dc.contributor.author | Pilehvar, MT | en_US |
dc.contributor.author | Bernard, A | en_US |
dc.contributor.author | Smedley, D | en_US |
dc.contributor.author | Collier, N | en_US |
dc.date.accessioned | 2023-03-07T10:53:07Z | |
dc.date.issued | 2022-01-27 | en_US |
dc.identifier.uri | https://qmro.qmul.ac.uk/xmlui/handle/123456789/84822 | |
dc.description.abstract | MOTIVATION: Significant effort has been spent by curators to create coding systems for phenotypes such as the Human Phenotype Ontology, as well as disease-phenotype annotations. We aim to support the discovery of literature-based phenotypes and integrate them into the knowledge discovery process. RESULTS: PheneBank is a Web-portal for retrieving human phenotype-disease associations that have been text-mined from the whole of Medline. Our approach exploits state-of-the-art machine learning for concept identification by utilizing an expert annotated rare disease corpus from the PMC Text Mining subset. Evaluation of the system for entities is conducted on a gold-standard corpus of rare disease sentences and for associations against the Monarch initiative data. AVAILABILITY AND IMPLEMENTATION: The PheneBank Web-portal freely available at http://www.phenebank.org. Annotated Medline data is available from Zenodo at DOI: 10.5281/zenodo.1408800. Semantic annotation software is freely available for non-commercial use at GitHub: https://github.com/pilehvar/phenebank. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. | en_US |
dc.format.extent | 1179 - 1180 | en_US |
dc.language | eng | en_US |
dc.relation.ispartof | Bioinformatics | en_US |
dc.rights | Attribution 3.0 United States | * |
dc.rights.uri | http://creativecommons.org/licenses/by/3.0/us/ | * |
dc.subject | Humans | en_US |
dc.subject | Rare Diseases | en_US |
dc.subject | Software | en_US |
dc.subject | Algorithms | en_US |
dc.subject | Data Mining | en_US |
dc.subject | Phenotype | en_US |
dc.title | PheneBank: a literature-based database of phenotypes. | en_US |
dc.type | Article | |
dc.identifier.doi | 10.1093/bioinformatics/btab740 | en_US |
pubs.author-url | https://www.ncbi.nlm.nih.gov/pubmed/34788791 | en_US |
pubs.issue | 4 | en_US |
pubs.notes | Not known | en_US |
pubs.publication-status | Published | en_US |
pubs.volume | 38 | en_US |
qmul.funder | PheneBank: automatic extraction and validation of a database of human phenotype-disease associations in the scientific literature::Medical Research Council | en_US |