On-Line Substructure Searching Utilizing Wiswesser Line Notations

Tomea, Albert V.; Sorter, Peter F.

doi:10.1021/ci60008a008

Cited by 2 publications

(2 citation statements)

References 2 publications

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“…Wiswesser Line Notation (WLN) [ 14 ] is one such line notation that predated SMILES, and saw widespread use amongst chemists and early cheminformatics software during its active years. Early look up systems such as the Index Chemicus Registry System (ICRS) [ 15 ] and the CROSSBOW software package [ 16 ] gave access to large chemical queries, and algorithms using WLN allowed for early substructure searching [ 17 ]. While the notation adheres to strict mathematical principles, the WLN language is conveyed through a set of verbose written English rules.…”

Section: Introductionmentioning

confidence: 99%

Zombie cheminformatics: extraction and conversion of Wiswesser Line Notation (WLN) from chemical documents

Blakey,

Pearman-Kanza,

Frey

2024

J Cheminform

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Purpose 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. Scientific contribution Tools for both the extraction and conversion of WLN from chemical documents have been successfully developed. Both the Deterministic Finite Automaton (DFA) and parser handle the majority of WLN rules officially endorsed in the three major WLN manuals, with the parser showing a clear jump in accuracy and chemical coverage over previous submissions. The GitHub repository can be found here: https://github.com/Mblakey/wiswesser.

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Section: Introductionmentioning

confidence: 99%

Zombie cheminformatics: extraction and conversion of Wiswesser Line Notation (WLN) from chemical documents

Blakey,

Pearman-Kanza,

Frey

2024

J Cheminform

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“…An example is the on-line substructure search used internally at Hoffmann-La Roche. 49 The use of rotated indexes at Hoffman-La Roche was replaced by a system that, in either on-line or batch mode, expands WLN notations containing contractions and converts them into atom-bond connection tables that are searched by a series of set reductions.…”

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confidence: 99%

Chemical substructure searching

Stobaugh¹

1985

J. Chem. Inf. Comput. Sci.

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On-Line Substructure Searching Utilizing Wiswesser Line Notations

Cited by 2 publications

References 2 publications

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

Chemical substructure searching

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