obophenotype / obophenotype/uberon

Experiment: materialize phylo-specific uberon classes as lattice

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Description

For context see https://github.com/obophenotype/uberon/issues/1635

The goal here is to make species-specific views as well as a pan-taxon view with materialized species-specific classes

These would have IDs like UBERON:nnnnnn.9606 (possibly new namespace.. not relevant yet as this is an experiment).

  • materialize the cross product of all Uberon x TaxonSubset (including intermediates, e.g Mammalia)
  • filter unsatisfiable (i.e. human feather) analogous to #1635
  • push down phyloGCIs
    • E.g. (C and part-of some T) sub R some D ==> CT sub R some D,
      • E.g. 'mammal naris part-of some mammal head`
  • insert horizontal homology axioms, from both curated table and inferred
  • merge with ssAOs if it exists (but note we will have nodes for ssAOs that do not exist). This is tricky as there is the possibility of bringing in things that mess with overall consistency and coherency, better if everyone is conforming to DPs etc

The results would be similar to the composite views https://github.com/obophenotype/uberon/wiki/Multi-species-composite-ontologies however, it would include taxa for which there is no curated ssAO.

The result would be very latticey which would confuse a lot of tools. We can set up a local OLS and test this as @matentzn did for upheno2.

We could also simply remove the taxon-generic groupings and have artefacts that are at a single taxonomic level

Same strategy could be applied to CL - this may be where we are headed with provisional CLs, transcriptomic-cluster CLs, marker-based CLs, all of which are rightly ss. cc @dosumis

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reading issue #1635, the Evolutionary variability GCIs wiki page, and the multi-species composite ontology documentation. Use the proposed local OLS experiment as the validation entry point. Done would mean a materialized species-specific and pan-taxon result that filters unsatisfiable classes and incorporates the described axioms without compromising consistency.

Written by the indexing model from the issue text.

Assessment

Domain
data
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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