Department of Computer Science, University of Toronto, Toronto, Ontario M5G 1L7, Canada.
Nucleic Acids Res. 2012 Jan;40(Database issue):D428-33. doi: 10.1093/nar/gkr919. Epub 2011 Nov 8.
The patent literature is a rich catalog of biologically relevant chemicals; many public and commercial molecular databases contain the structures disclosed in patent claims. However, patents are an equally rich source of metadata about bioactive molecules, including mechanism of action, disease class, homologous experimental series, structural alternatives, or the synthetic pathways used to produce molecules of interest. Unfortunately, this metadata is discarded when chemical structures are deposited separately in databases. SCRIPDB is a chemical structure database designed to make this metadata accessible. SCRIPDB provides the full original patent text, reactions and relationships described within any individual patent, in addition to the molecular files common to structural databases. We discuss how such information is valuable in medical text mining, chemical image analysis, reaction extraction and in silico pharmaceutical lead optimization. SCRIPDB may be searched by exact chemical structure, substructure or molecular similarity and the results may be restricted to patents describing synthetic routes. SCRIPDB is available at http://dcv.uhnres.utoronto.ca/SCRIPDB.
专利文献是生物相关化学物质的丰富目录；许多公共和商业分子数据库都包含专利权利要求中披露的结构。然而，专利也是关于生物活性分子的元数据的丰富来源，包括作用机制、疾病类别、同源实验系列、结构替代品或用于生产感兴趣分子的合成途径。不幸的是，当化学结构分别存储在数据库中时，此元数据会被丢弃。SCRIPDB 是一个化学结构数据库，旨在提供对这些元数据的访问。SCRIPDB 提供了完整的原始专利文本、任何单个专利中描述的反应和关系，以及结构数据库中常见的分子文件。我们讨论了此类信息在医学文本挖掘、化学图像分析、反应提取和药物虚拟先导优化中的价值。可以通过精确的化学结构、子结构或分子相似性搜索 SCRIPDB，并且结果可以限制为描述合成路线的专利。SCRIPDB 可在 http://dcv.uhnres.utoronto.ca/SCRIPDB 上获得。
