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

ABSTRACT: 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.

SUBMITTER: Liu C

PROVIDER: S-EPMC6602487 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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

Liu Cong C Peres Kury Fabricio Sampaio FS Li Ziran Z Ta Casey C Wang Kai K Weng Chunhua C

Nucleic acids research 20190701 W1

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 ...[more]

PMID: 31106327

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