Consistency of systematic chemical identifiers within and between small-molecule databases.
Consistency of systematic chemical identifiers within and between small-molecule databases.
复制标题
DOI：
10.1186/1758-2946-4-35
复制
发表时间：
2012-12-13
影响因子：
8.6
通讯作者：
Muresan S
中科院分区：
文献类型：
--
作者：
Akhondi SA;Kors JA;Muresan S
公共和商业化学数据库中结构和关联元数据的正确性极大地影响药物发现研究活动，如定量结构-性质关系建模和化合物新颖性检查。MOL文件、微笑符号、IUPAC名称和Inchi字符串是无处不在的文件格式和化学结构的系统标识符。尽管可互换用于许多化学信息学目的，但由于各种数据整合方法，包括使用不同的软件和不同的结构标准化规则，还没有关于这些结构识别符的不一致性的研究。我们调查了一些常用化学资源内部和之间的小分子系统识别符的一致性，有结构标准化和没有结构标准化。系统化学识别符与其对应的MOL表示之间的一致性在不同数据源之间差异很大(37.2%-98.5%)。我们观察到MOL-IUPAC名称的总体一致性最低。不考虑立体化学可以提高一致性(84.8%到99.9%)。通过交叉引用链接的化合物的MOL表示之间也存在很大的一致性差异(25.8%到93.7%)。去除立体化学提高了一致性(47.6%比95.6%)。我们已经表明，在数据库内和数据库之间的结构表示和系统的化学识别符方面存在相当大的不一致。这可能会产生很大的影响，特别是在合并数据时，以及如果系统标识符用作为结构集成或交叉查询多个数据库的关键索引时。从它们的MOL表示开始重新生成系统识别符，并在创建所有化合物之前对它们应用定义良好且有文档记录的化学标准化规则，可以极大地提高内部一致性。
Correctness of structures and associated metadata within public and commercial chemical databases greatly impacts drug discovery research activities such as quantitative structure–property relationships modelling and compound novelty checking. MOL files, SMILES notations, IUPAC names, and InChI strings are ubiquitous file formats and systematic identifiers for chemical structures. While interchangeable for many cheminformatics purposes there have been no studies on the inconsistency of these structure identifiers due to various approaches for data integration, including the use of different software and different rules for structure standardisation. We have investigated the consistency of systematic identifiers of small molecules within and between some of the commonly used chemical resources, with and without structure standardisation. The consistency between systematic chemical identifiers and their corresponding MOL representation varies greatly between data sources (37.2%-98.5%). We observed the lowest overall consistency for MOL-IUPAC names. Disregarding stereochemistry increases the consistency (84.8% to 99.9%). A wide variation in consistency also exists between MOL representations of compounds linked via cross-references (25.8% to 93.7%). Removing stereochemistry improved the consistency (47.6% to 95.6%). We have shown that considerable inconsistency exists in structural representation and systematic chemical identifiers within and between databases. This can have a great influence especially when merging data and if systematic identifiers are used as a key index for structure integration or cross-querying several databases. Regenerating systematic identifiers starting from their MOL representation and applying well-defined and documented chemistry standardisation rules to all compounds prior to creating them can dramatically increase internal consistency.
登录
查看更多内容
影响因子：
14.9
作者：
Wishart DS;Knox C;Guo AC;Eisner R;Young N;Gautam B;Hau DD;Psychogios N;Dong E;Bouatra S;Mandal R;Sinelnikov I;Xia J;Jia L;Cruz JA;Lim E;Sobsey CA;Shrivastava S;Huang P;Liu P;Fang L;Peng J;Fradette R;Cheng D;Tzur D;Clements M;Lewis A;De Souza A;Zuniga A;Dawe M;Xiong Y;Clive D;Greiner R;Nazyrova A;Shaykhutdinov R;Li L;Vogel HJ;Forsythe I
通讯作者：
Forsythe I
DOI：
10.1007/978-1-61779-965-5_8
发表时间：
2012-01-01
期刊：
Methods in molecular biology (Clifton, N.J.)
影响因子：
--
作者：
Muresan, Sorel;Sitzmann, Markus;Southan, Christopher
通讯作者：
Southan, Christopher
影响因子：
5.6
作者：
Fourches D;Muratov E;Tropsha A
通讯作者：
Tropsha A
影响因子：
8.6
作者：
O'Boyle NM
通讯作者：
O'Boyle NM
影响因子：
8.6
作者：
Martin, Elyette;Monge, Aurelien;Pospisil, Pavel
通讯作者：
Pospisil, Pavel