-
Notifications
You must be signed in to change notification settings - Fork 67
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
Using value set expansion with non-OBO annotator leads to 404 error #347
Comments
Partially related, but not sure what's going on with this line:
|
Can solve here by having OntoGPT create its own ValueSetExpander with its own config (not just the default oaklib one) |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Originally seen in #346.
Using a Bioportal ontology (like bioportal:SNOMEDCT) as an annotator works fine on its own.
If used in a value set expansion, e.g., with a
reachable_from
, it tries to download the corresponding semsql db.This doesn't work if the semsql db does not exist.
It should throw a warning instead of trying to access a nonexistent resource.
This is the offending line:
ontogpt/src/ontogpt/engines/knowledge_engine.py
Line 396 in bba9692
Example as per #346, from debugger:
The issue here arises because oaklib's
ValueSetExpander
requires a specific config to work with Bioportal. Otherwise it assumes it's in OBO space.See https://github.com/INCATools/ontology-access-kit/blob/a51929160549b160831474472f93ebc9a5a22c01/src/oaklib/utilities/subsets/value_set_expander.py#L263-L295
The text was updated successfully, but these errors were encountered: