obophenotype / obophenotype/uberon

Avoid logical definitions with two part-ofs as differentia

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design_pattern
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Emacs Lisp
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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

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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

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