Prediction and curation of missing biomedical identifier mappings with Biomappings.
Prediction and curation of missing biomedical identifier mappings with Biomappings.
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DOI：
10.1093/bioinformatics/btad130
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发表时间：
2023-04-03
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--
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生物医学标识符资源（如本体、分类法和受控词汇表）通常在范围上重叠，并在不同标识符下包含等效条目。维护这些条目之间的映射对于数据和知识的互操作性和集成至关重要。然而，在可用的映射中存在着大量的差距，这些差距激发了它们的半自动化策展。Biomappings为缺失的映射实现了一个策展工作流程，该工作流程将自动预测与人在环策展相结合。它支持多种预测方法，并提供了一个基于Web的用户界面，用于检查预测映射的正确性，并结合自动一致性检查。预测和策划的映射在GitHub上的公共、版本控制的资源文件中提供。Biomappings目前提供了9274个策划映射和40691个预测映射，提供了广泛使用的标识符资源之间的映射，涵盖小分子，细胞系，疾病和其他概念。我们证明了Biomappings在案例研究中的价值，这些案例研究涉及预测和管理癌细胞系以及临床试验中测试的小分子之间的缺失映射。我们还介绍了以前使用Biomappings策划的缺失映射如何被贡献回多个广泛使用的社区本体。这些数据和代码可以在https://github.com/biopragmatics/biomappings的CC0和MIT许可证下获得。
Biomedical identifier resources (such as ontologies, taxonomies, and controlled vocabularies) commonly overlap in scope and contain equivalent entries under different identifiers. Maintaining mappings between these entries is crucial for interoperability and the integration of data and knowledge. However, there are substantial gaps in available mappings motivating their semi-automated curation. Biomappings implements a curation workflow for missing mappings which combines automated prediction with human-in-the-loop curation. It supports multiple prediction approaches and provides a web-based user interface for reviewing predicted mappings for correctness, combined with automated consistency checking. Predicted and curated mappings are made available in public, version-controlled resource files on GitHub. Biomappings currently makes available 9274 curated mappings and 40 691 predicted ones, providing previously missing mappings between widely used identifier resources covering small molecules, cell lines, diseases, and other concepts. We demonstrate the value of Biomappings on case studies involving predicting and curating missing mappings among cancer cell lines as well as small molecules tested in clinical trials. We also present how previously missing mappings curated using Biomappings were contributed back to multiple widely used community ontologies. The data and code are available under the CC0 and MIT licenses at https://github.com/biopragmatics/biomappings.
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影响因子：
4.3
作者：
Ramsey J;McIntosh B;Renfro D;Aleksander SA;LaBonte S;Ross C;Zweifel AE;Liles N;Farrar S;Gill JJ;Erill I;Ades S;Berardini TZ;Bennett JA;Brady S;Britton R;Carbon S;Caruso SM;Clements D;Dalia R;Defelice M;Doyle EL;Friedberg I;Gurney SMR;Hughes L;Johnson A;Kowalski JM;Li D;Lovering RC;Mans TL;McCarthy F;Moore SD;Murphy R;Paustian TD;Perdue S;Peterson CN;Prüß BM;Saha MS;Sheehy RR;Tansey JT;Temple L;Thorman AW;Trevino S;Vollmer AC;Walbot V;Willey J;Siegele DA;Hu JC
通讯作者：
Hu JC
影响因子：
64.8
作者：
Ghandi, Mahmoud;Huang, Franklin W.;Sellers, William R.
通讯作者：
Sellers, William R.
DOI：
10.1093/bioinformatics/btac491
发表时间：
2022-09-02
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
通讯作者：
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影响因子：
14.9
作者：
Gaulton A;Hersey A;Nowotka M;Bento AP;Chambers J;Mendez D;Mutowo P;Atkinson F;Bellis LJ;Cibrián-Uhalte E;Davies M;Dedman N;Karlsson A;Magariños MP;Overington JP;Papadatos G;Smit I;Leach AR
通讯作者：
Leach AR
Gilda：通过机器学习消歧服务实现生物医学实体文本规范化。
DOI：
10.1093/bioadv/vbac034
发表时间：
2022
期刊：
BIOINFORMATICS ADVANCES
影响因子：
--
作者：
Gyori, Benjamin M.;Hoyt, Charles Tapley;Steppi, Albert
通讯作者：
Steppi, Albert