A UIMA wrapper for the NCBO annotator

A UIMA wrapper for the NCBO annotator

SUMMARY The Unstructured Information Management Architecture (UIMA) framework and web services are emerging as useful tools for integrating biomedical text mining tools. This note describes our work, which wraps the National Center for Biomedical Ontology (NCBO) Annotator-an ontology-based annotation service-to make it available as a component in UIMA workflows. AVAILABILITY This wrapper is f...

NCBO Annotator: Semantic Annotation of Biomedical Data

The National Center for Biomedical Ontology Annotator is an ontology-based web service for annotation of textual biomedical data with biomedical ontology concepts. The biomedical community can use the Annotator service to tag datasets automatically with concepts from more than 200 ontologies coming from the two most important set of biomedical ontology & terminology repositories: the UMLS Metat...

The NCBO Annotator: Ontology-Based Annotation as a Web Service

Scoring Semantic Annotations Returned by The NCBO Annotator

Semantic annotation using biomedical ontologies is required to enable data integration, interoperability, indexing and mining of biomedical data. When used to support semantic indexing the scoring and ranking of annotations become as important as provenance and metadata on the annotations themselves. In the biomedical domain, one broadly used service for annotations is the NCBO Annotator Web se...

Representing NCBO Annotator Results in Standard RDF with the Annotation Ontology

Semantic annotation is part of the Semantic Web vision. The Annotation Ontology is a model that have been proposed to represent any annotations in standard RDF. The NCBO Annotator Web service is a broadly used service for annotations in the biomedical domain, offered within the BioPortal platform and giving access to more than 350+ ontologies. This paper presents a new output format to represen...