Annotation Conf. Call 2019-09-10: Difference between revisions
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== October GOC Meeting - Berkeley == | == October GOC Meeting - Berkeley == | ||
* [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 == | |||
* 'cell part' and child terms | |||
** creation of new term ' cellular anatomical entity' | |||
== Guidelines: github annotation review tickets == | == Guidelines: github annotation review tickets == |
Revision as of 12:09, 9 September 2019
Agenda
October GOC Meeting - Berkeley
Ontology Updates
- 'cell part' and child terms
- creation of new term ' cellular anatomical entity'
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
- On today's call, we will review the annotation extension relations that need further discussion, starting with happens_during
- Google summary spreadsheet of MF extensions
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 ?
- WB had seven MF annotations with 'happens during' extensions that needed review.
- Updated documentation on 'happens during' usage: http://wiki.geneontology.org/index.php/Annotation_Extension_Relation:happens_during
Minutes
- Present: