Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

synonym parsing skips synonyms with xsd:string declared #534

Open
goodb opened this issue Mar 4, 2021 · 2 comments
Open

synonym parsing skips synonyms with xsd:string declared #534

goodb opened this issue Mar 4, 2021 · 2 comments

Comments

@goodb
Copy link

goodb commented Mar 4, 2021

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
Copy link
Author

goodb commented Mar 4, 2021

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

@goodb
Copy link
Author

goodb commented Mar 4, 2021

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).

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant