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

Automate mapping of infores in primary_knowledge_source #430

Open
caufieldjh opened this issue Mar 10, 2023 · 1 comment
Open

Automate mapping of infores in primary_knowledge_source #430

caufieldjh opened this issue Mar 10, 2023 · 1 comment
Labels
enhancement New feature or request

Comments

@caufieldjh
Copy link
Collaborator

In discussion with @cmungall, it sounds like there is a demand for consistent use of primary and aggregator knowledge source in KGX output, particularly for ingest into larger KGs. Can we make this fully automated within KGX? The goal would be to populate primary_knowledge_source for edges based on a basic heuristic of inferring the source from the namespace, though this makes assumptions about whether edges are from imports or base files, etc. There are cases like Upheno and Uberon in which it's immediately clear what the primary source is (e.g., it's not HP, it's Upheno).

I see that some work towards this happened in #314. I have a hacky approach in kg-phenio too.

@caufieldjh
Copy link
Collaborator Author

Working on this here: #434
I think most of this can go in utils/infores.py since that's already comprehensive re: provided_by and knowledge_source,
but ideally this should be as automatic as possible, so if there's an edge between two CHEBI nodes and we haven't been provided with other provenance then the edge gets infores:chebi for primary_knowledge_source.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request
Projects
None yet
Development

Successfully merging a pull request may close this issue.

1 participant