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

trapi validation issue with biolink:support_graphs #1363

Closed
colleenXu opened this issue Jul 21, 2023 · 3 comments
Closed

trapi validation issue with biolink:support_graphs #1363

colleenXu opened this issue Jul 21, 2023 · 3 comments

Comments

@colleenXu
Copy link
Contributor

Describe the bug
There's an issue with TRAPI validation where KG edges with the attribute biolink:support_graphs are being flagged with a warning. I think this is happening because support_graphs isn't an association slot in the biolink-model or is somehow not being recognized as a valid edge-attribute attribute_type_id...

This is an example warning message from BTE's validation report at this PK.

* Knowledge Graph Edge Attribute Type Id Not Association:
=> Edge has an attribute_type_id that is not an association slot
	$ infores:biothings-explorer
		# biolink:support_graphs:
		- edge_id: 
			MESH:C007789--biolink:treats->MONDO:0007035
	$ global
		# biolink:support_graphs:
		- edge_id: 
			CHEMBL.COMPOUND:CHEMBL4298120--biolink:treats->MONDO:0007035

What working group (or team) did this request originate from?
Exploring Agent / Service Provider

@sierra-moxon @RichardBruskiewich

@sierra-moxon
Copy link
Member

thanks @colleenXu.

@sierra-moxon
Copy link
Member

@colleenXu - #1364 for your review.

@colleenXu
Copy link
Contributor Author

Looks like the PR will help.

I'm unsure if there's a way to test whether PRs / latest versions of biolink-model help with reasoner-validator errors. Based on the docs for reasoner-validator, it looks like it depends on biolink-model toolkit. And it's unclear to me if biolink-model toolkit can handle PRs / latest versions of biolink-model (above 3.5.0?)....

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

No branches or pull requests

3 participants