This paper presents ClinIDMap, a tool for mapping identifiers between clinical ontologies and lexical resources. ClinIDMap interlinks identifiers from UMLS, SMOMED-CT, ICD-10 and the corresponding Wikipedia articles for concepts from the UMLS Metathesaurus. Our main goal is to provide semantic interoperability across the clinical concepts from various knowledge bases. As a side effect, the mapping enriches already annotated corpora in multiple languages with new labels. For instance, spans manually annotated with IDs from UMLS can be annotated with Semantic Types and Groups, and its corresponding SNOMED CT and ICD-10 IDs. We also experiment with sequence labelling models for detecting Diagnosis and Procedures concepts and for detecting UMLS Semantic Groups trained on Spanish, English, and bilingual corpora obtained with the new mapping procedure. The ClinIDMap tool is publicly available.