Manager Call 2020-03-11: Difference between revisions

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* Agenda: David
* Agenda: David
* Minutes: Kimberly
* Minutes: Kimberly
* Present: David, Huaiyu, Judy, Kimberly, Laurent-Philippe, Seth
* Present: Chris, David, Huaiyu, Judy, Kimberly, Laurent-Philippe, Pascale, Seth
* Regrets:
* Regrets:


Revision as of 11:02, 11 March 2020

Agenda

  • Agenda: David
  • Minutes: Kimberly
  • Present: Chris, David, Huaiyu, Judy, Kimberly, Laurent-Philippe, Pascale, Seth
  • Regrets:

Discussion points

GO meeting Paris

  • Back up plan: remote meeting at same dates ? delay meeting ?
  • When do we need to make the decision by ?


Extensions/exports concerns

From Ruth

  • Are we planning to exclude some relations (like 'acts upstream of')? If we don't export then we should not allow to use the relation to annotate
  • What do we plan to do for enrichment for the extension, while we wait for network enrichment tools to be available ? Some current annotations have lost information. For example:
  • miRNA inhibits production of some growth factor
    • With GO-CAM we propose to annotate to 'miRNA involved in -> gene silencing by siRNA -> acts upstream of, negative effect growth factor activity'. But this is missing the 'miRNA (indirectly) involved in negative regulation of growth factor signaling pathway'


===Proposed data flow from Alex (GOA)


1. All annotation sources/files are pulled to GO based on yaml files. (already implemented) 2. GOA pull them from GO based on yaml files data (partially implemented) 3. GOA perform all, so far known, sanity checks and constrains (already implemented) 4. GOA sends out reports to go-quality and group responsible for annotations (partially implemented) 5. GOA generate gpa/gpi (maybe gaf if you ask nicely) for 142 taxon for all annotations which are passed though step 3 (to be implemented) 6. GO using 142 taxon file for all their pipelines needs, no need to run their own set of checks, can be indexed directly to amigo and other tools. (to be implemented)


Paper identifying missing 'is_a' relations

David https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa106/5739437

Some missing relations are not: is it a version problem ? or maybe they aren't using the inferred version of the ontology ?

Is there any missing link that could be useful for the ontology ?

Non-GO editors people making PR in the ontology tracker

https://github.com/geneontology/go-ontology/issues/17091


Isn't our policy that *only* GO editors work on the ontology ? Or do we want to allow some other users to make PRs?

Pathway Genome Databases and the Alliance

See Chris' email

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