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SpacyProcessor's hard dependency on Forte's medical ontologies #95

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Piyush13y opened this issue Mar 2, 2022 · 0 comments · Fixed by #96
Closed

SpacyProcessor's hard dependency on Forte's medical ontologies #95

Piyush13y opened this issue Mar 2, 2022 · 0 comments · Fixed by #96

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@Piyush13y
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Piyush13y commented Mar 2, 2022

Describe the bug
With reference to the discussion thread in #89, we want to ensure multiple namespaces aren't created for the same use case.
Currently, Forte-Medicine has its own medical oriented ontology (ftx.medicine.clinical). Forte-wrappers, too works with a couple of ontology classes like MedicalEntityMention and UMLSConceptLink, but uses these from Forte (ftx.onto.clinical). These are used solely in the SpacyProcessor wrapper to work with umls_link flag. Hence, we need to modify SpacyProcessor in a way that it can use dynamically provided ontologies instead of having a hard dependency on Forte for medical related ontologies. This would ensure consistent package namespacing for all medical use cases going forward, especially as Forte-Medical grows.

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