Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community.
Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community.
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DOI：
10.1186/1471-2105-12-32
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发表时间：
2011-01-24
影响因子：
3
通讯作者：
Sternberg PW
中科院分区：
文献类型：
--
作者：
Schindelman G;Fernandes JS;Bastiani CA;Yook K;Sternberg PW
秀丽隐杆线虫基于基因的表型信息可以追溯到20世纪70年代，始于Sydney Brenner和通过经典遗传学表征行为和形态突变等位基因，以了解神经系统功能。自此秀丽隐杆线虫成为基础生物学和生物医学原理研究的重要遗传模型系统，主要是通过表型分析的使用。由于秀丽隐杆线虫作为一种遗传上可处理的模式生物的生长和大规模分析的发展，需要管理和向研究界提供的表型数据显着增加。为此，需要一个标准化词汇表来集成来自不同来源的表型数据，允许与其他数据类型集成，并以可计算的形式呈现数据。我们描述了一个层次结构，可用于标准化线虫表型描述的受控词汇表，即蠕虫表型本体（WPO）。WPO目前由1880个表型术语组成，其中74%已用于注释与超过18,000个秀丽隐杆线虫基因相关的表型。WPO的范围不仅限于秀丽隐杆线虫生物学，而且还包括在相关线虫物种中观察到的表型。我们通过将WPO与其他本体论整合，丰富了WPO的价值，从而增加了非线虫生物学家对蠕虫表型的可及性。我们正在积极发展世界气象组织，以继续满足科学界不断变化的需求，并希望让研究人员参与这项至关重要的努力。我们提供了一个表型本体论（WPO），这将有助于促进数据检索和线虫群落内的跨物种比较。在更大的科学界，WPO将允许不同模式生物数据库（MODs）和其他生物数据库之间的数据集成和互操作性。因此，这种标准化的表型本体将允许更复杂的数据查询和增强生物信息学分析。
Caenorhabditis elegans gene-based phenotype information dates back to the 1970's, beginning with Sydney Brenner and the characterization of behavioral and morphological mutant alleles via classical genetics in order to understand nervous system function. Since then C. elegans has become an important genetic model system for the study of basic biological and biomedical principles, largely through the use of phenotype analysis. Because of the growth of C. elegans as a genetically tractable model organism and the development of large-scale analyses, there has been a significant increase of phenotype data that needs to be managed and made accessible to the research community. To do so, a standardized vocabulary is necessary to integrate phenotype data from diverse sources, permit integration with other data types and render the data in a computable form. We describe a hierarchically structured, controlled vocabulary of terms that can be used to standardize phenotype descriptions in C. elegans, namely the Worm Phenotype Ontology (WPO). The WPO is currently comprised of 1,880 phenotype terms, 74% of which have been used in the annotation of phenotypes associated with greater than 18,000 C. elegans genes. The scope of the WPO is not exclusively limited to C. elegans biology, rather it is devised to also incorporate phenotypes observed in related nematode species. We have enriched the value of the WPO by integrating it with other ontologies, thereby increasing the accessibility of worm phenotypes to non-nematode biologists. We are actively developing the WPO to continue to fulfill the evolving needs of the scientific community and hope to engage researchers in this crucial endeavor. We provide a phenotype ontology (WPO) that will help to facilitate data retrieval, and cross-species comparisons within the nematode community. In the larger scientific community, the WPO will permit data integration, and interoperability across the different Model Organism Databases (MODs) and other biological databases. This standardized phenotype ontology will therefore allow for more complex data queries and enhance bioinformatic analyses.
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影响因子：
14.9
作者：
Grumbling G;Strelets V
通讯作者：
Strelets V
DOI：
10.1093/database/bap001
发表时间：
2009-01-01
影响因子：
5.8
作者：
Costanzo, Maria C.;Skrzypek, Marek S.;Cherry, J. Michael
通讯作者：
Cherry, J. Michael
影响因子：
11.8
作者：
Brisbin, Sarah;Liu, Jun;Chin-Sang, Ian
通讯作者：
Chin-Sang, Ian
影响因子：
11.8
作者：
Hannich, J. Thomas;Entchev, Eugeni V.;Kurzchalia, Teymuras V.
通讯作者：
Kurzchalia, Teymuras V.
影响因子：
56.9
作者：
Baldi, Chris;Cho, Soochin;Ellis, Ronald E.
通讯作者：
Ellis, Ronald E.