Aim 2.2.c. Develop and apply methods for mapping BioPortal ontology elements to Biolink model.

ncbo / BioPortal-to-KGX

Assemble a BioPortal Knowledge Graph

BSD 3-Clause "New" or "Revised" License

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Aim 2.2.c. Develop and apply methods for mapping BioPortal ontology elements to Biolink model. #39

Closed caufieldjh closed 2 years ago

caufieldjh commented 2 years ago

Tasks for this Aim are as follows.

During the transformation step, assign Biolink categories to nodes and edges based on:

[x] UMLS semantic types
[x] Known namespaces beyond those prefixes recognized by kgx already
[x] Ontology metadata, where possible

Also correct errors violating kgx format and Biolink:

[x] Replace URL node IDs with CURIEs specific to each ontology

Developments in kgx, OAK and Boomer may assist.

caufieldjh commented 2 years ago

RXNORM, NCBITAXON, and potentially other UMLS ontologies have STY categories stored in edges (RDF-style) rather than as node categories, where we'd prefer to store the Biolink category membership. Retrieve the node ID and STY from a hasSTY edge, then map it to the corresponding node in the nodes list.

caufieldjh commented 2 years ago

See also #44

caufieldjh commented 2 years ago

Issue #45 is a subtask here - if we know node prefixes, we can use them to:

retrieve class IDs from the API, and/or
generate class IDs based on what is after the prefix in each IRI of a given ontology

Then, the CURIE may be assembled as {ontologyID}:{classID}

caufieldjh commented 2 years ago

This can always be improved on, but is now effectively complete.