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monarch-initiative / mapping-walker

walks mapping graphs running boomer
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Add `BioportalEndpoint` implementation backed by latest oaklib version #7

Closed pkalita-lbl closed 2 years ago

pkalita-lbl commented 2 years ago

These changes add a BioportalEndpoint class which delegates most of the work to oaklib. It also adds an additional command line option to the main pipeline CLI to allow switching between endpoint classes. There are also some shenanigans in the pipeline to account for the fact that the mapping data produced by oaklib from the BioPortal API contains IRIs and not CURIEs.

cmungall commented 2 years ago

Thanks! Yes we need to sort out the identifier shenanigans!