KGX dropping terms from OBO ontologies (json -> tsv) with no 'name' attribute

[realmarcin]

Is your feature request related to a problem? Please describe.
Based on KG-Microbe builds there are terms from OBO ontologies (eg ChEBI and GO) which get dropped from the transform step because KGX is rejecting terms with no 'name' attribute.

The message is:
"Skipping line as it does not have a name field: CHEBI 21588 biolink:ChemicalSubstance chebi.json http://purl.obolibrary.org/obo/CHEBI_21588"

Looking at the CHEBI page for this chemical, it does display a name so perhaps there is an issue with parsing obo json?
https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:21588

ChEBI Name N-acetyl-β-D-glucosaminyl-1,3-β-D-galactosyl-1,4-N-acetyl-D-glucosaminyl group

Describe the solution you'd like
Ideally OBO ontologies would have a name for each term, but it looks like this is not a requirement/not enforced at OBOFoundry (or there is a KGX obo json parsing issue?). In the interim, and to be more flexible for inputs, can KGX not require a 'name' attribute, ie maybe just a warning?

[cmungall]

what is the source json file and where did you get it?

is this parsing chebi.json, or an ontology that uses chebi in axiomatization?

[realmarcin]

Good questions, thanks!

So it looks like we are downloading chebi.owl:
http://purl.obolibrary.org/obo/chebi.owl

And then converting to json using ROBOT:
https://github.com/Knowledge-Graph-Hub/kg-microbe/blob/5886197d5fa00ab4c2e6af09dd9f5a3bc453743f/kg_microbe/transform_utils/traits/traits.py#L85

Calling method here:
https://github.com/Knowledge-Graph-Hub/kg-microbe/blob/5886197d5fa00ab4c2e6af09dd9f5a3bc453743f/kg_microbe/utils/robot_utils.py#L27

And here is the line for the downstream transform code starting from 'obojson':
transform(inputs=[data_file], input_format='obojson', output= os.path.join(self.output_dir, name), output_format='tsv')

https://github.com/Knowledge-Graph-Hub/kg-microbe/blob/5886197d5fa00ab4c2e6af09dd9[…]3743f/kg_microbe/transform_utils/ontology/ontology_transform.py

From this import:
from kgx.cli.cli_utils import transform

[sierra-moxon]

@realmarcin - Is this still an issue?