Online Chemistry Nexus Proposal/Suitability of methods

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Suitability of methods

The method chosen for achieving the objectives of the project is a public website in wiki format powered by MediaWiki software.

A wiki is a website which allows the simple creation of multiple interlinked webpages, usually through the use of software which automatically converts relatively simple text-like coding (stored as a database) into standard HTML (for display on the web). MediaWiki is a popular software package for the creation of wikis, available under a free license (GPLv2+). The reasons for these technical choices are explained below.

Choice of wiki format

Wikis are a relatively common choice of tool for the collaborative creation of documents. A wiki may be public or private: the best known example of a public wiki is the online encyclopedia Wikipedia, although the wiki-hosting company Wikia, Inc., hosts more than 10,000 public wikis on a vast range of subjects; private wikis are used by many organizations (eg, Novell, Inc., the Royal Society of Chemistry) to prepare documents either for purely internal use or for subsequent publication in a different format. This proposal, for example, was drafted on a private wiki.

The technical requirements to contribute to a wiki document are access to the server (usually over the Internet) and a standard web browser: it is this simplicity of contribution which makes the format so popular for collaborative editing. The use of site preferences for converting the text into HTML ensures a homogenous appearance to the site. These are significant advantages over the production of multiple web pages by separate authors using more traditional HTML editors.

The use of multiple authors, and indeed the attraction of as many different contributors as possible, is an essential part of this proposal. This should enable a wide coverage of different fields with the chemical sciences, beyond the professional expertise of the PI and the workers funded under any award. More importantly, it ensures that the focus of the site remains on those areas which are most important to its users: the wiki format allows popular areas to expand with ease while still remaining integrated with the rest of the site content.

Choice of MediaWiki software

MediaWiki is the software used by the popular online encyclopedia Wikipedia and other projects of the Wikimedia Foundation, and also on the wikis hosted by Wikia, Inc., and elsewhere. It is probably the most popular wiki software, and is certainly the best known. This in itself would be a strong argument for using MediaWiki in this project, as it is the wiki software with which potential contributors are most likely to be familiar.

MediaWiki is available free of charge under the GNU General Public License 2.0 and later versions (GPLv2+). The documentation is freely available under both the GNU Free Documentation License 1.2 and later versions (GFDL1.2+) and the Creative Commons Attribution-Share Alike License version 3.0 Unported (CC-BY-SA-3.0). As such, it is classed as “free software”. It is supported by a community of several hundred volunteer developers (at at least one salaried staff member), and has proved both robust and simple to use. The latest release is version 1.15.1 (July 13, 2009).

MediaWiki functions as a database program combined with a parser to convert a text (containing simple markup) into HTML for page publication. The database contains tables for page content, internal links, users, page categorization, images and other non-text files, and other types of page: custom page types can also be created. The appearance of the site can be customized using CSS style sheets and Javascript functions are also supported. Individual users can also customize their view of the site without affecting the public view through personal CSS style sheets and Javascript functions.

In addition to the basic MediaWiki “core”, there are more than a thousand published “extensions” to MediaWiki, written (like the original program) in the PHP programming language. These extensions add optional functions to the main program: one example is cite.php, which simplifies the handling of references.

It is intended that the programming aspect of this project will concern the writing of extensions and/or Javascript functions, rather than the modification of the main MediaWiki program. All programs which are created during the project will be licensed under the GNU General Public License version 3.0 and later versions, and the accompanying documentation will be licensed under both the GNU Free Documentation License version 1.3 and later versions and under the Creative Commons Attribution-Share Alike License version 3.0 and later versions. This condition will be enforced contractually both for employees and for any contractors. In this way, the software resulting from this project will be freely available for reuse and modification by any other person.

Choice of creating a new website

The investigators have chosen to use the same format and basic software as the popular pre-existing website Wikipedia. However, the project concerns the development of a separate website.

The proposed website will be firmly focussed on the chemical sciences in all their forms, as opposed to the unashamed generalism of Wikipedia. The intention is to create a site “by chemists, for chemists” that will be also useful to all users of chemical information regardless of professional status or specialty. Wikipedia aims to make its articles accessible to a general audience, whereas the proposed website will allow (and encourage) more technical content where the subject matter justifies it.

The proposed website will also allow the use of functionalities which are specific to chemistry. One example is searching by chemical structure: a generalist site such as Wikipedia could never justify including structure searching as an integral part of its offer, as the proportion of chemistry searches among its usage is simply too low, but a site devoted to the chemical sciences can, indeed must, offer such a possibility.

The development of specialist content and functionality is all but impossible within the Wikipedia framework, hence the need for a new site. Chemistry is not unique in having these problems – subject-specific wikis such as PsychWiki for psychology and WikiDoc for medicine have existed for several years – but the range and complexity of chemical data present particular challenges. It is hoped that the software and content developed during this project will prove useful not only to users of the site itself but also to other sites dealing with chemical information: Wikipedia, certainly, but also other chemistry websites and private wikis.