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ChemScanner: extraction and re-use(ability) of chemical information from common scientific documents containing ChemDraw files
Journal of Cheminformatics ( IF 8.6 ) Pub Date : 2019-12-11 , DOI: 10.1186/s13321-019-0400-5
An Nguyen , Yu-Chieh Huang , Pierre Tremouilhac , Nicole Jung , Stefan Bräse

We developed ChemScanner, a software that can be used for the extraction of chemical information from ChemDraw binary (CDX) or ChemDraw XML-based (CDXML) files and to retrieve the ChemDraw scheme from DOC, DOCX or XML documents. This can facilitate the reuse of chemical information embedded into diverse documents used as standard storage and communication instrument in chemical sciences (e.g. for student’s theses, PhD theses, or publications). The extracted information is processed to reactions, molecules, as well as additional text and values and can be accessed via the ChemScanner UI. ChemScanner supports the export to Excel and CML, the direct import of the extracted data to the Open Source ELN Chemotion or the use via “copy and paste” of selected information. The software was designed with a focus on the processing of documents with embedded molecular structure information as CDX or CDXML as these are the most common file formats for chemical drawings. The project aims to support the chemists in their efforts to re-use chemistry research data by providing them missing tools for an automated assembly of reaction data.

中文翻译:

ç下摆小号罐头制造商:提取和再利用从包含文件的ChemDraw共同的科学文献化学信息(能力)

我们开发了ChemScanner,该软件可用于从ChemDraw二进制(CDX)或基于ChemDraw XML(CDXML)的文件中提取化学信息,并从DOC,DOCX或XML文档中检索ChemDraw方案。这可以促进化学信息的重复利用,这些化学信息嵌入了各种文档中,这些文档用作化学科学中的标准存储和通讯工具(例如,用于学生论文,博士学位论文或出版物)。提取的信息将处理为反应,分子以及其他文本和值,并可通过ChemScanner UI进行访问。ChemScanner支持导出到Excel和CML,将提取的数据直接导入到开源ELN Chemotion或通过“复制和粘贴”所选信息来使用。该软件的设计重点是处理具有嵌入式分子结构信息的文档,如CDX或CDXML,因为这些是化学制图的最常见文件格式。该项目旨在通过为化学家提供缺少的用于自动组装反应数据的工具,来支持他们进行化学研究数据的重用。
更新日期:2019-12-11
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