Department of Cheminformatics and Metabolism, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK.
Nucleic Acids Res. 2013 Jan;41(Database issue):D456-63. doi: 10.1093/nar/gks1146. Epub 2012 Nov 24.
ChEBI (http://www.ebi.ac.uk/chebi) is a database and ontology of chemical entities of biological interest. Over the past few years, ChEBI has continued to grow steadily in content, and has added several new features. In addition to incorporating all user-requested compounds, our annotation efforts have emphasized immunology, natural products and metabolites in many species. All database entries are now 'is_a' classified within the ontology, meaning that all of the chemicals are available to semantic reasoning tools that harness the classification hierarchy. We have completely aligned the ontology with the Open Biomedical Ontologies (OBO) Foundry-recommended upper level Basic Formal Ontology. Furthermore, we have aligned our chemical classification with the classification of chemical-involving processes in the Gene Ontology (GO), and as a result of this effort, the majority of chemical-involving processes in GO are now defined in terms of the ChEBI entities that participate in them. This effort necessitated incorporating many additional biologically relevant compounds. We have incorporated additional data types including reference citations, and the species and component for metabolites. Finally, our website and web services have had several enhancements, most notably the provision of a dynamic new interactive graph-based ontology visualization.
ChEBI（http://www.ebi.ac.uk/chebi）是一个具有生物学意义的化学实体数据库和本体。在过去的几年中，ChEBI 的内容持续稳定增长，并增加了几个新功能。除了包含所有用户请求的化合物外，我们的注释工作还强调了免疫学、天然产物和许多物种的代谢物。现在，所有数据库条目都在本体中被“is_a”分类，这意味着所有的化学物质都可以被利用分类层次结构的语义推理工具使用。我们已经将本体与开放生物医学本体（OBO）基金会推荐的上层基本形式本体完全对齐。此外，我们还将我们的化学分类与基因本体（GO）中涉及化学的过程分类对齐，由于这一努力，GO 中现在大多数涉及化学的过程都是根据参与其中的 ChEBI 实体来定义的。这一努力需要纳入许多其他具有生物学意义的化合物。我们已经纳入了其他数据类型，包括参考文献和代谢物的物种和成分。最后，我们的网站和网络服务进行了几次增强，最显著的是提供了一个新的动态交互式基于图形的本体可视化。
