wikipathways / wikipathways/GPML2RDF

Change from rdf:type wp:Pathway to rdfs:subClassOf wp:Pathway

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Dominant language
Java
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Description

Currently, the RDF is modelled using rdf:type on both skos:Collection and wp:Pathway. E.g.

<http://identifiers.org/wikipathways/WP4104_r113457>
        a                    skos:Collection , wp:Pathway ;

I am wondering about changing rdf:type to using rdfs:subClassOf for wp:Pathway part. This would put it inline with for example the Pathway Ontology.

Introducing this sublass model, where a Pathway is depicted as a class, would open up the possibility to query by traversing a hierarchical tree and extend that to for example the pathway ontology.

One example of this suggestion would be:

<http://identifiers.org/wikipathways/WP4104_r113457>
        a                            skos:Collection ;
        rdfs:subClassOf  wp:Pathway .

it will probably have some repercussions on how the same pathway in different species is modelled.
There might need to be species less pathway because in principle they are all subclasses of that pathway.

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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 locating the RDF generation entry point and reviewing how pathway and species data are currently represented. Compare the existing rdf:type output with the proposed rdfs:subClassOf model, including repercussions for pathways shared across species. Done means the modeling decision is resolved and the resulting RDF behavior is specified and verified.

Written by the indexing model from the issue text.

Assessment

Tech stack
java
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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