NCBO Annotator

NCBO Annotator

NCBO Annotator is a Web service that annotates text provided by the user (e.g. journal abstracts) with relevant ontology concepts. We provide this Web service as a direct service for our users, as part of the BioPortal software services. NCBO also uses this Web service to annotate resources in the NCBO Resource Index.

Go to NCBO Annotator (the direct service for users).

Currently, the annotation workflow is based on a highly efficient syntactic concept recognition (using concept names and synonyms) engine developed in collaboration with National Center for Integrative Biomedical Informatics and on a set of semantic expansion algorithms that leverage the semantics in ontologies (e.g., is_a relations and mappings). Our service methodology leverages ontologies to create annotations of raw text and returns them using semantic web standards.

Reference Paper - Clement Jonquet, Nigam H. Shah, Mark A. Musen, The Open Biomedical Annotator, AMIA Summit on Translational Bioinformatics, p. 56-60, March 2009, San Francisco, CA, USA.

NCBO Annotator Flyer - See an overview of the Annotator (pdf)

NCBO Annotator Poster

For more information see BioPortal and the NCBO wiki.

Annotator Workflow

The Annotator web service workflow. First, direct annotations are created from raw text according to a dictionary that uses terms from a set of ontologies. Second, different components expand the first set of annotations using ontology semantics.