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

Sebastian Köhler; Sandra C Doelken; Christopher J Mungall; Sebastian Bauer; Helen V Firth; Isabelle Bailleul-Forestier; Graeme C M Black; Danielle L Brown; Michael Brudno; Jennifer Campbell; David R Fitzpatrick; Janan T Eppig; Kathleen Freson; Marta Girdea; Ingo Helbig; Jane A Hurst; Johanna Jähn; Laird G Jackson; Anne M Kelly; David H Ledbetter; Christa L Martin; Celia Moss; Andrew Mumford; Willem H Ouwehand; Soo-Mi Park; Erin Rooney Riggs; Richard H Scott; Sanjay Sisodiya; Steven Van Vooren; Ronald J Wapner; Andrew O M Wilkie; Caroline F Wright; Anneke T Vulto-van Silfhout; Nicole de Leeuw; Bert B A de Vries; Nicole L Washingthon; Cynthia L Smith; Monte Westerfield; Paul Schofield; Barbara J Ruef; Georgios V Gkoutos; Melissa Haendel; Damian Smedley; Suzanna E Lewis; Andrew D Mumford

doi:10.1093/nar/gkt1026

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

Sebastian Köhler, Sandra C Doelken, Christopher J Mungall, Sebastian Bauer, Helen V Firth, Isabelle Bailleul-Forestier, Graeme C M Black, Danielle L Brown, Michael Brudno, Jennifer Campbell, David R Fitzpatrick, Janan T Eppig, Kathleen Freson, Marta Girdea, Ingo Helbig, Jane A Hurst, Johanna Jähn, Laird G Jackson, Anne M Kelly, David H LedbetterChrista L Martin, Celia Moss, Andrew Mumford, Willem H Ouwehand, Soo-Mi Park, Erin Rooney Riggs, Richard H Scott, Sanjay Sisodiya, Steven Van Vooren, Ronald J Wapner, Andrew O M Wilkie, Caroline F Wright, Anneke T Vulto-van Silfhout, Nicole de Leeuw, Bert B A de Vries, Nicole L Washingthon, Cynthia L Smith, Monte Westerfield, Paul Schofield, Barbara J Ruef, Georgios V Gkoutos, Melissa Haendel, Damian Smedley, Suzanna E Lewis, Andrew D Mumford

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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
Journal	Nucleic Acids Research
DOIs	https://doi.org/10.1093/nar/gkt1026
Publication status	Published - 11 Nov 2013

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Köhler, S., Doelken, S. C., Mungall, C. J., Bauer, S., Firth, H. V., Bailleul-Forestier, I., Black, G. C. M., Brown, D. L., Brudno, M., Campbell, J., Fitzpatrick, D. R., Eppig, J. T., Freson, K., Girdea, M., Helbig, I., Hurst, J. A., Jähn, J., Jackson, L. G., Kelly, A. M., ... Mumford, A. D. (2013). The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Research. https://doi.org/10.1093/nar/gkt1026

@article{99d87d09491a4595bb192bc81d162d23,

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 = "Sebastian K{\"o}hler and Doelken, {Sandra C} and Mungall, {Christopher J} and Sebastian Bauer and Firth, {Helen V} and Isabelle Bailleul-Forestier and Black, {Graeme C M} and Brown, {Danielle L} and Michael Brudno and Jennifer Campbell and Fitzpatrick, {David R} and Eppig, {Janan T} and Kathleen Freson and Marta Girdea and Ingo Helbig and Hurst, {Jane A} and Johanna J{\"a}hn and Jackson, {Laird G} and Kelly, {Anne M} and Ledbetter, {David H} and Martin, {Christa L} and Celia Moss and Andrew Mumford and Ouwehand, {Willem H} and Soo-Mi Park and Riggs, {Erin Rooney} and Scott, {Richard H} and Sanjay Sisodiya and Vooren, {Steven Van} and Wapner, {Ronald J} and Wilkie, {Andrew O M} and Wright, {Caroline F} and {Vulto-van Silfhout}, {Anneke T} and Leeuw, {Nicole de} and {de Vries}, {Bert B A} and Washingthon, {Nicole L} and Smith, {Cynthia L} and Monte Westerfield and Paul Schofield and Ruef, {Barbara J} and Gkoutos, {Georgios V} and Melissa Haendel and Damian Smedley and Lewis, {Suzanna E} and Mumford, {Andrew D}",

year = "2013",

month = nov,

day = "11",

doi = "10.1093/nar/gkt1026",

language = "English",

journal = "Nucleic Acids Research",

issn = "1362-4962",

publisher = "Oxford University Press",

}

Köhler, S, Doelken, SC, Mungall, CJ, Bauer, S, Firth, HV, Bailleul-Forestier, I, Black, GCM, Brown, DL, Brudno, M, Campbell, J, Fitzpatrick, DR, Eppig, JT, Freson, K, Girdea, M, Helbig, I, Hurst, JA, Jähn, J, Jackson, LG, Kelly, AM, Ledbetter, DH, Martin, CL, Moss, C, Mumford, A, Ouwehand, WH, Park, S-M, Riggs, ER, Scott, RH, Sisodiya, S, Vooren, SV, Wapner, RJ, Wilkie, AOM, Wright, CF, Vulto-van Silfhout, AT, Leeuw, ND, de Vries, BBA, Washingthon, NL, Smith, CL, Westerfield, M, Schofield, P, Ruef, BJ, Gkoutos, GV, Haendel, M, Smedley, D, Lewis, SE & Mumford, AD 2013, 'The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data', Nucleic Acids Research. https://doi.org/10.1093/nar/gkt1026

TY - JOUR

T1 - The Human Phenotype Ontology project

T2 - linking molecular biology and disease through phenotype data

AU - Köhler, Sebastian

AU - Doelken, Sandra C

AU - Mungall, Christopher J

AU - Bauer, Sebastian

AU - Firth, Helen V

AU - Bailleul-Forestier, Isabelle

AU - Black, Graeme C M

AU - Brown, Danielle L

AU - Brudno, Michael

AU - Campbell, Jennifer

AU - Fitzpatrick, David R

AU - Eppig, Janan T

AU - Freson, Kathleen

AU - Girdea, Marta

AU - Helbig, Ingo

AU - Hurst, Jane A

AU - Jähn, Johanna

AU - Jackson, Laird G

AU - Kelly, Anne M

AU - Ledbetter, David H

AU - Martin, Christa L

AU - Moss, Celia

AU - Mumford, Andrew

AU - Ouwehand, Willem H

AU - Park, Soo-Mi

AU - Riggs, Erin Rooney

AU - Scott, Richard H

AU - Sisodiya, Sanjay

AU - Vooren, Steven Van

AU - Wapner, Ronald J

AU - Wilkie, Andrew O M

AU - Wright, Caroline F

AU - Vulto-van Silfhout, Anneke T

AU - Leeuw, Nicole de

AU - de Vries, Bert B A

AU - Washingthon, Nicole L

AU - Smith, Cynthia L

AU - Westerfield, Monte

AU - Schofield, Paul

AU - Ruef, Barbara J

AU - Gkoutos, Georgios V

AU - Haendel, Melissa

AU - Smedley, Damian

AU - Lewis, Suzanna E

AU - Mumford, Andrew D

PY - 2013/11/11

Y1 - 2013/11/11

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 (Academic Journal)

C2 - 24217912

SN - 1362-4962

JO - Nucleic Acids Research

JF - Nucleic Acids Research

ER -

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

Abstract

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