obophenotype / obophenotype/upheno
Pattern for relaxing equivalence axioms to simple subclass graph
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Description
A common operation now part of standard OBO workflows via robot is the relaxation of equivalence axioms to weaker subClassOf axioms.
For the majority of ontologies this falls into one of two templates: C SubClassOf D or C SubClassOf R some D (i.e Basic Existential Graphs). These are typically treated as single edges in neo4j etc.
For phenotype ontologies we don't see this pattern due to the necessity for the extra has-part (used as a buffer against is-a overloading). In order to formally relax this into the pattern above we would need to name the has-part o inheres-in chain.
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
No files or tests are named. Start by reviewing the two equivalence-axiom relaxation templates described in the issue and the existing ROBOT/uPheno workflow, then determine how the has-part o inheres-in chain should be named. Done should be a formally defined relaxation into a simple subclass-graph pattern.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- neo4j
- Domain
- databases
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100