Annotation Conf. Call 2019-09-24: Difference between revisions
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* New ontology terms may not be available for use yet. | * 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. | * Software team is aware of the issues and working on restoring the pipeline to its regular schedule. | ||
* Any updates here? | |||
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== GO-CAMs and Annotation Extensions == | == GO-CAMs and Annotation Extensions == |
Revision as of 17:42, 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
- 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
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: Colin, David, Dmitry, Dustin, Edith, Giulia, Helen, Harold, Karen, Kimberly, Laurent-Philippe, Michelle, Midori, Pascale, Paul T., Sabrina, Seth, Stacia, Tanya, Petra
GO-CAMs and Annotation Extensions
happens_during
- We discussed review and use of 'happens during' as an annotation extension relation for MF terms.
- Use of 'happens during' with a biological phase of life cycle stage is allowed.
- Use of 'happens during' with a 'response to x' BP term is still under review.
- If the MF is an integral part of the 'response to' term, then the curator should update the annotation extension relation to 'part of'.
- Other 'response to' extensions will need to be examined in more detail to better understand what information we were trying to capture and how it would be modeled in a GO-CAM.
- PomBase has a number of these annotations and will get back to us on their thoughts.
- We will also address Barbara's questions about use of 'happens during' on a future call.
occurs_at
- We will not use SO terms with the 'occurs at' relation to capture the type of sequence or motif at which an MF occurs, e.g. 'occurs at' n_terminal_region (SO:0100014)