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dc.contributor.authorPilehvar, Mohammad Taher
dc.contributor.authorBernard, Adam
dc.contributor.authorSmedley, Damian
dc.contributor.authorCollier, Nigel
dc.date.accessioned2021-10-25T23:31:14Z
dc.date.available2021-10-25T23:31:14Z
dc.date.issued2021-11-12
dc.identifier.issn1367-4803
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/329879
dc.description.abstractMOTIVATION: Significant effort has been spent by curators to create coding systems for phenotypes such as the Human Phenotype Ontology (HPO), 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 utilising 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: 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 is available at Bioinformatics online.
dc.description.sponsorshipMedical Research Council (grant MR/M025160/1).
dc.languageeng
dc.publisherOxford University Press (OUP)
dc.rightsAll rights reserved
dc.rights.urihttp://www.rioxx.net/licenses/all-rights-reserved
dc.titlePheneBank: a literature-based database of phenotypes.
dc.typeArticle
prism.publicationDate2021
prism.publicationNameBioinformatics
dc.identifier.doi10.17863/CAM.77324
dcterms.dateAccepted2021-11-02
rioxxterms.versionofrecord10.1093/bioinformatics/btab740
rioxxterms.versionAM
rioxxterms.licenseref.urihttp://www.rioxx.net/licenses/all-rights-reserved
rioxxterms.licenseref.startdate2021-11-12
dc.contributor.orcidCollier, Nigel [0000-0002-7230-4164]
dc.identifier.eissn1367-4811
rioxxterms.typeJournal Article/Review
pubs.funder-project-idEngineering and Physical Sciences Research Council (EP/M005089/1)
pubs.funder-project-idMedical Research Council (MR/M025160/1)
cam.issuedOnline2021-11-12
cam.orpheus.success2021-10-25 - Embargo set during processing via Fast-track
rioxxterms.freetoread.startdate2022-10-27


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