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

Minerva returns labels with namespaces prefixed in some cases (e.g. GO:molecular_function) #195

Closed
kltm opened this issue Jun 26, 2018 · 7 comments

Comments

@kltm
Copy link
Member

kltm commented Jun 26, 2018

After the last minerva change (#194), it seems that Minerva returns labels with namespaces prefixed in some cases (e.g. GO:molecular_function). For example, see http://noctua.berkeleybop.org/editor/graph/gomodel:5ae3b0f600001743

The expectation is that labels should never be prefixed.

This does not seems to affect ids and labels on writeback. That said, it may confuse users and cause confusion if somebody tries to mimic it for input.

@kltm kltm added the bug label Jun 26, 2018
@kltm
Copy link
Member Author

kltm commented Jun 26, 2018

tagging @cmungall and @balhoff

@cmungall
Copy link
Member

The most obvious explanation is that the json-ld context mapping somehow injects this, but I don't see any evidence of this in the code. But the URI<->ID mapping is the most obvious place to check.

(I believe we still go through owltools for URI<->ID but this can now be entirely mediated through the json-ld context mechanism)

@cmungall
Copy link
Member

FWIW, doesn't seem to show up on inference explanations:

http://noctua.berkeleybop.org/workbench/inferredrelations/?model_id=gomodel:5525a0fc00000075&barista_token=

@balhoff
Copy link
Member

balhoff commented Jun 26, 2018

In the current ECO, the label for GO molecular_function is "GO:molecular_function": http://www.ontobee.org/ontology/ECO?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGO_0003674

@cmungall
Copy link
Member

Also reported here: evidenceontology/evidenceontology#168

@vanaukenk
Copy link

@kltm @balhoff
Is this issue fixed?
I looked at the referenced GO-CAM model but can't tell. There are other issues with that model, but I think it is just a test model so if we needed to fix those issues to check on the eco issue, I could do that.

@balhoff
Copy link
Member

balhoff commented Jan 26, 2019

This should be fixed now. We are not getting ECO's OBI import module anymore at all.

@balhoff balhoff closed this as completed Jan 26, 2019
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

4 participants