Removed some unnecessary RDF properties #87
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While we need this in JSON, we probably don't need to include this in RDF (see #78). If we do need to insert it, we can add it back pretty easily.
We previously used this for letting JPhyloRef know when a phyloref was malformed, but it no longer checks this property -- it now just throws an error if reasoning fails.
gaurav
changed the title
testcase:internal_specifier and testcase:external_specifier
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BTW we might consider using |
Or perhaps you are suggesting that we record the internal and external specifiers using subclass statements, such as by describing the phyloref Alligatoridae as a subclass of I have opened an issue for converting the |
We can discuss this at the next call, but I didn't think this what we wanted Phyx to look like, right? (As opposed to the generated OWL expressions) |
Sounds good, I'll put it on the agenda! |
Instead, it returns the full component class the first time it is called, and subsequently returns an ID to that component class.
This PR removes some RDF properties from the JSON Schema:
internalSpecifiersandexternalSpecifiersproperties in JSON, we probably don't need to include them in RDF (see Figure out what to do about the top-level object in a Phyx file #78, An object property for associating an internal specifier with a phyloreference phyloref-ontology#7, An object property for associating an external specifier with a phyloreference phyloref-ontology#8). If we change our mind later, we can add them back pretty easily.malformedPhyloreferencefield to let JPhyloRef know when a particular phyloreference was malformed (such as when it had no internal specifiers, or if one of its specifiers could not be mapped to a particular phylogeny node). JPhyloRef no longer checks this field at all, so we might as well remove it from here as well.subClassesfield (which is the@reverseofrdfs:subClassOf).#phyloref1had 4 component classes, the first component class for#phyloref2would be identified as#phyloref2_component5). I've changed this so that each phyloreference's component classes start counting from 1.Closes #78.