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Wikipedia Chemical Structure Explorer: substructure and similarity searching of molecules from Wikipedia.

Ertl P, Patiny L, Sander T, Rufener C, Zasso M - J Cheminform (2015)

Bottom Line: The web-based Wikipedia Chemical Structure Explorer provides a useful resource for research as well as for chemical education enabling both researchers and students easy and user friendly chemistry searching and identification of relevant information in Wikipedia.And last but not least this search system is a nice example of how the modern web technology can be applied in the field of cheminformatics.Graphical abstractWikipedia Chemical Structure Explorer allows substructure and similarity searches on molecules referenced in Wikipedia.

View Article: PubMed Central - PubMed

Affiliation: Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland.

ABSTRACT

Background: Wikipedia, the world's largest and most popular encyclopedia is an indispensable source of chemistry information. It contains among others also entries for over 15,000 chemicals including metabolites, drugs, agrochemicals and industrial chemicals. To provide an easy access to this wealth of information we decided to develop a substructure and similarity search tool for chemical structures referenced in Wikipedia.

Results: We extracted chemical structures from entries in Wikipedia and implemented a web system allowing structure and similarity searching on these data. The whole search as well as visualization system is written in JavaScript and therefore can run locally within a web page and does not require a central server. The Wikipedia Chemical Structure Explorer is accessible on-line at www.cheminfo.org/wikipedia and is available also as an open source project from GitHub for local installation.

Conclusions: The web-based Wikipedia Chemical Structure Explorer provides a useful resource for research as well as for chemical education enabling both researchers and students easy and user friendly chemistry searching and identification of relevant information in Wikipedia. The tool can also help to improve quality of chemical entries in Wikipedia by providing potential contributors regularly updated list of entries with problematic structures. And last but not least this search system is a nice example of how the modern web technology can be applied in the field of cheminformatics. Graphical abstractWikipedia Chemical Structure Explorer allows substructure and similarity searches on molecules referenced in Wikipedia.

No MeSH data available.


Wikipedia Chemical Structure Explorer interface.
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Fig4: Wikipedia Chemical Structure Explorer interface.

Mentions: The user interface (FigureĀ 4) consists of several modules. The JSME editor [15] in the top-left module allows to draw a query structure easily. Below is a selector for the search mode (substructure, similarity or exact match) and a text field that allows to filter the results by keeping only molecules whose names contain the entered text. Matching molecules are sorted by relevance and displayed in a table with the structure and name. Chemical structure images are generated by JavaScript code that was also derived from the OpenChemLib project [23]. First the SMILES code is converted into a chemical graph, then 2-dimensional atom coordinates are generated and bonds and atom labels are drawn esthetically optimized considering details like aromaticity and implicit hydrogens. The actual molecule display, where the molecule is rendered on a HTML5 canvas using a JavaScript library, is done by using a structure drawing package from Actelion [21]. The original Java source code has been compiled via GWT into the corresponding JavaScript files.Figure 4


Wikipedia Chemical Structure Explorer: substructure and similarity searching of molecules from Wikipedia.

Ertl P, Patiny L, Sander T, Rufener C, Zasso M - J Cheminform (2015)

Wikipedia Chemical Structure Explorer interface.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4374119&req=5

Fig4: Wikipedia Chemical Structure Explorer interface.
Mentions: The user interface (FigureĀ 4) consists of several modules. The JSME editor [15] in the top-left module allows to draw a query structure easily. Below is a selector for the search mode (substructure, similarity or exact match) and a text field that allows to filter the results by keeping only molecules whose names contain the entered text. Matching molecules are sorted by relevance and displayed in a table with the structure and name. Chemical structure images are generated by JavaScript code that was also derived from the OpenChemLib project [23]. First the SMILES code is converted into a chemical graph, then 2-dimensional atom coordinates are generated and bonds and atom labels are drawn esthetically optimized considering details like aromaticity and implicit hydrogens. The actual molecule display, where the molecule is rendered on a HTML5 canvas using a JavaScript library, is done by using a structure drawing package from Actelion [21]. The original Java source code has been compiled via GWT into the corresponding JavaScript files.Figure 4

Bottom Line: The web-based Wikipedia Chemical Structure Explorer provides a useful resource for research as well as for chemical education enabling both researchers and students easy and user friendly chemistry searching and identification of relevant information in Wikipedia.And last but not least this search system is a nice example of how the modern web technology can be applied in the field of cheminformatics.Graphical abstractWikipedia Chemical Structure Explorer allows substructure and similarity searches on molecules referenced in Wikipedia.

View Article: PubMed Central - PubMed

Affiliation: Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland.

ABSTRACT

Background: Wikipedia, the world's largest and most popular encyclopedia is an indispensable source of chemistry information. It contains among others also entries for over 15,000 chemicals including metabolites, drugs, agrochemicals and industrial chemicals. To provide an easy access to this wealth of information we decided to develop a substructure and similarity search tool for chemical structures referenced in Wikipedia.

Results: We extracted chemical structures from entries in Wikipedia and implemented a web system allowing structure and similarity searching on these data. The whole search as well as visualization system is written in JavaScript and therefore can run locally within a web page and does not require a central server. The Wikipedia Chemical Structure Explorer is accessible on-line at www.cheminfo.org/wikipedia and is available also as an open source project from GitHub for local installation.

Conclusions: The web-based Wikipedia Chemical Structure Explorer provides a useful resource for research as well as for chemical education enabling both researchers and students easy and user friendly chemistry searching and identification of relevant information in Wikipedia. The tool can also help to improve quality of chemical entries in Wikipedia by providing potential contributors regularly updated list of entries with problematic structures. And last but not least this search system is a nice example of how the modern web technology can be applied in the field of cheminformatics. Graphical abstractWikipedia Chemical Structure Explorer allows substructure and similarity searches on molecules referenced in Wikipedia.

No MeSH data available.