Building a biomedical ontology recommender web service.

Journal of Biomedical Semantics
Clement JonquetNigam H Shah

Abstract

Researchers in biomedical informatics use ontologies and terminologies to annotate their data in order to facilitate data integration and translational discoveries. As the use of ontologies for annotation of biomedical datasets has risen, a common challenge is to identify ontologies that are best suited to annotating specific datasets. The number and variety of biomedical ontologies is large, and it is cumbersome for a researcher to figure out which ontology to use. We present the Biomedical Ontology Recommender web service. The system uses textual metadata or a set of keywords describing a domain of interest and suggests appropriate ontologies for annotating or representing the data. The service makes a decision based on three criteria. The first one is coverage, or the ontologies that provide most terms covering the input text. The second is connectivity, or the ontologies that are most often mapped to by other ontologies. The final criterion is size, or the number of concepts in the ontologies. The service scores the ontologies as a function of scores of the annotations created using the National Center for Biomedical Ontology (NCBO) Annotator web service. We used all the ontologies from the UMLS Metathesaurus and the NCBO B...Continue Reading

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Citations

Dec 26, 2012·Bioinformatics·Eamonn MaguirePhilippe Rocca-Serra
Nov 15, 2011·Nucleic Acids Research·Lynn Marie SchrimlWarren Alden Kibbe
Jul 16, 2010·Journal of Biomedical Semantics·Larisa N SoldatovaNigam H Shah
Dec 20, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Liang ChengYadong Wang
Feb 28, 2014·Computer Methods and Programs in Biomedicine·Marcos Martínez-RomeroAlejandro Pazos
May 15, 2015·Journal of Biomedical Semantics·Kiyoko F Aoki-KinoshitaSoichi Ogishima
Apr 9, 2013·Computer Methods and Programs in Biomedicine·H López-FernándezF Fdez-Riverola
Mar 31, 2015·Journal of Biomedical Semantics·Janna HastingsEgon Willighagen
Aug 23, 2016·PloS One·Feichen Shen, Yugyung Lee
Nov 15, 2011·Journal of the American Medical Informatics Association : JAMIA·Mark A MusenUNKNOWN NCBO team
Nov 15, 2011·Journal of the American Medical Informatics Association : JAMIA·Lucila Ohno-MachadoUNKNOWN iDASH team
Jun 16, 2011·Journal of the American Medical Informatics Association : JAMIA·Russ B Altman, Katharine S Miller
Feb 13, 2016·PLoS Computational Biology·James MaloneCath Brooksbank
Jul 27, 2012·Briefings in Bioinformatics·Udo HahnNigam H Shah
Jun 9, 2017·Journal of Biomedical Semantics·Marcos Martínez-RomeroMark A Musen

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Software Mentioned

UMLS
ArrayExpress
BioPortal Search
NCBO Annotator Web Service
Biomedical Ontology Recommender
BioPortal
WebCORE
Magpie
OntoKhoj
NCBO BioPortal

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