obophenotype / obophenotype/uberon
Avoid logical definitions with two part-ofs as differentia
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- Emacs Lisp
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- 1d 17h
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Description
this is an antipattern:
id: UBERON:0017612
name: cingulum of lower jaw molar
def: "A ridge that girdles the base of a lower molar tooth." [http://en.wiktionary.org/wiki/cingulid]
synonym: "cingulid" BROAD []
synonym: "cingulid of molar tooth" EXACT []
synonym: "tooth cingulid" RELATED []
intersection_of: UBERON:0017295 ! cingulum of tooth
intersection_of: part_of UBERON:0001710 ! lower jaw region
intersection_of: part_of UBERON:0003655 ! molar tooth
Rationale: we have a precoordinated term "lower jaw molar", and this DP and OWL reasoning is insufficient to infer the crucial part-of between these two.
Formally this is the co-reference problem, so I would classify as a co-reference antipattern. Even if we use a method like materialize or RG to materialize A sub R some B, formally we have models in which the MT is not part of the LJR
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the UBERON:0017612 example and its three intersection_of axioms; the issue names no repository file or test. Determine a modeling approach that avoids two part_of differentiae while preserving the intended relationship, then validate the ontology reasoning and update affected terms.
Written by the indexing model from the issue text.
Assessment
- Domain
- data
- Issue type
- Refactor
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100