DermO; an ontology for the description of dermatologic disease

Handle URI:
http://hdl.handle.net/10754/614411
Title:
DermO; an ontology for the description of dermatologic disease
Authors:
Fisher, Hannah M.; Hoehndorf, Robert ( 0000-0001-8149-5890 ) ; Bazelato, Bruno S.; Dadras, Soheil S.; King, Lloyd E.; Gkoutos, Georgios V.; Sundberg, John P.; Schofield, Paul N.
Abstract:
Background There have been repeated initiatives to produce standard nosologies and terminologies for cutaneous disease, some dedicated to the domain and some part of bigger terminologies such as ICD-10. Recently, formally structured terminologies, ontologies, have been widely developed in many areas of biomedical research. Primarily, these address the aim of providing comprehensive working terminologies for domains of knowledge, but because of the knowledge contained in the relationships between terms they can also be used computationally for many purposes. Results We have developed an ontology of cutaneous disease, constructed manually by domain experts. With more than 3000 terms, DermO represents the most comprehensive formal dermatological disease terminology available. The disease entities are categorized in 20 upper level terms, which use a variety of features such as anatomical location, heritability, affected cell or tissue type, or etiology, as the features for classification, in line with professional practice and nosology in dermatology. Available in OBO flatfile and OWL 2 formats, it is integrated semantically with other ontologies and terminologies describing diseases and phenotypes. We demonstrate the application of DermO to text mining the biomedical literature and in the creation of a network describing the phenotypic relationships between cutaneous diseases. Conclusions DermO is an ontology with broad coverage of the domain of dermatologic disease and we demonstrate here its utility for text mining and investigation of phenotypic relationships between dermatologic disorders. We envision that in the future it may be applied to the creation and mining of electronic health records, clinical training and basic research, as it supports automated inference and reasoning, and for the broader integration of skin disease information with that from other domains.
KAUST Department:
Computational Bioscience Research Center (CBRC)
Citation:
DermO; an ontology for the description of dermatologic disease 2016, 7 (1) Journal of Biomedical Semantics
Publisher:
Springer Nature
Journal:
Journal of Biomedical Semantics
Issue Date:
13-Jun-2016
DOI:
10.1186/s13326-016-0085-x
Type:
Article
ISSN:
2041-1480
Sponsors:
The authors acknowledge National Institutes of Health Grants R21-AR063781 to JPS and SSD, and R01HG004838-03 supported PNS and GVG. We thank Prof. Jonathan Bard for helpful comments on the manuscript and Prof. Amanda Oakley, for the support of DermNet NZ.
Additional Links:
http://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0085-x
Appears in Collections:
Articles

Full metadata record

DC FieldValue Language
dc.contributor.authorFisher, Hannah M.en
dc.contributor.authorHoehndorf, Roberten
dc.contributor.authorBazelato, Bruno S.en
dc.contributor.authorDadras, Soheil S.en
dc.contributor.authorKing, Lloyd E.en
dc.contributor.authorGkoutos, Georgios V.en
dc.contributor.authorSundberg, John P.en
dc.contributor.authorSchofield, Paul N.en
dc.date.accessioned2016-06-23T11:09:39Z-
dc.date.available2016-06-23T11:09:39Z-
dc.date.issued2016-06-13-
dc.identifier.citationDermO; an ontology for the description of dermatologic disease 2016, 7 (1) Journal of Biomedical Semanticsen
dc.identifier.issn2041-1480-
dc.identifier.doi10.1186/s13326-016-0085-x-
dc.identifier.urihttp://hdl.handle.net/10754/614411-
dc.description.abstractBackground There have been repeated initiatives to produce standard nosologies and terminologies for cutaneous disease, some dedicated to the domain and some part of bigger terminologies such as ICD-10. Recently, formally structured terminologies, ontologies, have been widely developed in many areas of biomedical research. Primarily, these address the aim of providing comprehensive working terminologies for domains of knowledge, but because of the knowledge contained in the relationships between terms they can also be used computationally for many purposes. Results We have developed an ontology of cutaneous disease, constructed manually by domain experts. With more than 3000 terms, DermO represents the most comprehensive formal dermatological disease terminology available. The disease entities are categorized in 20 upper level terms, which use a variety of features such as anatomical location, heritability, affected cell or tissue type, or etiology, as the features for classification, in line with professional practice and nosology in dermatology. Available in OBO flatfile and OWL 2 formats, it is integrated semantically with other ontologies and terminologies describing diseases and phenotypes. We demonstrate the application of DermO to text mining the biomedical literature and in the creation of a network describing the phenotypic relationships between cutaneous diseases. Conclusions DermO is an ontology with broad coverage of the domain of dermatologic disease and we demonstrate here its utility for text mining and investigation of phenotypic relationships between dermatologic disorders. We envision that in the future it may be applied to the creation and mining of electronic health records, clinical training and basic research, as it supports automated inference and reasoning, and for the broader integration of skin disease information with that from other domains.en
dc.description.sponsorshipThe authors acknowledge National Institutes of Health Grants R21-AR063781 to JPS and SSD, and R01HG004838-03 supported PNS and GVG. We thank Prof. Jonathan Bard for helpful comments on the manuscript and Prof. Amanda Oakley, for the support of DermNet NZ.en
dc.language.isoenen
dc.publisherSpringer Natureen
dc.relation.urlhttp://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0085-xen
dc.rightsThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.en
dc.subjectDermatologyen
dc.subjectOntologyen
dc.subjectDiseaseen
dc.subjectDermatopathologyen
dc.titleDermO; an ontology for the description of dermatologic diseaseen
dc.typeArticleen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.identifier.journalJournal of Biomedical Semanticsen
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionDept. of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UKen
dc.contributor.institutionDept. of Computer Science, Llandinam Building, Aberystwyth University, Aberystwyth, Ceredigion SY23 3DB, UKen
dc.contributor.institutionDept. Dermatology and Pathology, University of Connecticut Health Center, 263, Farmington Avenue, Farmington, CT 06030, USAen
dc.contributor.institutionDept. of Medicine, Div. Dermatology, Vanderbilt University, Nashville, Tennessee, USAen
dc.contributor.institutionCollege of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, Centre for Computational Biology, University of Birmingham, Birmingham B15 2TT, UKen
dc.contributor.institutionInstitute of Translational Medicine, University Hospitals Birmingham NHS Foundation Trust, Birmingham B15 2TT, UKen
dc.contributor.institutionThe Jackson Laboratory, 600, Main Street, Bar Harbor Maine ME 04609-1500, USAen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorHoehndorf, Roberten
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