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尸化学信息学:从化学文档中提取和转换Wiswesser线标记 (WLN)

Michael Blakey¹, Samantha Pearman-Kanza², Jeremy G Frey²

¹Department of Chemistry, University of Southampton, University Road, Southampton, Hampshire, SO17 1BJ, UK. M.Blakey@soton.ac.uk.

Journal of cheminformatics

|April 15, 2024

概括

我们开发了一个Wiswesser Line Notation (WLN) 解析器和有限态机来转换和提取化学数据. 该工具通过提高遗留WLN记录的准确性和覆盖范围来实现化学数据的现代化.

科学领域:

计算化学是一种计算化学.
化学信息学化学信息学

背景情况:

威斯韦塞线符号 (Wiswesser Line Notation,简称WLN) 是一种较旧的化学符号系统.
化学数据的现代化需要工具来处理像WLN这样的遗留格式.
现有的WLN数据往往不准确,缺乏现代等价值 (SMILES,InChI).

研究的目的:

使用OpenBabel工具包开发一个针对Wiswesser Line Notation (WLN) 的综合解析器.
创建一个专门的有限状态机器 (FSM) 来识别和从文本中提取WLN字符串.
为了解决现有的WLN数据库条目中的不准确性,并提高数据质量.

主要方法:

开发一个利用OpenBabel工具包进行格式转换的WLN解析器.
基于WLN字符串识别规则的确定性有限自动机 (DFA) 的构建.
使用来自ChEMBL,ChemSpider和PubChem的数据进行转换得分和错误纠正.

主要成果:

成功开发了用于WLN提取和转换的工具.
与以前的方法相比,解析器显示了更好的准确性和化学覆盖率.
识别和纠正WLN数据库条目中的不准确性.

结论:

开发的WLN解析器和DFA有效地处理了大多数WLN规则.
这些工具有助于化学数据的现代化,使遗留的WLN信息能够更好地处理.
该项目为WLN数据处理和纠正提供了一个开放式访问解决方案.

关键词:

化学化合物是一种化学化合物.化学线条表示化学线条表示斯米莱斯 (SMILES) 是一个有趣的小孩.文本解析文本解析在WLN中使用.

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