Difference between revisions of "Annotation Conf. Call 2019-09-24"

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m (GO-CAMs and Annotation Extensions)
m (GO-CAMs and Annotation Extensions)
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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 12:58, 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)
  • 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
    • 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
  • 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

Minutes

  • Present: