Development of a Cognitive Paradigm Ontology: BrainMap and BIRN Intergration

认知范式本体的开发：BrainMap 和 BIRN 集成

• 批准号: 8091394
• 负责人: PETER Thornton FOX
• 金额: $ 27.14万
• 依托单位: UNIVERSITY OF TEXAS HLTH SCIENCE CENTER
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-08-01 至 2013-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8091394
• 关键词: Adopted; Adoption; Advisory Committees; Anatomy; Archives; Back; Biomedical Informatics Research Network; Characteristics; Classification; Code; Cognitive; Cognitive Science; Collaborations; Communication; Communities; Conflict (Psychology); Consult; Controlled Vocabulary; Data; Data Set; Data Sources; Data Storage and Retrieval; Databases; Development; Educational workshop; Electroencephalography; Electromagnetics; Feedback; Functional Imaging; Functional Magnetic Resonance Imaging; Funding; Genes; Goals; Health; Human; Image; Informatics; Instruction; Label; Letters; Link; Literature; Maps; Measures; Medical; Medical Imaging; Memory; Meta-Analysis; Methods; Mining; Mission; Modality; Modeling; Names; Neurosciences; Ontology; PTPNS1 gene; Performance; Procedures; PubMed; Publications; Research; Resolution; Resources; Response to stimulus physiology; Sampling; Scheme; Series; Societies; Stimulus; Structure; Systematized Nomenclature of Medicine; Techniques; Technology; Terminology; Testing; Work; abstracting; base; biomedical ontology; clinical care; community planning; data sharing; design; efficacy testing; image archival system; information framework; interest; interoperability; member; neuroimaging; neuroinformatics; novel; relating to nervous system; response; time use; tool; wiki

DESCRIPTION (provided by applicant): The objective of this proposal is to develop, evaluate, and distribute a domain ontology of cognitive paradigms for application and use in the functional neuroimaging community. This cognitive paradigm ontology, CogPO, will be developed through the integration of two well known and established databases, the Functional Imaging Biomedical Informatics Research Network (FBIRN) Human Imaging Database (HID) and the BrainMap database. The design of CogPO concentrates on what can be observed directly: categorization of each paradigm in terms of (1) the stimulus presented to the subjects, (2) the requested instructions, and (3) the returned response. All paradigms are essentially comprised of these three orthogonal components, and formalizing an ontology around them is a clear and direct approach to describing paradigms. This structured, well-defined, common and controlled vocabulary will be capable of representing the cognitive paradigms in the FBIRN Data Repository, which stores structural and functional imaging datasets for later analysis, and in BrainMap, which stores analyzed results from the functional imaging literature. This proposal has been designed to include strong collaboration with the National Center for Biomedical Ontology (NCBO) and the Neuroinformatics Information Framework (NIF). Neither the NCBO nor the NIF currently seeks to develop an ontology of cognitive paradigms; thus, the current proposal is novel and does not conflict with any existing ontology efforts, but is a complementary endeavor. Through a series of workshops, CogPO developers will consult both the domain experts (the neuroimaging research community) and the ontological experts (NCBO) and the BIRN Ontology Task Force (OTF). CogPO developers also plan to allow user input and feedback from the entire neuroimaging community through the Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC). This proposal includes a formal plan for community acceptance of the developed ontology, complete with a list of concrete deliverables in Protigi-OWL format to be distributed by the end of the funding period, which can be utilized not only by FBIRN and BrainMap users, but also by the entire neuroimaging community. It is our ultimate aim that CogPO be designed to enable its extension to a broader context in cognitive sciences. PUBLIC HEALTH RELEVANCE: CogPO, a domain ontology of cognitive paradigms, would facilitate descriptions of cognitive experimental paradigms in ways that are machine-readable and machine-interpretable, to allow communication and automated data sharing across diverse databases and data sources. This ontology will be made available for adoption not only by other fMRI databases, but also for archives of other neuroimaging modalities (e.g., EEG or MEG data), such as the Neural ElectroMagnetic Ontologies (NEMO), and literature neuroinformatics efforts such as the Society for Neuroscience's PubMed Plus. It is our ultimate aim that CogPO be designed to enable its extension to a broader context in cognitive sciences.

描述(由申请人提供)：本提案的目标是开发、评估和分发认知范例的领域本体，以便在功能神经成像社区中应用和使用。这一认知范式本体论CogPO将通过整合两个著名和成熟的数据库--功能成像生物医学信息学研究网络(FBIRN)人类成像数据库(HID)和脑图数据库(BrainMap)来开发。CogPO的设计集中在可以直接观察到的东西上：根据(1)呈现给受试者的刺激，(2)请求的指令，以及(3)返回的响应，对每种范式进行分类。所有范例基本上都由这三个相互垂直的组成部分组成，形式化它们周围的本体是描述范例的一种明确而直接的方法。这种结构化的、定义明确的、通用的和受控的词汇将能够在FBIRN数据储存库和BrainMap中表示认知范式，FBIRN数据储存库存储结构和功能成像数据集，供以后分析，BrainMap存储来自功能成像文献的分析结果。这项提议旨在包括与国家生物医学本体论中心(NCBO)和神经信息学信息框架(NIF)的密切合作。NCBO和NIF目前都没有寻求开发认知范式的本体论；因此，目前的提议是新颖的，并不与任何现有的本体论努力相冲突，而是一项相辅相成的努力。通过一系列研讨会，CogPO开发人员将咨询领域专家(神经成像研究社区)、本体专家(NCBO)和BIRN本体任务组(OTF)。CogPO开发人员还计划通过神经成像信息学工具和资源信息交换中心(NITRC)允许用户输入和来自整个神经成像社区的反馈。这项提议包括一项社区接受已开发的本体的正式计划，以及在资助期结束前分发的Protigi-Owl格式的具体交付成果清单，这些清单不仅可供FBIRN和BrainMap用户使用，而且可供整个神经成像社区使用。我们的最终目标是将CogPO设计为能够将其扩展到认知科学的更广泛的背景中。公共卫生相关性：CogPO是认知范式的一个领域本体论，它将促进以机器可读和机器可解释的方式描述认知实验范式，以便在不同的数据库和数据源之间进行通信和自动数据共享。该本体不仅可供其他fMRI数据库使用，还可用于其他神经成像模式(例如，EEG或MEG数据)的存档，如神经电磁本体(NEMO)，以及文献神经信息学努力，如神经科学学会的PubMed Plus。我们的最终目标是将CogPO设计为能够将其扩展到认知科学的更广泛的背景中。

项目成果

Automated annotation of functional imaging experiments via multi-label classification.

• DOI: 10.3389/fnins.2013.00240
• 发表时间: 2013
• 期刊: Frontiers in neuroscience
• 影响因子: 4.3
• 作者: Turner MD;Chakrabarti C;Jones TB;Xu JF;Fox PT;Luger GF;Laird AR;Turner JA
• 通讯作者: Turner JA

Interdisciplinary perspectives on the development, integration, and application of cognitive ontologies.

• DOI: 10.3389/fninf.2014.00062
• 发表时间: 2014
• 期刊: Frontiers in neuroinformatics
• 影响因子: 3.5
• 作者: Hastings J;Frishkoff GA;Smith B;Jensen M;Poldrack RA;Lomax J;Bandrowski A;Imam F;Turner JA;Martone ME
• 通讯作者: Martone ME

Modeling biomedical experimental processes with OBI.

• DOI: 10.1186/2041-1480-1-s1-s7
• 发表时间: 2010-06-22
• 期刊: Journal of biomedical semantics
• 影响因子: 1.9
• 作者: Brinkman RR;Courtot M;Derom D;Fostel JM;He Y;Lord P;Malone J;Parkinson H;Peters B;Rocca-Serra P;Ruttenberg A;Sansone SA;Soldatova LN;Stoeckert CJ Jr;Turner JA;Zheng J;OBI consortium
• 通讯作者: OBI consortium