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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.


An example of a Chembox in Wiki markup format.
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Fig2: An example of a Chembox in Wiki markup format.

Mentions: Among other chemical content Wikipedia contains numerous entries describing specific chemicals. Such entries are using a special chemical template [3], either an “Infobox drug” (also called Drugbox) used for drugs or a Chembox used for other chemicals. These chemical templates (also called infoboxes) are pieces of Wikipedia markup embedded into chemistry pages that contain the most important information about molecules, allowing to present chemical data in a standardized way and support also computer mining of the data. The templates have a modular design. After general information including chemical name and structure depiction, possibly also a 3D molecule image, SMILES code [4] and links to other chemical databases like PubChem [5] or ChEMBL [6] these boxes often contain also other data like physicochemical and pharmacological properties, information about chemical hazard and so on. They can be built from multiple sections, each covering a group of information. Depending on the compound, sections can be added or left out, and within a section parameters can be added or omitted. An example of Wikipedia page with a Chembox is shown in Figure 1 and its encoding in Wiki markup in Figure 2.Figure 1


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)

An example of a Chembox in Wiki markup format.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig2: An example of a Chembox in Wiki markup format.
Mentions: Among other chemical content Wikipedia contains numerous entries describing specific chemicals. Such entries are using a special chemical template [3], either an “Infobox drug” (also called Drugbox) used for drugs or a Chembox used for other chemicals. These chemical templates (also called infoboxes) are pieces of Wikipedia markup embedded into chemistry pages that contain the most important information about molecules, allowing to present chemical data in a standardized way and support also computer mining of the data. The templates have a modular design. After general information including chemical name and structure depiction, possibly also a 3D molecule image, SMILES code [4] and links to other chemical databases like PubChem [5] or ChEMBL [6] these boxes often contain also other data like physicochemical and pharmacological properties, information about chemical hazard and so on. They can be built from multiple sections, each covering a group of information. Depending on the compound, sections can be added or left out, and within a section parameters can be added or omitted. An example of Wikipedia page with a Chembox is shown in Figure 1 and its encoding in Wiki markup in Figure 2.Figure 1

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.