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

Journal: Nucleic acids research
PMID: 31106327

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.

Authors

  • Cong Liu
    Department of Bioengineering, University of Illinois at Chicago, 851 S Morgan St, Chicago, IL, 60607, USA.
  • Fabricio Sampaio Peres Kury
    Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA.
  • Ziran Li
    Department of Biomedical Informatics, Columbia University, New York, New York, USA.
  • Casey Ta
    Department of Biomedical Informatics, Columbia University, New York, New York, USA.
  • Kai Wang
    Department of Rheumatology, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, Jiangsu, China.
  • Chunhua Weng
    Department of Biomedical Informatics, Columbia University.

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