Zombie cheminformatics: extraction and conversion of Wiswesser Line Notation (WLN) from chemical documents
Zombie cheminformatics: extraction and conversion of Wiswesser Line Notation (WLN) from chemical documents
Wiswesser Line Notation (WLN) is a old line notation for encoding chemical compounds for storage and processing by computers. Whilst the notation itself has long since been surpassed by SMILES and InChI, distribution of WLN during its active years was extensive. In the context of modernising chemical data, we present a comprehensive WLN parser developed using the OpenBabel toolkit, capable of translating WLN strings into various formats supported by the library. Furthermore, we have devised a specialised Finite State Machine l, constructed from the rules of WLN, enabling the recognition and extraction of chemical strings out of large bodies of text. Available open-access WLN data with corresponding SMILES or InChI notation is rare, however ChEMBL, ChemSpider and PubChem all contain WLN records which were used for conversion scoring. Our investigation revealed a notable proportion of inaccuracies within the database entries, and we have taken steps to rectify these errors whenever feasible.
Chemical Compounds, Chemical Line Notation, SMILES, Text Parsing, WLN
Blakey, Michael
dd52ac5f-a5f5-4698-8099-712f410fa92e
Pearman-Kanza, Samantha
b73bcf34-3ff8-4691-bd09-aa657dcff420
Frey, Jeremy G.
ba60c559-c4af-44f1-87e6-ce69819bf23f
15 April 2024
Blakey, Michael
dd52ac5f-a5f5-4698-8099-712f410fa92e
Pearman-Kanza, Samantha
b73bcf34-3ff8-4691-bd09-aa657dcff420
Frey, Jeremy G.
ba60c559-c4af-44f1-87e6-ce69819bf23f
Blakey, Michael, Pearman-Kanza, Samantha and Frey, Jeremy G.
(2024)
Zombie cheminformatics: extraction and conversion of Wiswesser Line Notation (WLN) from chemical documents.
Journal of Cheminformatics, 16 (1), [42].
(doi:10.1186/s13321-024-00831-2).
Abstract
Wiswesser Line Notation (WLN) is a old line notation for encoding chemical compounds for storage and processing by computers. Whilst the notation itself has long since been surpassed by SMILES and InChI, distribution of WLN during its active years was extensive. In the context of modernising chemical data, we present a comprehensive WLN parser developed using the OpenBabel toolkit, capable of translating WLN strings into various formats supported by the library. Furthermore, we have devised a specialised Finite State Machine l, constructed from the rules of WLN, enabling the recognition and extraction of chemical strings out of large bodies of text. Available open-access WLN data with corresponding SMILES or InChI notation is rare, however ChEMBL, ChemSpider and PubChem all contain WLN records which were used for conversion scoring. Our investigation revealed a notable proportion of inaccuracies within the database entries, and we have taken steps to rectify these errors whenever feasible.
Text
Zombie_Cheminformatics___Extraction_and_Conversion_of_Wiswesser_Line_Notation__WLN__from_Chemical_Documents_Version_2
- Accepted Manuscript
Text
s13321-024-00831-2
- Version of Record
More information
Accepted/In Press date: 23 March 2024
Published date: 15 April 2024
Keywords:
Chemical Compounds, Chemical Line Notation, SMILES, Text Parsing, WLN
Identifiers
Local EPrints ID: 489426
URI: http://eprints.soton.ac.uk/id/eprint/489426
ISSN: 1758-2946
PURE UUID: 332b118c-e01c-4ca0-96bc-d20621d06059
Catalogue record
Date deposited: 24 Apr 2024 16:30
Last modified: 27 Apr 2024 02:04
Export record
Altmetrics
Contributors
Author:
Michael Blakey
Download statistics
Downloads from ePrints over the past year. Other digital versions may also be available to download e.g. from the publisher's website.
View more statistics
