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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.


The 250 most common scaffolds of molecules from Wikipedia presented as a Molecule Cloud diagram [11] documenting diversity of entries.
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Fig3: The 250 most common scaffolds of molecules from Wikipedia presented as a Molecule Cloud diagram [11] documenting diversity of entries.

Mentions: After final processing the database of SMILES codes of Wikipedia molecules contained 13,072 entries. To document diversity of this molecule collection the 250 most frequent scaffolds present in this set are shown in Figure 3 in form of a Molecule Cloud diagram [11]. The size of the scaffold image is proportional to the number of molecules containing this scaffold, ranging from the largest benzene (there are 1116 entries for benzene derivatives in Wikipedia) down to the smallest images representing 5 Wikipedia entries. The 250 scaffolds displayed in the Figure 3 represent together 4294 Wikipedia molecules. Although detailed analysis of Wikipedia chemical content is out of scope of this communication, it is interesting to compare at least briefly the Wikipedia scaffolds with those present in the common synthetic molecules and bioactive molecules (Figures four and five in ref. [11]). In Wikipedia one can see clear preference for more complex structures, like structures of natural products, steroids or cores of common drugs. This is, of course, nothing surprising, because the Wikipedia chemical entries are created subjectively based on the usefulness and application area of the respective molecules.Figure 3


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)

The 250 most common scaffolds of molecules from Wikipedia presented as a Molecule Cloud diagram [11] documenting diversity of entries.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig3: The 250 most common scaffolds of molecules from Wikipedia presented as a Molecule Cloud diagram [11] documenting diversity of entries.
Mentions: After final processing the database of SMILES codes of Wikipedia molecules contained 13,072 entries. To document diversity of this molecule collection the 250 most frequent scaffolds present in this set are shown in Figure 3 in form of a Molecule Cloud diagram [11]. The size of the scaffold image is proportional to the number of molecules containing this scaffold, ranging from the largest benzene (there are 1116 entries for benzene derivatives in Wikipedia) down to the smallest images representing 5 Wikipedia entries. The 250 scaffolds displayed in the Figure 3 represent together 4294 Wikipedia molecules. Although detailed analysis of Wikipedia chemical content is out of scope of this communication, it is interesting to compare at least briefly the Wikipedia scaffolds with those present in the common synthetic molecules and bioactive molecules (Figures four and five in ref. [11]). In Wikipedia one can see clear preference for more complex structures, like structures of natural products, steroids or cores of common drugs. This is, of course, nothing surprising, because the Wikipedia chemical entries are created subjectively based on the usefulness and application area of the respective molecules.Figure 3

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.