Annotation Conf. Call 2019-09-10: Difference between revisions
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** creation of new term ' cellular anatomical entity' | ** creation of new term ' cellular anatomical entity' | ||
=== Protein multimerization terms === | === Protein multimerization terms === | ||
* How are the reviews going? | |||
* Next terms up: protein homodimerization, protein heterodimerization (non-IPI evidence codes) | |||
=== Transcription terms === | === Transcription terms === | ||
* Any issues or questions here? | |||
= Minutes = | = Minutes = | ||
*Present: | *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) | |||
[[Category:Annotation Working Group]] | [[Category:Annotation Working Group]] |
Latest revision as of 14:47, 10 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
- 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)