Doc2Hpo: a web application for efficient and accurate HPO concept curation

We present Doc2Hpo, an interactive web application that enables interactive and efficient phenotype concept curation from clinical text with automated concept normalization using the Human Phenotype Ontology (HPO). Users can edit the HPO concepts automatically extracted by Doc2Hpo in real time, and...

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Detalles Bibliográficos
Autores principales: Liu, Cong, Peres Kury, Fabricio Sampaio, Li, Ziran, Ta, Casey, Wang, Kai, Weng, Chunhua
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
Materias:
Web Server Issue
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602487/
https://www.ncbi.nlm.nih.gov/pubmed/31106327
http://dx.doi.org/10.1093/nar/gkz386
Descripción
Sumario:We present Doc2Hpo, an interactive web application that enables interactive and efficient phenotype concept curation from clinical text with automated concept normalization using the Human Phenotype Ontology (HPO). Users can edit the HPO concepts automatically extracted by Doc2Hpo in real time, and export the extracted HPO concepts into gene prioritization tools. Our evaluation showed that Doc2Hpo significantly reduced manual effort while achieving high accuracy in HPO concept curation. Doc2Hpo is freely available at https://impact2.dbmi.columbia.edu/doc2hpo/. The source code is available at https://github.com/stormliucong/doc2hpo for local installation for protected health data.

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