The Ontology for Biomedical Investigations.
The Ontology for Biomedical Investigations.
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DOI：
10.1371/journal.pone.0154556
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发表时间：
2016
期刊：
影响因子：
3.7
通讯作者：
Zheng J
中科院分区：
文献类型：
--
作者：
Bandrowski A;Brinkman R;Brochhausen M;Brush MH;Bug B;Chibucos MC;Clancy K;Courtot M;Derom D;Dumontier M;Fan L;Fostel J;Fragoso G;Gibson F;Gonzalez-Beltran A;Haendel MA;He Y;Heiskanen M;Hernandez-Boussard T;Jensen M;Lin Y;Lister AL;Lord P;Malone J;Manduchi E;McGee M;Morrison N;Overton JA;Parkinson H;Peters B;Rocca-Serra P;Ruttenberg A;Sansone SA;Scheuermann RH;Schober D;Smith B;Soldatova LN;Stoeckert CJ Jr;Taylor CF;Torniai C;Turner JA;Vita R;Whetzel PL;Zheng J
生物医学研究本体论（OBI）是一种本体论，它提供了具有精确定义含义的术语，以描述生物和医学领域中如何进行研究的各个方面。OBI重新使用来自开放生物学和生物医学本体（OBO）项目的生物医学知识表示，并增加了描述这些知识是如何获得的能力。我们在这里描述的状态OBI和几个应用程序，使用它，如添加语义表达到现有的数据库，建立数据输入表单，并实现知识资源之间的互操作性。OBI涵盖调查过程的所有阶段，例如规划、执行和报告。它代表参与这些过程的信息和物质实体，以及角色和功能。在OBI之前，不可能使用单个内部一致的资源来应用于这些应用程序的多种类型的实验。OBI通过为生物和医学研究中涉及的实体创建术语，并通过导入其他生物医学本体的部分内容，如GO，生物学感兴趣的化学实体（ChEBI）和表型属性和性状本体（PATO）而不改变其含义，从而使这一点成为可能。OBI正在广泛的项目中使用，涵盖基因组学，多组学，免疫学和服务目录。OBI还衍生了其他本体（信息本体）和导入本体部分的方法（引用外部本体术语的最小信息（MIREOT））。OBI项目是一个开放的跨学科合作项目，包括来自地球仪的多个研究社区。迄今为止，OBI已经创建了2366个类和40个关系沿着文本和形式定义。OBI Consortium维护一个网络资源（obi-ontology.org），提供与OBI相关的人员、政策和问题的详细信息。OBI的当前版本可在http://purl.obolibrary.org/obo/obi.owl上获得。
The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource (http://obi-ontology.org) providing details on the people, policies, and issues being addressed in association with OBI. The current release of OBI is available at http://purl.obolibrary.org/obo/obi.owl.