Ontology meeting 2016-09-22

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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]]

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.
+id: GO:0075251 ! uredospore formation
+is_a: GO:0044711 {is_inferred="true"} ! single-organism biosynthetic process

So now which ontologies get precedence for axioms?


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

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.

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


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.

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:


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.

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

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