Evaluating a dictionary of human phenotype terms focusing on rare diseases
Simon Kocbek, Toyofumi Fujiwara, Jin-Dong Kim, Toshihisa Takagi, Tudor Groza
Abstract
Annotating medical text such as clinical notes with human phenotype descriptors is an important task that can, for example, assist in building patient profiles. To automatically annotate text one usually needs a dictionary of predefined terms. However, do to the variety of human expressiveness, current state-of-the art phenotype concept recognizers and automatic annotators struggle with specific domain issues and challenges. In this paper we present results of an-notating gold standard corpus with a dictionary containing lexical variants for the Human Phenotype Ontology terms. The main purpose of the dictionary is to improve the recall of phenotype concept recognition systems. We compare the method with four other approaches and present results.- Anthology ID:
- W16-4712
- Volume:
- Proceedings of the 5th International Workshop on Computational Terminology (Computerm2016)
- Month:
- December
- Year:
- 2016
- Address:
- Osaka, Japan
- Venue:
- CompuTerm
- SIG:
- Publisher:
- The COLING 2016 Organizing Committee
- Note:
- Pages:
- 104–109
- Language:
- URL:
- https://aclanthology.org/W16-4712
- DOI:
- Cite (ACL):
- Simon Kocbek, Toyofumi Fujiwara, Jin-Dong Kim, Toshihisa Takagi, and Tudor Groza. 2016. Evaluating a dictionary of human phenotype terms focusing on rare diseases. In Proceedings of the 5th International Workshop on Computational Terminology (Computerm2016), pages 104–109, Osaka, Japan. The COLING 2016 Organizing Committee.
- Cite (Informal):
- Evaluating a dictionary of human phenotype terms focusing on rare diseases (Kocbek et al., CompuTerm 2016)
- PDF:
- https://preview.aclanthology.org/ingestion-script-update/W16-4712.pdf