Clinical phenotype-based gene prioritization: an initial study using semantic similarity and the human phenotype ontology

Over the course of the last few years there has been a significant amount of research performed on ontology-based formalization of phenotype descriptions. The intrinsic value and knowledge captured within such descriptions can only be expressed by taking advantage of their inner structure that implicitly combines qualities and anatomical entities. We present a meta-model (the Phenotype Fragment Ontology) and a processing pipeline that enable together the automatic decomposition and conceptualization of phenotype descriptions for the human skeletal phenome. We use this approach to showcase the usefulness of the generic concept of phenotype decomposition by performing an experimental study on all skeletal phenotype concepts defined in the Human Phenotype Ontology.

Download Full-text

Annotating Diseases Using Human Phenotype Ontology Improves Prediction of Disease-Associated Long Non-coding RNAs

Journal of Molecular Biology ◽

10.1016/j.jmb.2018.05.006 ◽

2018 ◽

Vol 430 (15) ◽

pp. 2219-2230 ◽

Cited By ~ 8

Author(s):

Duc-Hau Le ◽

Lan T.M. Dao

Keyword(s):

Human Phenotype Ontology ◽

Phenotype Ontology ◽

Human Phenotype ◽

Non Coding Rnas

Download Full-text

Integrating exome and whole genome analysis with the Human Phenotype Ontology for discovery of new genes in rare eye diseases

Acta Ophthalmologica ◽

10.1111/j.1755-3768.2019.5001 ◽

2019 ◽

Vol 97 (S263) ◽

Author(s):

Nikolas Pontikos

Keyword(s):

Genome Analysis ◽

Eye Diseases ◽

Human Phenotype Ontology ◽

Whole Genome ◽

Phenotype Ontology ◽

Whole Genome Analysis ◽

Human Phenotype ◽

New Genes

Download Full-text

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

Nucleic Acids Research ◽

10.1093/nar/gkz386 ◽

2019 ◽

Vol 47 (W1) ◽

pp. W566-W570 ◽

Cited By ~ 5

Author(s):

Cong Liu ◽

Fabricio Sampaio Peres Kury ◽

Ziran Li ◽

Casey Ta ◽

Kai Wang ◽

...

Keyword(s):

Real Time ◽

Web Application ◽

Source Code ◽

High Accuracy ◽

Health Data ◽

Gene Prioritization ◽

Phenotype Ontology ◽

Human Phenotype ◽

Clinical Text ◽

Local Installation

AbstractWe 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.

Download Full-text