The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data.
The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data.
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DOI：
10.1093/nar/gkt1026
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发表时间：
2014-01
影响因子：
14.9
通讯作者：
Robinson PN
中科院分区：
文献类型：
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作者：
Köhler 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;Jähn 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
可在http://www.human-phenotype-ontology.org，获得的人类表型本体论项目提供了一套结构化、全面和定义良好的10,088个类别(术语)，描述了人类表型异常和HPO类别之间的13,326个子类关系。此外，我们使用解剖学、细胞类型、功能、胚胎学、病理学和其他领域的本体论术语，为所有HPO类别中的46%开发了逻辑定义。这允许与几个资源的互操作性，特别是那些包含小鼠和斑马鱼等模式生物的表型信息的资源。在这里，我们描述了更新的HPO数据库，它提供了OMIM、孤儿网和解密中列出的7,278个人类遗传综合征的注释。不同的元属性，如频率、指称和否定，与每个注释相关联。世界各地的几个大型项目利用HPO来描述其数据集中的表型信息。因此，我们生成了到其他表型词汇表的等价映射，如LDDB、Orphanet、MedDRA、UMLS和henoDB，从而允许集成现有数据集并与多个生物医学资源互操作。我们使用平面文件、MySQL数据库和基于Web的工具创建了访问HPO数据库内容的各种方法。关于HPO项目的所有数据和文件都可以在网上找到。
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.