Cargando…

Consistency of systematic chemical identifiers within and between small-molecule databases

BACKGROUND: 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, an...

Descripción completa

Detalles Bibliográficos
Autores principales: Akhondi, Saber A, Kors, Jan A, Muresan, Sorel
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3539895/
https://www.ncbi.nlm.nih.gov/pubmed/23237381
http://dx.doi.org/10.1186/1758-2946-4-35
_version_ 1782255159459446784
author Akhondi, Saber A
Kors, Jan A
Muresan, Sorel
author_facet Akhondi, Saber A
Kors, Jan A
Muresan, Sorel
author_sort Akhondi, Saber A
collection PubMed
description BACKGROUND: 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. RESULTS: 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%). CONCLUSIONS: 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.
format Online
Article
Text
id pubmed-3539895
institution National Center for Biotechnology Information
language English
publishDate 2012
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-35398952013-01-10 Consistency of systematic chemical identifiers within and between small-molecule databases Akhondi, Saber A Kors, Jan A Muresan, Sorel J Cheminform Research Article BACKGROUND: 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. RESULTS: 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%). CONCLUSIONS: 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. BioMed Central 2012-12-13 /pmc/articles/PMC3539895/ /pubmed/23237381 http://dx.doi.org/10.1186/1758-2946-4-35 Text en Copyright ©2012 Akhondi et al.; licensee Chemistry Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Akhondi, Saber A
Kors, Jan A
Muresan, Sorel
Consistency of systematic chemical identifiers within and between small-molecule databases
title Consistency of systematic chemical identifiers within and between small-molecule databases
title_full Consistency of systematic chemical identifiers within and between small-molecule databases
title_fullStr Consistency of systematic chemical identifiers within and between small-molecule databases
title_full_unstemmed Consistency of systematic chemical identifiers within and between small-molecule databases
title_short Consistency of systematic chemical identifiers within and between small-molecule databases
title_sort consistency of systematic chemical identifiers within and between small-molecule databases
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3539895/
https://www.ncbi.nlm.nih.gov/pubmed/23237381
http://dx.doi.org/10.1186/1758-2946-4-35
work_keys_str_mv AT akhondisabera consistencyofsystematicchemicalidentifierswithinandbetweensmallmoleculedatabases
AT korsjana consistencyofsystematicchemicalidentifierswithinandbetweensmallmoleculedatabases
AT muresansorel consistencyofsystematicchemicalidentifierswithinandbetweensmallmoleculedatabases