An Ontology of Qualities for the Annotation of Biomedical Data

生物医学数据注释的质量本体论

• 批准号: 8127993
• 负责人: Suzanna E Lewis
• 金额: $ 52.49万
• 依托单位: UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-09-30 至 2013-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8127993
• 关键词: Abbreviations; Adopted; Advocate; Anatomy; Biological Process; Characteristics; Clinical Data; Collaborations; Data; Data Set; Databases; Deposition; Disease; Drosophila genus; Exercise; Glossary; Health; Human; Knowledge; Letters; Modeling; Molecular Genetics; Mus; Mutation; Online Mendelian Inheritance In Man; Ontology; Organism; Phenotype; Records; Research Project Grants; Resources; Structure; Terminology; Text; Translational Research; Work; Zebrafish; acronyms; base; biomedical ontology; comparative; genome database; human data; human disease; improved; interoperability; model organisms databases; mouse genome; mutant; research study

DESCRIPTION (provided by applicant): Our proposal is to develop an ontology of qualities (i.e. distinguishing characteristics such as: long, short, increased, decreased, red, blue, and so on) and use it, in conjunction with ontologies of particular anatomies and biological processes, to describe phenotypic data from zebrafish, fruit fly, mouse, and human rigorously. This work will provide one of the integral components necessary for integrating phenotypic descriptions semantically with other aspects of biomedical knowledge. Currently these descriptions are recorded either as free text or using a terminology that is idiosyncratic to a single organism or research project. We have chosen these particular data sets because of the preliminary work that has already been carried out on these data, because they provide a wide spectrum of descriptive situations that will fully exercise the ontology, and particularly because, with the human data, we will be able to explore how unifying these data sets can enable translational research. We will also work with other database resources, such as BIRN [BIRN], WormBase [WormBase], dictyBase [dictyBase], and PhenoScape [PhenoScape], who are also adopting the approach we advocate (see letters of support). We will contribute PATO and the other ontologies that we develop to the OBO Foundry [OBO], and we will deposit our phenotypic annotations into the OBD [OBD] database of the National Center for Biomedical Ontology [NCBO] to facilitate comparisons between these and other data. The Quality Ontology [PATO] will provide one essential part of the unifying framework needed to surmount the difficult problem of integrating phenotypic data sets. PUBLIC HEALTH RELEVANCE: The underlying principle of this proposal is that the comparative approach can be used to further our understanding of the genetic and molecular bases of human diseases. Experiments that study the phenotypic consequences of mutations in non-human organisms are justified by the fact that they provide valuable models for a better understanding of human diseases.

描述（由申请人提供）：我们的建议是开发质量的本体论（即，诸如：长，短，增加，减少，红色，蓝色等的区别特征），并与特定的解剖学和生物学过程的本体结合使用，以描述Zebrafish，Fruf Fluer Fly Fly Fly，鼠标和人类的特定表型数据。这项工作将提供将表型描述与生物医学知识的其他方面相结合所必需的组成部分之一。目前，这些描述是将其记录为自由文本，也可以使用对单个生物体或研究项目具有特质的术语。我们之所以选择这些特定的数据集，是因为已经在这些数据上进行的初步工作，因为它们提供了各种描述性情况，这些情况将充分行使本体论，尤其是因为借助人类数据，我们将能够探索如何统一这些数据集可以启用转换研究。我们还将与其他数据库资源一起工作，例如Birn [Birn]，Wormbase [wormbase]，dictybase [dictybase]和Phenoscape [Phenoscape]，他们也采用了我们提倡的方法（请参阅支持信）。我们将为OBO铸造厂[OBO]贡献Pato和其他本体论，并将表型注释将我们的表型注释沉积到国家生物医学本体论中心[NCBO]的OBD [OBD]数据库中，以促进这些数据和其他数据之间的比较。质量本体论[PATO]将为统一框架的重要组成部分，以克服整合表型数据集的困难问题。公共卫生相关性：该提案的基本原则是，可以使用比较方法来进一步了解人类疾病的遗传和分子基础。研究非人类生物中突变的表型后果的实验是合理的，因为它们为更好地理解人类疾病提供了宝贵的模型。