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

被引：552

作者：

Koehler, Sebastian ^{[1
,2
]}

Doelken, Sandra C. ^{[1
]}

Mungall, Christopher J. ^{[3
]}

Bauer, Sebastian ^{[1
]}

Firth, Helen V. ^{[4
,5
]}

Bailleul-Forestier, Isabelle ^{[6
]}

Black, Graeme C. M. ^{[7
,8
]}

Brown, Danielle L. ^{[9
]}

Brudno, Michael ^{[10
,11
]}

Campbell, Jennifer ^{[9
,12
]}

FitzPatrick, David R. ^{[13
]}

Eppig, Janan T. ^{[14
]}

Jackson, Andrew P. ^{[13
]}

Freson, Kathleen ^{[15
]}

Girdea, Marta ^{[10
,11
]}

Helbig, Ingo ^{[16
]}

Hurst, Jane A. ^{[17
]}

Jaehn, Johanna ^{[16
]}

Jackson, Laird G. ^{[18
]}

Kelly, Anne M. ^{[19
,20
]}

Ledbetter, David H. ^{[21
]}

Mansour, Sahar ^{[22
]}

Martin, Christa L. ^{[21
]}

Moss, Celia ^{[23
]}

Mumford, Andrew ^{[24
]}

Ouwehand, Willem H. ^{[4
,19
,20
]}

Park, Soo-Mi ^{[5
]}

Riggs, Erin Rooney ^{[21
]}

Scott, Richard H. ^{[25
,26
]}

Sisodiya, Sanjay ^{[27
]}

Van Vooren, Steven ^{[28
]}

Wapner, Ronald J. ^{[29
]}

Wilkie, Andrew O. M. ^{[30
]}

Wright, Caroline F. ^{[4
]}

Vulto-van Silfhout, Anneke T. ^{[31
]}

de Leeuw, Nicole ^{[31
]}

de Vries, Bert B. A. ^{[31
]}

Washingthon, Nicole L. ^{[3
]}

Smith, Cynthia L. ^{[14
]}

Westerfield, Monte ^{[32
]}

Schofield, Paul ^{[14
,33
]}

Ruef, Barbara J. ^{[32
]}

Gkoutos, Georgios V. ^{[34
]}

Haendel, Melissa ^{[35
]}

Smedley, Damian ^{[4
]}

Lewis, Suzanna E. ^{[3
]}

Robinson, Peter N. ^{[1
,2
,36
]}

机构：

[1] Charite, Inst Med Genet & Human Genet, D-13353 Berlin, Germany

[2] Charite, Berlin Brandenburg Ctr Regenerat Therapies, D-13353 Berlin, Germany

[3] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA

[4] Wellcome Trust Sanger Inst, Hinxton CB10 1SA, Cambs, England

[5] Univ Cambridge, Addenbrookes Hosp, Dept Med Genet, Cambridge CB2 2QQ, England

[6] Univ Toulouse 3, Fac Chirurg Dent, CHU Toulouse, F-31062 Toulouse, France

[7] Cent Manchester Univ Hosp NHS Fdn Trust, Manchester Acad Hlth Sci Ctr, Ctr Genom Med, Manchester, Lancs, England

[8] Univ Manchester, MAHSC, Fac Med & Human Sci, Inst Human Dev,Ctr Genom Med, Manchester M13 9WL, Lancs, England

[9] Newcastle Univ, Inst Med Genet, Newcastle Upon Tyne NE1 3BZ, Tyne & Wear, England

[10] Univ Toronto, Dept Comp Sci, Toronto, ON M5S 1A1, Canada

[11] Hosp Sick Children, Ctr Computat Med, Toronto, ON M5G 1X8, Canada

[12] Leeds Teaching Hosp NHS Trust, Dept Clin Genet, Leeds LS2 9NS, W Yorkshire, England

[13] Univ Edinburgh, MRC Inst Genet & Mol Med, MRC Human Genet Unit, Edinburgh EH4 2XU, Midlothian, Scotland

[14] Jackson Lab, Bar Harbor, ME 04609 USA

[15] Univ Leuven, Ctr Mol & Vasc Biol, Louvain, Belgium

[16] Univ Med Ctr Schleswig Holstein, Dept Neuropediat, D-24105 Kiel, Germany

[17] Great Ormond St Hosp Sick Children, NE Thames Genet Serv, London WC1N 3JH, England

[18] Drexel Univ, Coll Med, Philadelphia, PA 19102 USA

[19] Univ Cambridge, Dept Haematol, Cambridge CB2 0PT, England

[20] NHS Blood & Transplant Cambridge, Cambridge CB2 0PT, England

[21] Geisinger Hlth Syst, Autism & Dev Med Inst, Danville, PA 17822 USA

[22] St Georges Healthcare NHS Trust, SW Thames Reg Genet Serv, London SW17 0RE, England

[23] Birmingham Childrens Hosp, Dept Dermatol, Birmingham, W Midlands, England

[24] Univ Bristol, Bristol Heart Inst, Bristol, Avon, England

[25] Great Ormond St Hosp Sick Children, Dept Clin Genet, London, England

[26] UCL Inst Child Hlth, Clin & Mol Genet Unit, London, England

[27] UCL Inst Neurol, Dept Clin & Expt Epilepsy, London, England

[28] Cartagenia, Louvain, Belgium

[29] Columbia Univ, Med Ctr, Dept Obstet & Gynecol, New York, NY 10032 USA

[30] Univ Oxford, John Radcliffe Hosp, Weatherall Inst Mol Med, Oxford OX3 9DS, England

[31] Radboud Univ Nijmegen, Med Ctr, Dept Human Genet, NL-6500 HB Nijmegen, Netherlands

[32] Univ Oregon, ZFIN, Eugene, OR 97403 USA

[33] Dept Physiol Dev & Neurosci, Cambridge CB2 3EG, England

[34] Aberystwyth Univ, Dept Comp Sci, Aberystwyth SY23 3DB, Ceredigion, Wales

[35] Oregon Hlth & Sci Univ, Dept Med Informat & Clin Epidemiol, Portland, OR 97239 USA

[36] Max Planck Inst Mol Genet, D-14195 Berlin, Germany

来源：

NUCLEIC ACIDS RESEARCH | 2014年 / 42卷 / D1期

基金：

美国国家卫生研究院;

关键词：

INTERNATIONAL STANDARDS; GENE DISCOVERY; INFORMATICS; INTEGRATION; EVOLUTION; MEDICINE; SEARCHES;

D O I：

10.1093/nar/gkt1026

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

070307 [化学生物学]; 071010 [生物化学与分子生物学];

摘要：

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.

引用

页码：D966 / D974

页数：9

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