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
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author Liu, Cong
Peres Kury, Fabricio Sampaio
Li, Ziran
Ta, Casey
Wang, Kai
Weng, Chunhua
author_facet Liu, Cong
Peres Kury, Fabricio Sampaio
Li, Ziran
Ta, Casey
Wang, Kai
Weng, Chunhua
author_sort Liu, Cong
collection PubMed
description 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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spelling pubmed-66024872019-07-05 Doc2Hpo: a web application for efficient and accurate HPO concept curation Liu, Cong Peres Kury, Fabricio Sampaio Li, Ziran Ta, Casey Wang, Kai Weng, Chunhua Nucleic Acids Res Web Server Issue 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. Oxford University Press 2019-07-02 2019-05-20 /pmc/articles/PMC6602487/ /pubmed/31106327 http://dx.doi.org/10.1093/nar/gkz386 Text en © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Web Server Issue
Liu, Cong
Peres Kury, Fabricio Sampaio
Li, Ziran
Ta, Casey
Wang, Kai
Weng, Chunhua
Doc2Hpo: a web application for efficient and accurate HPO concept curation
title Doc2Hpo: a web application for efficient and accurate HPO concept curation
title_full Doc2Hpo: a web application for efficient and accurate HPO concept curation
title_fullStr Doc2Hpo: a web application for efficient and accurate HPO concept curation
title_full_unstemmed Doc2Hpo: a web application for efficient and accurate HPO concept curation
title_short Doc2Hpo: a web application for efficient and accurate HPO concept curation
title_sort doc2hpo: a web application for efficient and accurate hpo concept curation
topic Web Server Issue
url 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
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