PGxCorpus, a manually annotated corpus for pharmacogenomics
Open Access
- 2 January 2020
- journal article
- research article
- Published by Springer Science and Business Media LLC in Scientific Data
- Vol. 7 (1), 1-13
- https://doi.org/10.1038/s41597-019-0342-9
Abstract
Pharmacogenomics (PGx) studies how individual gene variations impact drug response phenotypes, which makes PGx-related knowledge a key component towards precision medicine. A significant part of the state-of-the-art knowledge in PGx is accumulated in scientific publications, where it is hardly reusable by humans or software. Natural language processing techniques have been developed to guide experts who curate this amount of knowledge. But existing works are limited by the absence of a high quality annotated corpus focusing on PGx domain. In particular, this absence restricts the use of supervised machine learning. This article introduces PGxCorpus, a manually annotated corpus, designed to fill this gap and to enable the automatic extraction of PGx relationships from text. It comprises 945 sentences from 911 PubMed abstracts, annotated with PGx entities of interest (mainly gene variations, genes, drugs and phenotypes), and relationships between those. In this article, we present the corpus itself, its construction and a baseline experiment that illustrates how it may be leveraged to synthesize and summarize PGx knowledge.Funding Information
- Agence Nationale de la Recherche (ANR-15-CE23-0028, ANR-15-CE23-0028, ANR-15-CE23-0028, ANR-15-CE23-0028, ANR-15-CE23-0028, ANR-15-CE23-0028)
- Université de Lorraine (15-IDEX-0004)
- Snowball Inria Associate Team
This publication has 41 references indexed in Scilit:
- DNorm: disease name normalization with pairwise learning to rankBioinformatics, 2013
- PubTator: a web-based text mining tool for assisting biocurationNucleic Acids Research, 2013
- A knowledge-driven conditional approach to extract pharmacogenomics specific drug–gene relationships from free textJournal of Biomedical Informatics, 2012
- Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011BMC Bioinformatics, 2012
- Collaborative biocuration--text-mining development task for document prioritization for curationDatabase: The Journal of Biological Databases and Curation, 2012
- GeneTUKit: a software for document-level gene normalizationBioinformatics, 2011
- PubMed and beyond: a survey of web tools for searching biomedical literatureDatabase: The Journal of Biological Databases and Curation, 2011
- Using text to build semantic networks for pharmacogenomicsJournal of Biomedical Informatics, 2010
- Corpus annotation for mining biomedical events from literatureBMC Bioinformatics, 2008
- A Coefficient of Agreement for Nominal ScalesEducational and Psychological Measurement, 1960