The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data
نویسندگان
چکیده
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.
منابع مشابه
Molecular mechanisms involved in multidrug resistance in breast cancer therapy
Breast cancer is the most prevalent cancer in women. Chemotherapy is the main strategy in the treatment of this disease especially in the advanced form of the disease. Despite the recent progress in the development of new chemotherapy, the effectiveness of these drugs has dramatically reduced due to multidrug resistance. The phenotype of multidrug resistance (MDR) can occur through different me...
متن کاملاثرات متقابل ژن- ماده مغذی در بروز سرطان؛ یک مطالعه مروری سیستماتیک
--Advances in molecular biology over the past decades have contributed to a profound understanding of the function of genes in the development of diseases. The environment and nutritional factors interact with the genetic background of subject results in development of various diseases including cancer, cardiovascular disease and degenerative nervous disorders. However, the exact mechanisms o...
متن کاملPhenoMiner: quantitative phenotype curation at the rat genome database
The Rat Genome Database (RGD) is the premier repository of rat genomic and genetic data and currently houses >40 000 rat gene records as well as human and mouse orthologs, >2000 rat and 1900 human quantitative trait loci (QTLs) records and >2900 rat strain records. Biological information curated for these data objects includes disease associations, phenotypes, pathways, molecular functions, bio...
متن کاملI-49: Human Y Chromosome ProteomeProject
The success of the Human Genome Project (HGP) has provided a blueprint for the approximately 20,000 gene-encoded proteins potentially active in all of the hundreds of cell types that make up the human body. Yet we still have limited knowledge about a majority of the gene-encoded proteins which are the “building blocks of life” and “cellular machinery”. It is estimated that for nearly half of th...
متن کاملBuilding a dictionary of lexical variants for human phenotype de- scriptors
Detecting phenotype descriptors in text and linking them to ontology concepts is a challenging task. Current state-of-the art concept recognizers struggle with several issues due the variety of human expressiveness. Here we present initial results of creating a dictionary of lexical variants for the Human Phenotype Ontology. This work is a smaller but important part of a larger project with a g...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
دوره 42 شماره
صفحات -
تاریخ انتشار 2014