Ontology meeting 2016-09-22

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Attendees: Paola, David H, Harold, Melanie, Moni, Tanya, Petra, Jim, Chris, David OS, Paul T, Diane (towards the end)

Regrets:

Minutes: Paola

New high level terms for fungal processes (population of unicellular organisms vs. multicellular organism)

Diane Inglis, Val Wood and Petra Fey will join us for this discussion.

See NTR: population of unicellular-organism process terms [[1]]

Tanya gives a summary of the issue (see GH ticket).
Petra: would need some way to have a top level; how would it fit with species such as Dicty?
Tanya: do you really need a high-level grouping term such as that?
Petra: maybe not. Use taxon restrictions from some term levels down? 
DOS: we have over 50 terms with multicellular in their name
T: which makes me reluctant to create parallel ones
DH agree. Was originally done because Val asked for cellular terms, but we were unsure
DOS: we shouldn’t get confused with use of cellular. Maybe easier to state that if a species has a multicellular stage, it’s multicellular
Tanya: we already have terms for biofilm. DOS: flocking is another case, and we have terms.
Tanya: Issue stemmed from PAINT annotation. Chris: But that should be all resolved now. 
AI: we’d prefer not to create that set of terms at high level, but rather map to fungal terms. Tanya will post this in the GH ticket. 
Petra agrees. She may request new terms after we’ve arranged the hierarchy as resolved and cleaned up.
DOS: fine with me that in the end stuff will end up under development for Dicty.
Petra: I’ll probably ask to create ‘social cooperation’.
Chris: we should start axiomatising Dicty terms using Dicty anatomy ontology. Petra: agree. They’ll talk more at the GO meeting.
Who’d be a good person from the anatomy ontology to follow the FAO tracker and look into FAO terms? 
We don’t know. Maybe Diane could ask Petra or Stacia to take a look if she has specific questions? 
DOS could help with some relations.

FAO update

  • FAO now has a home on github
  • We have a partial axiomatization of some fungal CCs and BPs using FAO - now in import chain
  • See Inferences Changes Report for: 2016-08-24 - e.g.
[Term]
+id: GO:0075251 ! uredospore formation
+is_a: GO:0044711 {is_inferred="true"} ! single-organism biosynthetic process

So now which ontologies get precedence for axioms?

[Term]

id: GO:0048315
name: conidium formation
namespace: biological_process
def: "Formation of asexual, nonmotile spores in fungi, by conversion of hyphal elements or arising from specialized sporogenous cells." [ISBN:0963117211, PMID:2524423, PMID:9529886]
synonym: "conidia biosynthesis" EXACT []
synonym: "conidia formation" EXACT []
is_a: GO:0030436 ! asexual sporulation
is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis
intersection_of: GO:0048646 ! anatomical structure formation involved in morphogenesis
intersection_of: results_in_formation_of CL:0000599 ! conidium

But conidium is also: FAO:0000024 conidium

DH: some CL terms mean the same as some FAO terms. He tried double axiomatisation (i.e. using both CL AND FAO) and it didn’t break anything. 
But should one ontology take precedence? 
Chris: we should have CL be metazoan, and use FAO for Fungi. But let’s check the state of FAO first. We should make a gap analysis first. 
AI: Cede cells to FAO: https://github.com/obophenotype/cell-ontology/issues/447

Reinstate daily report of terms and stats

Ticket: https://github.com/geneontology/go-site/issues/217

The ticket says that this is fixed, but no one has seen the report.

AI: Chris will check. Annoying because everything looks correct…

Implement a system for keeping partonomies in sync (Uberon & CC -> BP)

https://github.com/geneontology/go-ontology/issues/12658

We have many cases where we manually maintain partonomies between Uberon and BP (most notably under the development branch, and between CC and BP (most notably in the organization branch). Ideally we'd have some way to keep these part hierarchies in sync automatically. Not having such a system causes problems and adds unnecessary work for editors.

We can solve the problem by using GCIs to infer partonomy

  • These GCIs can be incorporated into Design patterns, TermGenie etc.
  • GCIs are visible in Protege 5 under terms used in them
  • We have a system for generating inferred partonomies. This will allow an edit file pipeline analogous to the one we use to generate automated classifications at each commit and add them to an imported file so that they are visible in OE or Protege.

I propose we test this out on the organization branch.

DOS Goes over the GH ticket. Hard to start with UBERON, but we could test the organization branch more easily. He put a proposal at the end of the ticket.
Melanie: is there a chance to impact reasoning by adding many GCIs? 
Chris: takes a while but it’s done as a batch process, so shouldn’t really impact. 
DOS: there may be some scaling issues. But we’re probably fine for now. 
AI: DOS, Chris and Jim will discuss and look at how to implement.

Follow-up: Modified proteins

See background discussion here: http://wiki.geneontology.org/index.php/Ontology_meeting_2016-09-15#Modified_proteins

Some of us still need to comment on the draft proposal. Please do so. Keep in mind that not everyone attends the annotation calls and not everyone will be at USC. Link:

https://docs.google.com/document/d/17U1TD3n_QI9coCycJcOUBDa2nRf3ggPR-tKjDMa_ff8/edit

AI: all those who haven’t, please comment, even if it’s just to say you agree. 
Then Paola will wrap up - or we could do it as a group.
Then we’ll present, whether it’s at an annotation call, by email to the wider group, in person at the GOC meeting, or all of the above.

Follow-up: How to report potential/necessary changes to annotations resulting from edits

See background discussion here http://wiki.geneontology.org/index.php/Ontology_meeting_2016-09-15#How_to_report_potential.2Fnecessary_changes_to_annotations_resulting_from_edits

Table is here https://docs.google.com/spreadsheets/d/1nAquF0oXHU6d638Q97ZeQ7K7DOhuru84-rOMEL4A114/edit#gid=0. At time of writing, it still needs input from some groups - these have been reminded.

AI: Paola will send reminder to go-consortium and go-discuss and to addresses that Moni collected on the Google spreadsheet.
Then let Paul T know if we still miss any replies, and he’ll contact people if needed. 
AI: Paola will then liaise with DOS so he can include the table in GH. Give it to him as a tsv file.

Follow-up: Metadata update - Move GO_REFs over to go-site

FYI, plan is here: https://github.com/geneontology/go-site/issues/214

Melanie: Is there a timeline? 
Moni: Hasn’t been switched over yet, but everything is in place. An announcement will be sent when ready. 
Chris can help establish a timeline.