Online Chemistry Nexus Proposal/Activity and effect

Proposed activity and effect on infrastructure

The proposed activity has been divided into three sections:

• technical activity, which requires a high-degree of programming skill and familiarity with the various software environments;
• technical-content activity, which requires a low-to-moderate degree of programming skill (or at least a collaboration with someone with some programming skills) or which requires specific expertise in the functioning of wikis;
• content activity, which requires a good general knowledge of chemistry and wiki markup, but little or no programming or other technical expertise.

As with any novel project, it is impossible to give an exact description of the activity that will be necessary or desirable. While the activity in an experimental project depends intimately on the experimental results obtained, the activity in developing the proposed site will necessarily depend on feedback from its users. The activity described here is intended to acheive the objectives described above.

Technical activity

Set up site, including choice and installation of appropriate pre-existing MediaWiki extensions

An ad hoc test site has already been set up at SUNY Potsdam. However it is expected that the installation will have to be reviewed in the light of the objectives of this proposal to ensure that it takes full advantage of the software tools which are already available for MediaWiki sites.

Incorporation of a Jmol extension to allow display of .mol files

A Jmol extension for MediaWiki wikis already exists. Hence this activity would first involve installing and testing this extension, and then modifying it if enhanced functionality and/or usability are deemed necessary.

Incorporation of an extension to allow searching by structure

At first, this would be a simple search on exact structure matches. However it is hoped to extend the structure searching options to include searching by molecular fragments and reaction searching, and it is expected that development of searching options will occupy a large proportion of the technical activity of the project. There are some structure searching tools in the Chemistry Development Kit (CDK), written in JavaScript and released under the Lesser General Public License (LGPL), and the free molecule editor BKChem, written in Python, also provides a basis from which to create new free software molecular structure searching tools.

Development of an extension to support (and, if possible include semi-automatically) CML markup

Chemical markup language (CML) is a dialect of XML allowing the transfer of chemical information between different software applications [REF].

Development of extensions to support and facilitate Open Laboratory Notebooks

Preparation of usage statistics and regular database dumps

Technical-content activity

Choice of supported filetypes and MediaWiki "namespaces"

Ensuring correct procedures for the labelling of contributed content with its correct copyright license

Development of automated and semi-automated methods for the validation and correction of certain content

Development of methods to ensure the machine-readability of content at the minimum effort for the contributor

Content activity

Development of a robust categorization system

Creation of portals to enable access to initial material

Selection of initial material, including creation of material where necessary

Development of a robust set of policies and guidelines

Identification of online chemistry resources

Moderation and arbitration, while maintaining a culture of openness and diversity of opinions.

Policing of vandalism and copyright violations