Difference between revisions of "Annotation Conf. Call 2019-09-10"

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* [http://wiki.geneontology.org/index.php/2019_Berkeley_GOC_Meeting_Logistics Logistics and Sign-Up]
 
* [http://wiki.geneontology.org/index.php/2019_Berkeley_GOC_Meeting_Logistics Logistics and Sign-Up]
  
== Ontology Updates ==
+
== Pipeline ==
* 'cell part' and child terms
+
* There have been some glitches with the GOC pipeline.
** creation of new term ' cellular anatomical entity'
+
* 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.
  
 
== Guidelines: github annotation review tickets ==
 
== Guidelines: github annotation review tickets ==
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* Updated documentation on 'happens during' usage:  http://wiki.geneontology.org/index.php/Annotation_Extension_Relation:happens_during
 
* Updated documentation on 'happens during' usage:  http://wiki.geneontology.org/index.php/Annotation_Extension_Relation:happens_during
  
 
+
== Ontology Updates ==
 +
* 'cell part' and child terms
 +
** creation of new term ' cellular anatomical entity'
  
 
= Minutes =
 
= Minutes =
 
*Present:  
 
*Present:  
 
[[Category:Annotation Working Group]]
 
[[Category:Annotation Working Group]]

Revision as of 11:51, 9 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.

Guidelines: github annotation review tickets

  • Group contacts are listed as 'assignees'
  • Please remove your name from the assignee list when you are finished
  • Some tickets also have lists or tables listing each group - good to add info here, too, but assignee list is most important

GO-CAMs and Annotation Extensions

  • After USC hackathon in June, we formed a small working group to fully articulate the GO-CAM model specifications
  • This will allow for consistent GO-CAM curation using Noctua workbenches, import projects (e.g. Reactome and MOD imports)
  • Will also allow us to move forward with harmonizing AE relations used in GO-CAM and conventional annotation

happens_during

  • Google spreadsheet for happens during
  • Current recommendations are that 'happens during' is used to define a biological phase or life stage during which a molecular function occurs
  • However, happens_during is not defined in the relations ontology
  • There is a comment, however:
    • X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))
    • This implies that the start and end of the molecular function and phase are known
    • For things like cell cycle phases or development stages this seems fairly straightforward
  • But what about annotations that referred to a function that 'happens during' a biological process, such as 'response to oxidative stress'?
  • What do we mean when we make these statements?
    • WB had seven MF annotations with 'happens during' extensions that needed review.
      • One used a WBls term, so that was okay.
      • The remaining six used 'response to' terms and in reviewing them, I changed the extension relation to 'part of' the 'response to' term. The MFs were all transcription-related functions that mediated the transcriptional response to unfolded protein, or hypoxia, or heat.
    • (Pascale): If we want to allow happens_during for 'response to' terms, then we should treat them as 'biological phases', and disallow direct annotations. Are there cases where using 'part_of' versus 'happens_during' makes sense ?
  • Updated documentation on 'happens during' usage: http://wiki.geneontology.org/index.php/Annotation_Extension_Relation:happens_during

Ontology Updates

  • 'cell part' and child terms
    • creation of new term ' cellular anatomical entity'

Minutes

  • Present: