search

pato-ontology / pato

PATO - the Phenotype And Trait Ontology
https://pato-ontology.github.io/pato/
BSD 3-Clause "New" or "Revised" License
58 stars 18 forks source link

Missing value in `basicPropertyValues` of latest JSON graph #530

Open althonos opened 2 years ago

althonos commented 2 years ago

Hi!

The last version of pato.json has an invalid property-value node: at line 510134 of pato.json, there is a predicate appearing twice but once without a value, which I think is an error:

            "basicPropertyValues": [
              { 
                "pred": "http://purl.obolibrary.org/obo/IAO_0000112"
              },
              {
                "pred": "http://purl.obolibrary.org/obo/IAO_0000112",
                "val": "This a general term that can include every organism of a species living in an area or any subset of them.  Subclasses can be more specific as needed."
              },
cmungall commented 2 years ago

This is in PCO which is imported by PATO

<Class rdf:about="http://purl.obolibrary.org/obo/PCO_0000001">
    <rdfs:label xml:lang="en">population of organisms</rdfs:label>
    <rdfs:subClassOf rdf:resource="

http://purl.obolibrary.org/obo/PCO_0000018"/>

A collection of organisms, all of the same species, that live in the same place. This is valid OWL but clearly still reflects a mistake. I suppose the owl2json should not try and be smart and omit vals with empty strings, and should either omit the annotation altogether, or following principle of least surprise, reflect the owl in the json with an empty string. On Thu, Oct 13, 2022 at 7:18 AM Martin Larralde ***@***.***> wrote: > Hi! > > The last version of pato.json has an invalid property-value node: at line > 510134 of pato.json, there is a predicate appearing twice but once > without a value, which I think is an error: > > "basicPropertyValues": [ > { > "pred": "http://purl.obolibrary.org/obo/IAO_0000112" > }, > { > "pred": "http://purl.obolibrary.org/obo/IAO_0000112", > "val": "This a general term that can include every organism of a species living in an area or any subset of them. Subclasses can be more specific as needed." > }, > > — > Reply to this email directly, view it on GitHub > , or unsubscribe > > . > You are receiving this because you are subscribed to this thread.Message > ID: ***@***.***> >