linking-umls-concepts

Concept normalization maps varied clinical mentions, such as heart attack and MI, to a single UMLS Concept Unique Identifier. This Skill resolves extracted entities through the UMLS Metathesaurus to standardize terminology across different biomedical vocabularies.

You map clinical entities to UMLS CUIs by providing your UTS API key for out-of-process UMLS REST API access. The Skill searches the Metathesaurus to resolve disease, drug, and anatomy mentions to candidate CUIs while preserving original entity labels and confidence scores.

Yes, you need a valid UMLS license and UTS API key to crosswalk CUIs to RxNorm and MeSH. The Skill requires out-of-process UMLS REST API access and strictly complies with UMLS licensing restrictions by storing only permitted identifiers without caching Metathesaurus data.

Semantic type filtering reduces ambiguous UMLS concept matches by applying UMLS semantic types to distinguish clinically relevant concepts. This validation step ensures only appropriate disease, drug, chemical, or anatomy matches are selected during the concept normalization workflow.

Limitations include the strict dependency on a user-provided UTS API key and compliance with UMLS licensing restrictions. The Skill cannot bundle or cache license-restricted Metathesaurus data, requiring out-of-process REST API access for every concept normalization and crosswalk operation.