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biolink / ontobio

python library for working with ontologies and ontology associations
https://ontobio.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
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synonym parsing skips synonyms with xsd:string declared #534

Open goodb opened 3 years ago

goodb commented 3 years ago

I came across this processing the cell ontology. The class 'naive B cell' provides an example. As you can see in the screenshot, the two synonyms without xsd:type string declarations get added to the ontobio 'node' dictionary but the others do not.

With a pointer to the code that gets these out, maybe I can fix it quickly. (observed in ontobio 2.4 and 2.6)

Screen Shot 2021-03-04 at 9 38 31 AM
goodb commented 3 years ago

I think this is actually a problem with the OWLTools json exporter that gets used when processing a local owl file with ontobio.

goodb commented 3 years ago

Problem goes all the way up into the OWL API. Not merging annotations from imported ontologies.. Anyway, not an ontobio issue after all! (Solve by robot merge before processing with ontobio).