ***others | ||
*Definitely out | **Definitely out | ||
**chained relations, e.g. regulates_o_occurs_in | ***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 | ****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 | ***others | ||
* [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] | ||
**Definitely in: | |||
***part_of | |||
**In but usage restricted to extending specific component terms | |||
***adjacent_to | |||
****extracellular region | |||
***overlaps | |||
****cell junction-type terms | |||
= Minutes = | = Minutes = |
Revision as of 15:58, 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
- 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
- Cellular Component
- Definitely in:
- part_of
- In but usage restricted to extending specific component terms
- adjacent_to
- extracellular region
- overlaps
- cell junction-type terms
- adjacent_to
- Definitely in:
Minutes
- Present: