remove dependency on ontobee SPARQL endpoint

geneontology / go-fastapi

https://api.geneontology.org/

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Closed sierra-moxon closed 1 year ago

sierra-moxon commented 1 year ago

replace expand_uri method with linkml_runtime.utils.namespaces equivalent (which has access to merged context and go context from prefixmaps)
replace run_sparql method from ontobio with oaklib.Sparqlmplementation and SparqlQuery builder.

this will also help with porting GO-CAM API SPARQL query architecture to go-fastapi and unify handling of prefix mappings

sierra-moxon commented 1 year ago

noting this issue in oaklib: https://github.com/INCATools/ontology-access-kit/issues/318 (thinking of pulling out SparqlQuery builder into its own repository).