Skip to Main content Skip to Navigation
Conference papers

Scoring semantic annotations returned by the NCBO Annotator

Abstract : 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 service, offered within the BioPortal platform and giving access to more than 350+ ontologies or terminologies. This paper presents a new scoring method for the NCBO Annotator allowing to rank the annotation results and enabling to use such scores for better indexing of the annotated data. By using a natural language processing-based term extraction measure, C-Value, we are able to enhance the original scoring algorithm which uses basic frequencies of the matches and in addition to positively discriminate multi-words term annotations. We show results obtained by comparing three different methods with a reference corpus of PubMed-MeSH manual annotations.
Document type :
Conference papers
Complete list of metadata

Cited literature [26 references]  Display  Hide  Download
Contributor : Clement Jonquet Connect in order to contact the contributor
Submitted on : Monday, January 5, 2015 - 2:39:10 PM
Last modification on : Tuesday, September 6, 2022 - 4:57:50 PM
Long-term archiving on: : Monday, April 6, 2015 - 11:25:11 AM


Publisher files allowed on an open archive


  • HAL Id : lirmm-01099860, version 1



Soumia Melzi, Clement Jonquet. Scoring semantic annotations returned by the NCBO Annotator. SWAT4LS: Semantic Web Applications and Tools for Life Sciences, Dec 2014, Berlin, Germany. ⟨lirmm-01099860⟩



Record views


Files downloads