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: 7559228
• 负责人: Suzanna E Lewis
• 金额: $ 53.39万
• 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 2012-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7559228
• 关键词: Abbreviations; Adopted; Advocate; Anatomy; Biological Process; Characteristics; Clinical Data; Collaborations; Data; Data Set; Databases; Deposition; Disease; Drosophila genus; Exercise; Glossary; 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; public health relevance; 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本体（即区分特征，例如：长、短、增加、减少、红色、蓝色等），并将其与特定解剖学和生物学过程的本体结合使用，以严格描述来自斑马鱼、果蝇、小鼠和人类的表型数据。这项工作将提供一个必要的组成部分整合表型描述语义与其他方面的生物医学知识。目前，这些描述要么以自由文本的形式记录，要么使用一个术语，该术语对单个生物体或研究项目来说是特殊的。我们之所以选择这些特定的数据集，是因为已经对这些数据进行了初步的工作，因为它们提供了广泛的描述性情况，可以充分运用本体论，特别是因为，通过人类数据，我们将能够探索如何统一这些数据集才能实现转化研究。我们还将与其他数据库资源合作，例如BIRN [BIRN]，WormBase [WormBase]，dictyBase [dictyBase]和PhenoScape [PhenoScape]，他们也采用我们提倡的方法（请参阅支持函）。我们将把我们开发的PATO和其他本体贡献给OBO Foundry [OBO]，我们将把我们的表型注释存款国家生物医学本体中心[NCBO]的OBD [OBD]数据库，以便于这些数据和其他数据之间的比较。质量本体[PATO]将提供一个必要的组成部分，统一的框架需要克服困难的问题，整合表型数据集。公共卫生关系：这一建议的基本原则是，比较的方法可以用来进一步了解人类疾病的遗传和分子基础。研究非人类生物体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有价值的模型。