NCBO Annotator +

The NCBO Annotator+ is a proxy calling the NCBO Annotator Web service on the NCBO BioPortal.

Tchechmedjiev, A., Abdaoui, A., Emonet, V., Melzi, S., Jonnagaddala, J., & Jonquet, C. (2018). Enhanced functionalities for annotating and indexing clinical text with the NCBO Annotator+. Bioinformatics, 34(11), 1962-1965.

If using the API, please provide a valid NCBO BioPortal apikey and hit the service at http://services.bioportal.lirmm.fr/ncbo_annotatorplus
Text submitted to the NCBO Annotator+ must be in English.

insert sample text

Show advanced options >>

Select ontologies Start typing to select ontologies or leave blank to use all

Select UMLS semantic types Start typing to select UMLS semantic types or leave blank to use all

Select UMLS semantic groups Start typing to select UMLS semantic groups or leave blank to use all

Include ancestors up to level:

Include score: Score annotations following the previous 2009 NCBO measure (old) or the C-Value measure (cvalue). If hierarchy expansion is used, then prefer cvalueh.

Filter by score threshold: Specify the minimum score value for annotations

Filter confidence threshold: Specify the minimum position in the scoring distribution (between 1 and 100)

FastContext Enable FastContext to detect : if a concept has been negated (affirmed, negated), who experienced the found concept (patient, other), when the annotated concept occurred (recent, historical, hypothetical), and/or if the annotated concept is uncertain (certain, uncertain).

Annotations

Class filter	Ontology filter	Type filter	UMLS Sem Type	Context	Matched Class filter	Matched Ontology filter	Score	Negation	Experiencer	Temporality	Certainty

Format results as:

Reproduce these results using the

Additional parameters explained at Annotator API documentation