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

Cong Liu; Fabricio Sampaio Peres Kury; Ziran Li; Casey Ta; Kai Wang; Chunhua Weng

doi:10.1093/nar/gkz386

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

Nucleic Acids Res. 2019 Jul 2;47(W1):W566-W570. doi: 10.1093/nar/gkz386.

Authors

Cong Liu¹, Fabricio Sampaio Peres Kury¹, Ziran Li¹, Casey Ta¹, Kai Wang^{2

3}, Chunhua Weng¹

Affiliations

¹ Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA.
² Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
³ Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

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.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Biological Ontologies*
Data Curation*
Genes
Humans
Internet
Phenotype*
Software*
User-Computer Interface

Abstract

Publication types

MeSH terms

Grants and funding