An Ontology of Qualities for the Annotation of Biomedical Data

描述(由申请人提供)：我们的建议是开发一个质量本体(即区分特征，如：长、短、增、减、红、蓝等)，并将其与特定解剖和生物过程的本体结合使用，以严格描述斑马鱼、果蝇、老鼠和人类的表型数据。这项工作将提供将表型描述与生物医学知识的其他方面进行语义整合所必需的组成部分之一。目前，这些描述要么以自由文本的形式记录，要么使用单个有机体或研究项目特有的术语。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工作，因为它们提供了广泛的描述性情况，将充分运用本体论，特别是因为，有了人类数据，我们将能够探索统一这些数据集如何使翻译研究成为可能。我们还将与其他数据库资源合作，如BIRN[BIRN]、WormBase[WormBase]、dictyBase[dictyBase]和PhenoScape[PhenoScape]，它们也采用我们倡导的方法(请参阅支持函)。我们将把PATO和我们开发的其他本体贡献给OBO Foundry[OBO]，我们将把我们的表型注释存储到国家生物医学本体中心[NCBO]的OBD[OBD]数据库中，以便于这些数据与其他数据之间的比较。质量本体论[PATO]将提供统一框架的一个重要部分，该框架需要克服整合表型数据集的难题。公共卫生相关性：这项建议的基本原则是，可以使用比较方法来加深我们对人类疾病的遗传和分子基础的理解。研究非人类有机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。

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.