Manager Call 2020-03-11

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Agenda

  • Agenda: David
  • Minutes: Kimberly
  • Present: Chris, David, Huaiyu, Judy, Kimberly, Laurent-Philippe, Pascale, Paul T., Seth, Suzi
  • 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 ?
  • PIs will discuss on go-top call today and decide what to do.
    • Hold the current dates for the meeting; announce decision to GOC within a week

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'
  • In a GAF, there is no indication of the 'acts upstream of', or similar, gp2term relations, which can lead to misleading annotations.
  • We need to double-check what the behavior is for current annotation tools and output files.
  • Proposal: do *not* include asserted 'acts upstream of' annotations in the GAF; GPAD would be okay because users have access to the expanded set of gp2term relations?
  • Proposal: do a one-time incremental update to the GAF to include full set of gp2term relations and prioritize providing annotation file subsets
    • There seems to be agreement that this is the most reasonable approach but we need to formulate a specific plan for execution.
    • This change will be an officially versioned increment of GAF file format (exact level of new format naming TBD).
    • Communicate with our users about the changes and what files will/are available for analyses.
    • Other issues to address: impact on enrichment tools, e.g. PANTHER

Proposed data flow from Alex (GOA)

  • Based on decision at PI retreat to only show in AmiGO the 142 species also included in PANTHER, i.e. fewer species but all available annotations for those species.
  • This would be a new pipeline to supplant the current UniProtGOA-all pipeline, i.e. the MODs will still be the source of their species annotations


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 ?

  • At the moment, we will not pursue a collaboration with this group, but this paper highlights that we need to spend more time on the logical definitions and DOS-DPs project.

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?

  • We don't want a blanket rule that no one outside of the ontology editors can make pull requests, but we need to be vigilant in monitoring the types and content of pull requests.

Pathway Genome Databases and the Alliance

See Chris' email

  • Explore bringing in other existing curated pathways in a similar way that we did for Reactome