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

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          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 abstract

          Wikipedia Chemical Structure Explorer allows substructure and similarity searches on molecules referenced in Wikipedia.

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          Most cited references6

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          JSME: a free molecule editor in JavaScript

          Bruno Bienfait, Peter Ertl (2013)
          Background A molecule editor, i.e. a program facilitating graphical input and interactive editing of molecules, is an indispensable part of every cheminformatics or molecular processing system. Today, when a web browser has become the universal scientific user interface, a tool to edit molecules directly within the web browser is essential. One of the most popular tools for molecular structure input on the web is the JME applet. Since its release nearly 15 years ago, however the web environment has changed and Java applets are facing increasing implementation hurdles due to their maintenance and support requirements, as well as security issues. This prompted us to update the JME editor and port it to a modern Internet programming language - JavaScript. Summary The actual molecule editing Java code of the JME editor was translated into JavaScript with help of the Google Web Toolkit compiler and a custom library that emulates a subset of the GUI features of the Java runtime environment. In this process, the editor was enhanced by additional functionalities including a substituent menu, copy/paste, drag and drop and undo/redo capabilities and an integrated help. In addition to desktop computers, the editor supports molecule editing on touch devices, including iPhone, iPad and Android phones and tablets. In analogy to JME the new editor is named JSME. This new molecule editor is compact, easy to use and easy to incorporate into web pages. Conclusions A free molecule editor written in JavaScript was developed and is released under the terms of permissive BSD license. The editor is compatible with JME, has practically the same user interface as well as the web application programming interface. The JSME editor is available for download from the project web page http://peter-ertl.com/jsme/
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            JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied toProteopedia

            Robert Hanson, Jaime Prilusky, Zhou Renjian … (2013)
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              The Molecule Cloud - compact visualization of large collections of molecules

              Peter Ertl, Bernhard Rohde (2012)
              Background Analysis and visualization of large collections of molecules is one of the most frequent challenges cheminformatics experts in pharmaceutical industry are facing. Various sophisticated methods are available to perform this task, including clustering, dimensionality reduction or scaffold frequency analysis. In any case, however, viewing and analyzing large tables with molecular structures is necessary. We present a new visualization technique, providing basic information about the composition of molecular data sets at a single glance. Summary A method is presented here allowing visual representation of the most common structural features of chemical databases in a form of a cloud diagram. The frequency of molecules containing particular substructure is indicated by the size of respective structural image. The method is useful to quickly perceive the most prominent structural features present in the data set. This approach was inspired by popular word cloud diagrams that are used to visualize textual information in a compact form. Therefore we call this approach “Molecule Cloud”. The method also supports visualization of additional information, for example biological activity of molecules containing this scaffold or the protein target class typical for particular scaffolds, by color coding. Detailed description of the algorithm is provided, allowing easy implementation of the method by any cheminformatics toolkit. The layout algorithm is available as open source Java code. Conclusions Visualization of large molecular data sets using the Molecule Cloud approach allows scientists to get information about the composition of molecular databases and their most frequent structural features easily. The method may be used in the areas where analysis of large molecular collections is needed, for example processing of high throughput screening results, virtual screening or compound purchasing. Several example visualizations of large data sets, including PubChem, ChEMBL and ZINC databases using the Molecule Cloud diagrams are provided.
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                Author and article information

                Contributors
                Peter Ertl: peter.ertl@novartis.com
                Luc Patiny: luc.patiny@epfl.ch
                Thomas Sander: thomas.sander@actelion.com
                Christian Rufener: christian.rufener@actelion.com
                Michaël Zasso: michael.zasso@epfl.ch
                Journal
                Journal ID (nlm-ta): J Cheminform
                Journal ID (iso-abbrev): J Cheminform
                Title: Journal of Cheminformatics
                Publisher: Springer International Publishing (Cham )
                ISSN (Electronic): 1758-2946
                Publication date (Electronic): 22 March 2015
                Publication date PMC-release: 22 March 2015
                Publication date Collection: 2015
                Volume: 7
                Electronic Location Identifier: 10
                Affiliations
                [ ]Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
                [ ]Ecole Polytechnique Fédérale de Lausanne (EPFL), Institute of Chemical Sciences and Engineering (ISIC), 1015 Lausanne, Switzerland
                [ ]Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
                Article
                Publisher ID: 61
                DOI: 10.1186/s13321-015-0061-y
                PMC ID: 4374119
                PubMed ID: 25815062
                SO-VID: 6ab44a73-da0a-4607-beab-d81503f1faa2
                Copyright statement: © Ertl et al.; licensee Springer. 2015
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.

                History
                Date received : 3 February 2015
                Date accepted : 5 March 2015
                Categories
                Subject: Software
                Custom metadata
                issue-copyright-statement © The Author(s) 2015

                ScienceOpen disciplines: Chemoinformatics
                Keywords: wikipedia,smiles,substructure search,similarity search,chemical database,javascript
                Data availability:
                ScienceOpen disciplines: Chemoinformatics
                Keywords: wikipedia, smiles, substructure search, similarity search, chemical database, javascript

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