CL has KeyError: 'CARO:0000000'

[quirinmanz]

Hi,

Overall, I find this package pretty useful.

I tried to load the Cell Ontology as described in the Examples:

cl = Ontology("http://purl.obolibrary.org/obo/cl.obo")

Unfortunately, I get the following error:

It looks like is_a relationships are only expected from the same ontology.

Any help would be appreciated.

Best,
Quirin

[althonos]

This is an problem on the CL side, I'll get in touch with the developers. It is not expected for an OBO ontology to contain dangling clauses (referencing undeclared entities), so they should fix it.

In the meantime, you can try using the cl-basic.obo release, which is lacking some axioms and relationships to other ontologies, but doesn't have this problem:

>>> import pronto
>>> cl = pronto.Ontology("http://purl.obolibrary.org/obo/cl-basic.obo")

[quirinmanz]

Thank you, that is very helpful!

Interestingly, I get the following error, when using from_obo_library:

I have the same problem with other local obo files (not cl):

Do you have an idea on how to solve this?

UPDATE:
Just realized that there is no basic version for uberon.
I managed to load cl, uberon and efo using a local owl file from https://www.ebi.ac.uk/ols/ontologies.
There are a lot of SyntaxWarnings but I guess I can ignore them.

[althonos]

You need to specify the extension with Ontology.from_obo_library:

cl = pronto.Ontology.from_obo_library("cl-basic.obo")

and there is also a basic uberon (it will raise some warnings):

uberon = pronto.Ontology.from_obo_library("uberon/basic.obo")

[cmungall]

I agree these ontologies should be fixed as its confusing to have these dangling classes - but it's not a violation of the spec, and it can be useful to be able to parse these