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

Cong Liu | Zendy; Fabrício S. P. Kury | Zendy; Ziran Li | Zendy; Casey Ta | Zendy; Kai Wang | Zendy; Chunhua Weng | Zendy

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

Author(s) -

Cong Liu,

Fabrício S. P. Kury,

Ziran Li,

Casey Ta,

Kai Wang,

Chunhua Weng

Publication year - 2019

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gkz386

Subject(s) - data curation , normalization (sociology) , computer science , prioritization , biology , information retrieval , source code , computational biology , world wide web , programming language , management science , sociology , anthropology , economics

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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