The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience.
The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience.
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DOI：
10.1007/s12021-008-9032-z
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发表时间：
2008-09
期刊：
影响因子：
3
通讯作者：
Martone, Maryann E.
中科院分区：
文献类型：
--
作者：
Bug, William J.;Ascoli, Giorgio A.;Grethe, Jeffrey S.;Gupta, Amarnath;Fennema-Notestine, Christine;Laird, Angela R.;Larson, Stephen D.;Rubin, Daniel;Shepherd, Gordon M.;Turner, Jessica A.;Martone, Maryann E.
关键词：
神经科学信息框架（NIF）项目的一个关键组成部分是用于描述和检索神经科学相关资源的一致，灵活的术语。虽然最初的NIF规范要求使用松散结构的受控词汇表来描述神经科学资源，但随着NIF系统的发展，对具有足够粒度的神经科学正式结构化本体的需求变得明显，以描述和访问各种信息。这一要求导致了NIF标准化（NIFSTD）本体，这是一个通用神经科学领域术语的全面集合，这些术语被编织成通常用于描述神经科学数据的生物医学领域的本体一致的统一表示（例如，解剖学、细胞类型、技术），以及整个神经科学界正在创建的数字资源（工具、数据库）。NIFSTD建立在由BIRNLex建立的结构之上，BIRNLex是由生物医学信息学研究网络（BIRN）项目开发的涵盖临床神经成像研究的概念词典。每个不同的领域模块都使用Web本体语言（OWL）表示。NIFSTD尽可能地重用现有的涵盖所需生物医学领域的社区本体，构建注释NIF资源所需的更具体的概念。通过遵循这一原则，在相对较短的时间内以促进容易扩展和修改的形式组装了用于NIF信息注释、组织和检索的广泛词汇表。我们在这里报告的NIFSTD的结构，其前身BIRNLex，在其建设遵循的原则，并提供其在NIF内使用的例子。
A critical component of the Neuroscience Information Framework (NIF) project is a consistent, flexible terminology for describing and retrieving neuroscience-relevant resources. Although the original NIF specification called for a loosely structured controlled vocabulary for describing neuroscience resources, as the NIF system evolved, the requirement for a formally structured ontology for neuroscience with sufficient granularity to describe and access a diverse collection of information became obvious. This requirement led to the NIF standardized (NIFSTD) ontology, a comprehensive collection of common neuroscience domain terminologies woven into an ontologically consistent, unified representation of the biomedical domains typically used to describe neuroscience data (e.g., anatomy, cell types, techniques), as well as digital resources (tools, databases) being created throughout the neuroscience community. NIFSTD builds upon a structure established by the BIRNLex, a lexicon of concepts covering clinical neuroimaging research developed by the Biomedical Informatics Research Network (BIRN) project. Each distinct domain module is represented using the Web Ontology Language (OWL). As much as has been practical, NIFSTD reuses existing community ontologies that cover the required biomedical domains, building the more specific concepts required to annotate NIF resources. By following this principle, an extensive vocabulary was assembled in a relatively short period of time for NIF information annotation, organization, and retrieval, in a form that promotes easy extension and modification. We report here on the structure of the NIFSTD, and its predecessor BIRNLex, the principles followed in its construction and provide examples of its use within NIF.
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影响因子：
21.1
作者：
Catterall, WA;Striessnig, J;Perez-Reyes, E
通讯作者：
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作者：
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作者：
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Julius, D
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作者：
Larson SD;Fong LL;Gupta A;Condit C;Bug WJ;Martone ME
通讯作者：
Martone ME
影响因子：
34.7
作者：
Ascoli, Giorgio A.;Alonso-Nanclares, Lidia;Anderson, Stewart A.;Barrionuevo, German;Benavides-Piccione, Ruth;Burkhalter, Andreas;Buzsaki, Gyoergy;Cauli, Bruno;DeFelipe, Javier;Fairen, Alfonso;Feldmeyer, Dirk;Fishell, Gord;Fregnac, Yves;Freund, Tamas F.;Gardner, Daniel;Gardner, Esther P.;Goldberg, Jesse H.;Helmstaedter, Moritz;Hestrin, Shaul;Karube, Fuyuki;Kisvarday, Zoltan F.;Lambolez, Bertrand;Lewis, David A.;Marin, Oscar;Markram, Henry;Munoz, Alberto;Packer, Adam;Petersen, Carl C. H.;Rockland, Kathleen S.;Rossier, Jean;Rudy, Bernardo;Somogyi, Peter;Staiger, Jochen F.;Tamas, Gabor;Thomson, Alex M.;Toledo-Rodriguez, Maria;Wang, Yun;West, David C.;Yuste, Rafael
通讯作者：
Yuste, Rafael