SPONSOR’S SPOTLIGHT: ChemSpider

ChemSpider (www.chemspider.com) was developed with the intention of aggregating and indexing available sources of chemical structures and their associated information into a single searchable repository and making it available to everybody, at no charge.

One of the initial concepts for ChemSpider was to aggregate into a single database all chemical structures available within open access and commercial databases, and to provide the necessary pointers from the ChemSpider search engine to the information of interest. The ChemSpider database has now indexed over 20 million unique chemical compounds and hosts data from almost 100 different data sources (and growing). These data sources include chemical vendors, chemistry database vendors, online chemistry resources, blog postings, Wikipedia, online patent services, Open Access publishers, Open Notebook Science projects and user submissions.

ChemSpider is a free Open Access website for chemists. The site provides access to almost 20 million individual chemical structures and their related properties from almost 100 different data sources and suppliers. The system can be used for the purpose of:

• Converting chemical names to chemical structures
• Flexible text and structure-based searching to facilitate structure identification
• Text-based searching of over 150,000 Open Access chemistry articles including integrated Entrez searching
• Structure/substructure based searching of US and European patents
• Structure and spectra deposition to share data with the chemistry community
• Support of both personal, group and community Open Notebook Science
• Prediction of physicochemical properties such as logP and Lipinski Rule of 5

ChemSpider continues to grow in its reach into the chemistry community with a number of specific missions.

1. Improving the quality of available information

   ChemSpider has enabled a community-based curation process to help identify errors in the data and improve the quality of available information. This ‘crowd-sourced’ approach to data cleansing has already removed many tens of thousands of incorrect identifiers associated with chemical structures and has resulted in the deposition of hundreds of spectra to the database to provide a free access spectral library database.

2. Increased access to chemistry-related information

   There are many types of data and information which can be associated with chemical compounds and made available to the benefit of the chemistry community. As an example of this the association of analytical data, the integration to patent searches and to QSAR-based modelling has been enabled.

3. Provide access to online tools and service

   ChemSpider enables online prediction of certain chemical properties. Web services such as the recently exposed InChI and OpenBabel services will continue to expand in number.

ChemSpider will continue remain true to its initial vision – to build a structure-centric community for chemists. We will continue to demonstrate the potential of the semantic web by forming virtual online connections and real-life necessary relationships to help build a chemical structure community for chemists.

ChemSpider encourages groups and individuals who are interested in making their data available to contact them directly. This includes for the purpose of business generation by exposing a subset of information and directing chemists to your website for further commercial activities.

ChemSpider celebrated its first anniversary in March 2008 and currently averages over 4000 unique visitors per day. The possibilities of the semantic web are being delivered.

ChemBioOffice Workgroup 2008

The ChemBioOffice Workgroup 2008 suite from CambridgeSoft is ideal for smaller organisations or groups that want to organise and search over their inventory, purchase reagents, and manipulate and store chemical and biological data in a collaborative fashion.

ChemBioOffice Workgroup Pro 2008 is comprised of BioAssay Workgroup 11.0, Inventory Workgroup 11.0, and E-Notebook Workgroup 11.0. These applications offer much of the functionality delivered in ChemOffice Enterprise, while using Microsoft SQL Server as the database (instead of Oracle as the enterprise applications use).

ChemBioOffice Workgroup Ultra 2008 adds CambridgeSoft’s complete suite of desktop applications to the workgroup applications. ChemBioDraw provides structural drawing, analysis and querying for chemists, and offers biologists tools for drawing and annotating biological pathways. ChemBio3D affords molecular modelling and graphical visualisation of small molecules and proteins. ChemBioViz with ChemFinder gives users a chemically intelligent database tools and provides visualisation tools to correlate chemical data with biological activity. Also included is ChemBioScript, a Python extension language from CambridgeSoft which provides a set of classes and methods for working with atoms, bonds, and the other properties of molecules, reactions, and 3D models.

More details can be found at http://www.cambridgesoft.com.

Topomer Search and Topomer CoMFA

Tripos International has announced the availability of integrated versions of its recently patented Topomer Search and Topomer CoMFA technologies. These Topomer technologies accelerate the speed and enhance the accuracy of predicting the biological activity and properties of compounds, and enable researchers to search vast numbers of compounds rapidly (1 million compounds overnight).

Topomers fundamentally characterise the shapes of organic compounds, and emphasise consistency over reproducing experimental or low energy geometries. The idea behind Topomer generation is that similar chemical connectivity will yield similar shapes. Structures with similar shapes based on Topomer similarity are more likely to have similar biological properties.

Scientists can create quantitative, predictive 3D QSAR models in Topomer CoMFA and use Topomer Search to identify new substituents and R-groups, which are predicted to improve biological activity and have already been synthetically realised in their corporate collection. Enhancements are planned for both Topomer Search and Topomer CoMFA later in 2008. Tripos also plans to release a new informatics system based on the Topomers technology that allows chemists to consider simultaneously synthetic cost as well as therapeutic benefit during lead discovery and optimisation decisions.

More information is available at http://www.tripos.com/.

SciTegic Pipeline Pilot new releases

Accerlys has released three new component collections for SciTegic Pipeline Pilot. The new collections feature functionality in the areas of advanced image analysis, chemical mining and gene expression.

The Advanced Imaging Collection brings SciTegic Pipeline Pilot’s data integration capabilities to research and development workflows enabling learning, clustering, modelling, statistical analysis, reporting and archiving of images, video and associated data. Template protocols allow rapid development of custom applications such as drill-down reporting and image link capabilities.

The ChemMining Collection allows scientists to mine and analyse the world’s patent literature and find opportunities for new drug candidates. The Collection facilitates the creation of flexible workflows that search text documents to find chemical names, convert them to live structures, and create a searchable chemical database.

The Gene Expression Collection helps researchers to identify potential drug targets and biomarker candidates. Scientists can process, analyse, explore and report on gene expression experiments. Robust and flexible BioConductor-based workflows deliver automation and web-based bioinformatics solutions that allow increased productivity in research laboratories.

More details can be found at http://accelrys.com/products/scitegic/.

SciFinder via the Web

CAS is launching a web version of SciFinder in phases throughout 2008. This new platform is especially designed for the Web and does not simply duplicate the look and feel of the current SciFinder product. The newest SciFinder experience will be offered to commercial, government and academic users as the product launch proceeds.

More information can be found at http://www.cas.org/products/scifindr/sfweb/index.html.

STN Express, Version 8.3

Now available for Windows, this new version includes several important updates. The Select Discover! Wizard window has been redesigned to provide greater utility and better visibility of the search session. The search history window now displays the search strategy and the L-number of the items retrieved. The Search and Results wizards are now accessible within tabbed menus with an option to Hide or Show the tabbed menus. A new wizard in Version 8.3 creates a fully-functional L-number from a saved STN AnaVist answer set (.xta file format). In addition to searching, the L-number can be used to display answers from STN AnaVist in any format, and move full-text patent documents from STN AnaVist to STN Viewer via the Evaluate with STN Viewer wizard.

More details are to be found at http://www.cas.org/support/stngen/stnews/takenote/expressv83.html.