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

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* This will allow for consistent GO-CAM curation using Noctua workbenches, import projects (e.g. Reactome and MOD imports)
 
* 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
 
* Will also allow us to move forward with harmonizing AE relations used in GO-CAM and conventional annotation
** On today's call, we will review the annotation extension relations that need further discussion, starting with happens_during
 
** [https://docs.google.com/spreadsheets/d/1zB8UKtG3JRGMkHgXmMpby-K5RFmYxGGRMEXULCCtcPo/edit#gid=1539887761 Google summary spreadsheet of MF extensions]
 
 
=== happens_during ===
 
* [https://docs.google.com/spreadsheets/d/1qoxnXM3q59jcZLIxnX5SY0H5syfK7GJc38s0VGxx2jM/edit#gid=0 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 [https://www.ebi.ac.uk/ols/ontologies/ro/properties?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_0002092 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 and Annotation Reviews ==
 
== Ontology Updates and Annotation Reviews ==

Revision as of 14:43, 22 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

  • 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

Ontology Updates and Annotation Reviews

Cellular Component

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

Protein multimerization terms

  • How are the reviews going?
  • Next terms up: protein homodimerization, protein heterodimerization (non-IPI evidence codes)

Transcription terms

  • Any issues or questions here?

Minutes

  • Present: