OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies.
OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies.
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DOI：
10.1093/database/baab069
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发表时间：
2021-10-26
期刊：
影响因子：
--
通讯作者：
Peters B
中科院分区：
文献类型：
--
作者：
Jackson R;Matentzoglu N;Overton JA;Vita R;Balhoff JP;Buttigieg PL;Carbon S;Courtot M;Diehl AD;Dooley DM;Duncan WD;Harris NL;Haendel MA;Lewis SE;Natale DA;Osumi-Sutherland D;Ruttenberg A;Schriml LM;Smith B;Stoeckert CJ Jr;Vasilevsky NA;Walls RL;Zheng J;Mungall CJ;Peters B
生物本体用于组织、整理和解释从生物实验中产生的大量数据。虽然这在使用单个本体时工作得很好，但集成多个本体可能会有问题，因为它们是独立开发的，这可能导致不兼容。开放生物和生物医学本体（OBO）铸造厂的创建是为了在一套总体原则的指导下，通过促进本体的开发、协调、应用和共享来解决这个问题。实现这些目标的一个挑战是，最初并没有以精确的方式编码OBO原则，并且解释是主观的。在这里，我们通过将OBO原则正式编码为操作规则，并实现一套自动验证检查和一个仪表板来客观地评估每个本体对每个原则的遵从性，来展示我们是如何解决这个问题的。这需要大量的工作来管理所有本体的元数据，并与各个涉众进行协调。我们已经在整个OBO本体套件中应用了这些检查，揭示了各个本体需要更改以符合我们原则的区域。我们的工作展示了如何根据客观标准组织和评估一个规模可观的联合社区，这些标准有助于提高总体质量和互操作性，这对于OBO项目的维持和实现使数据可查找、可访问、可互操作和可重用（FAIR）的总体目标至关重要。数据库地址http://obofoundry.org/
Biological ontologies are used to organize, curate and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies (OBO) Foundry was created to address this by facilitating the development, harmonization, application and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here, we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable, federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data Findable, Accessible, Interoperable, and Reusable (FAIR). Database URL http://obofoundry.org/
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影响因子：
46.9
作者：
Smith, Barry;Ashburner, Michael;Lewis, Suzanna
通讯作者：
Lewis, Suzanna
DOI：
10.1101/sqb.2003.68.227
发表时间：
2003-01-01
期刊：
COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY
影响因子：
--
作者：
Ashburner, M;Mungall, CJ;Lewis, SE
通讯作者：
Lewis, SE
影响因子：
4.5
作者：
Blake, Judith A.;Bult, Carol J.
通讯作者：
Bult, Carol J.
Miro：关于本体论报告的最低信息指南。
影响因子：
1.9
作者：
Matentzoglu N;Malone J;Mungall C;Stevens R
通讯作者：
Stevens R
影响因子：
9.8
作者：
Wilkinson MD;Dumontier M;Aalbersberg IJ;Appleton G;Axton M;Baak A;Blomberg N;Boiten JW;da Silva Santos LB;Bourne PE;Bouwman J;Brookes AJ;Clark T;Crosas M;Dillo I;Dumon O;Edmunds S;Evelo CT;Finkers R;Gonzalez-Beltran A;Gray AJ;Groth P;Goble C;Grethe JS;Heringa J;'t Hoen PA;Hooft R;Kuhn T;Kok R;Kok J;Lusher SJ;Martone ME;Mons A;Packer AL;Persson B;Rocca-Serra P;Roos M;van Schaik R;Sansone SA;Schultes E;Sengstag T;Slater T;Strawn G;Swertz MA;Thompson M;van der Lei J;van Mulligen E;Velterop J;Waagmeester A;Wittenburg P;Wolstencroft K;Zhao J;Mons B
通讯作者：
Mons B