The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data

S. Kohler; S. C. Doelken; C. J. Mungall; S. Bauer; H. V. Firth; I. Bailleul-Forestier; G. C. Black; D. L. Brown; M. Brudno; J. Campbell; D. R. FitzPatrick; J. T. Eppig; A. P. Jackson; K. Freson; M. Girdea; I. Helbig; J. A. Hurst; J. Jahn; L. G. Jackson; A. M. Kelly; D. H. Ledbetter; S. Mansour; C. L. Martin; C. Moss; A. Mumford; W. H. Ouwehand; S. M. Park; E. R. Riggs; R. H. Scott; S. Sisodiya; S. Van Vooren; R. J. Wapner; A. O. Wilkie; C. F. Wright; A. T. Vulto-van Silfhout; N. de Leeuw; B. B. de Vries; N. L. Washingthon; C. L. Smith; M. Westerfield; P. Schofield; B. J. Ruef; G. V. Gkoutos; M. Haendel; D. Smedley; S. E. Lewis; P. N. Robinson

doi:10.1093/nar/gkt1026

The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data

S. Kohler, S. C. Doelken, C. J. Mungall, S. Bauer, H. V. Firth, I. Bailleul-Forestier, G. C. Black, D. L. Brown, M. Brudno, J. Campbell, D. R. FitzPatrick, J. T. Eppig, A. P. Jackson, K. Freson, M. Girdea, I. Helbig, J. A. Hurst, J. Jahn, L. G. Jackson, A. M. KellyD. H. Ledbetter, S. Mansour, C. L. Martin, C. Moss, A. Mumford, W. H. Ouwehand, S. M. Park, E. R. Riggs, R. H. Scott, S. Sisodiya, S. Van Vooren, R. J. Wapner, A. O. Wilkie, C. F. Wright, A. T. Vulto-van Silfhout, N. de Leeuw, B. B. de Vries, N. L. Washingthon, C. L. Smith, M. Westerfield, P. Schofield, B. J. Ruef, G. V. Gkoutos, M. Haendel, D. Smedley, S. E. Lewis, P. N. Robinson

Cancer and Genomic Sciences

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Abstract

The Human Phenotype Ontology (HPO) project, available at http://www.human-phenotype-ontology.org, provides a structured, comprehensive and well-defined set of 10,088 classes (terms) describing human phenotypic abnormalities and 13,326 subclass relations between the HPO classes. In addition we have developed logical definitions for 46% of all HPO classes using terms from ontologies for anatomy, cell types, function, embryology, pathology and other domains. This allows interoperability with several resources, especially those containing phenotype information on model organisms such as mouse and zebrafish. Here we describe the updated HPO database, which provides annotations of 7,278 human hereditary syndromes listed in OMIM, Orphanet and DECIPHER to classes of the HPO. Various meta-attributes such as frequency, references and negations are associated with each annotation. Several large-scale projects worldwide utilize the HPO for describing phenotype information in their datasets. We have therefore generated equivalence mappings to other phenotype vocabularies such as LDDB, Orphanet, MedDRA, UMLS and phenoDB, allowing integration of existing datasets and interoperability with multiple biomedical resources. We have created various ways to access the HPO database content using flat files, a MySQL database, and Web-based tools. All data and documentation on the HPO project can be found online.

Original language	English
Pages (from-to)	D966-974
Journal	Nucleic Acids Research
Volume	42
Issue number	Database issue
Early online date	11 Nov 2013
DOIs	https://doi.org/10.1093/nar/gkt1026
Publication status	Published - 1 Jan 2014

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10.1093/nar/gkt1026Licence: Creative Commons: Attribution (CC BY)

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Kohler, S., Doelken, S. C., Mungall, C. J., Bauer, S., Firth, H. V., Bailleul-Forestier, I., Black, G. C., Brown, D. L., Brudno, M., Campbell, J., FitzPatrick, D. R., Eppig, J. T., Jackson, A. P., Freson, K., Girdea, M., Helbig, I., Hurst, J. A., Jahn, J., Jackson, L. G., ... Robinson, P. N. (2014). The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Research, 42(Database issue), D966-974. https://doi.org/10.1093/nar/gkt1026

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title = "The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data",

abstract = "The Human Phenotype Ontology (HPO) project, available at http://www.human-phenotype-ontology.org, provides a structured, comprehensive and well-defined set of 10,088 classes (terms) describing human phenotypic abnormalities and 13,326 subclass relations between the HPO classes. In addition we have developed logical definitions for 46% of all HPO classes using terms from ontologies for anatomy, cell types, function, embryology, pathology and other domains. This allows interoperability with several resources, especially those containing phenotype information on model organisms such as mouse and zebrafish. Here we describe the updated HPO database, which provides annotations of 7,278 human hereditary syndromes listed in OMIM, Orphanet and DECIPHER to classes of the HPO. Various meta-attributes such as frequency, references and negations are associated with each annotation. Several large-scale projects worldwide utilize the HPO for describing phenotype information in their datasets. We have therefore generated equivalence mappings to other phenotype vocabularies such as LDDB, Orphanet, MedDRA, UMLS and phenoDB, allowing integration of existing datasets and interoperability with multiple biomedical resources. We have created various ways to access the HPO database content using flat files, a MySQL database, and Web-based tools. All data and documentation on the HPO project can be found online. ",

author = "S. Kohler and Doelken, {S. C.} and Mungall, {C. J.} and S. Bauer and Firth, {H. V.} and I. Bailleul-Forestier and Black, {G. C.} and Brown, {D. L.} and M. Brudno and J. Campbell and FitzPatrick, {D. R.} and Eppig, {J. T.} and Jackson, {A. P.} and K. Freson and M. Girdea and I. Helbig and Hurst, {J. A.} and J. Jahn and Jackson, {L. G.} and Kelly, {A. M.} and Ledbetter, {D. H.} and S. Mansour and Martin, {C. L.} and C. Moss and A. Mumford and Ouwehand, {W. H.} and Park, {S. M.} and Riggs, {E. R.} and Scott, {R. H.} and S. Sisodiya and {Van Vooren}, S. and Wapner, {R. J.} and Wilkie, {A. O.} and Wright, {C. F.} and {Vulto-van Silfhout}, {A. T.} and {de Leeuw}, N. and {de Vries}, {B. B.} and Washingthon, {N. L.} and Smith, {C. L.} and M. Westerfield and P. Schofield and Ruef, {B. J.} and Gkoutos, {G. V.} and M. Haendel and D. Smedley and Lewis, {S. E.} and Robinson, {P. N.}",

year = "2014",

month = jan,

day = "1",

doi = "10.1093/nar/gkt1026",

language = "English",

volume = "42",

pages = "D966--974",

journal = "Nucleic Acids Research",

issn = "0305-1048",

publisher = "Oxford University Press",

number = "Database issue",

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Kohler, S, Doelken, SC, Mungall, CJ, Bauer, S, Firth, HV, Bailleul-Forestier, I, Black, GC, Brown, DL, Brudno, M, Campbell, J, FitzPatrick, DR, Eppig, JT, Jackson, AP, Freson, K, Girdea, M, Helbig, I, Hurst, JA, Jahn, J, Jackson, LG, Kelly, AM, Ledbetter, DH, Mansour, S, Martin, CL, Moss, C, Mumford, A, Ouwehand, WH, Park, SM, Riggs, ER, Scott, RH, Sisodiya, S, Van Vooren, S, Wapner, RJ, Wilkie, AO, Wright, CF, Vulto-van Silfhout, AT, de Leeuw, N, de Vries, BB, Washingthon, NL, Smith, CL, Westerfield, M, Schofield, P, Ruef, BJ, Gkoutos, GV, Haendel, M, Smedley, D, Lewis, SE & Robinson, PN 2014, 'The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data', Nucleic Acids Research, vol. 42, no. Database issue, pp. D966-974. https://doi.org/10.1093/nar/gkt1026

TY - JOUR

T1 - The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data

AU - Kohler, S.

AU - Doelken, S. C.

AU - Mungall, C. J.

AU - Bauer, S.

AU - Firth, H. V.

AU - Bailleul-Forestier, I.

AU - Black, G. C.

AU - Brown, D. L.

AU - Brudno, M.

AU - Campbell, J.

AU - FitzPatrick, D. R.

AU - Eppig, J. T.

AU - Jackson, A. P.

AU - Freson, K.

AU - Girdea, M.

AU - Helbig, I.

AU - Hurst, J. A.

AU - Jahn, J.

AU - Jackson, L. G.

AU - Kelly, A. M.

AU - Ledbetter, D. H.

AU - Mansour, S.

AU - Martin, C. L.

AU - Moss, C.

AU - Mumford, A.

AU - Ouwehand, W. H.

AU - Park, S. M.

AU - Riggs, E. R.

AU - Scott, R. H.

AU - Sisodiya, S.

AU - Van Vooren, S.

AU - Wapner, R. J.

AU - Wilkie, A. O.

AU - Wright, C. F.

AU - Vulto-van Silfhout, A. T.

AU - de Leeuw, N.

AU - de Vries, B. B.

AU - Washingthon, N. L.

AU - Smith, C. L.

AU - Westerfield, M.

AU - Schofield, P.

AU - Ruef, B. J.

AU - Gkoutos, G. V.

AU - Haendel, M.

AU - Smedley, D.

AU - Lewis, S. E.

AU - Robinson, P. N.

PY - 2014/1/1

Y1 - 2014/1/1

N2 - The Human Phenotype Ontology (HPO) project, available at http://www.human-phenotype-ontology.org, provides a structured, comprehensive and well-defined set of 10,088 classes (terms) describing human phenotypic abnormalities and 13,326 subclass relations between the HPO classes. In addition we have developed logical definitions for 46% of all HPO classes using terms from ontologies for anatomy, cell types, function, embryology, pathology and other domains. This allows interoperability with several resources, especially those containing phenotype information on model organisms such as mouse and zebrafish. Here we describe the updated HPO database, which provides annotations of 7,278 human hereditary syndromes listed in OMIM, Orphanet and DECIPHER to classes of the HPO. Various meta-attributes such as frequency, references and negations are associated with each annotation. Several large-scale projects worldwide utilize the HPO for describing phenotype information in their datasets. We have therefore generated equivalence mappings to other phenotype vocabularies such as LDDB, Orphanet, MedDRA, UMLS and phenoDB, allowing integration of existing datasets and interoperability with multiple biomedical resources. We have created various ways to access the HPO database content using flat files, a MySQL database, and Web-based tools. All data and documentation on the HPO project can be found online.

AB - The Human Phenotype Ontology (HPO) project, available at http://www.human-phenotype-ontology.org, provides a structured, comprehensive and well-defined set of 10,088 classes (terms) describing human phenotypic abnormalities and 13,326 subclass relations between the HPO classes. In addition we have developed logical definitions for 46% of all HPO classes using terms from ontologies for anatomy, cell types, function, embryology, pathology and other domains. This allows interoperability with several resources, especially those containing phenotype information on model organisms such as mouse and zebrafish. Here we describe the updated HPO database, which provides annotations of 7,278 human hereditary syndromes listed in OMIM, Orphanet and DECIPHER to classes of the HPO. Various meta-attributes such as frequency, references and negations are associated with each annotation. Several large-scale projects worldwide utilize the HPO for describing phenotype information in their datasets. We have therefore generated equivalence mappings to other phenotype vocabularies such as LDDB, Orphanet, MedDRA, UMLS and phenoDB, allowing integration of existing datasets and interoperability with multiple biomedical resources. We have created various ways to access the HPO database content using flat files, a MySQL database, and Web-based tools. All data and documentation on the HPO project can be found online.

U2 - 10.1093/nar/gkt1026

DO - 10.1093/nar/gkt1026

M3 - Article

SN - 0305-1048

VL - 42

SP - D966-974

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - Database issue

ER -

The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data

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