Archive for the Open PHACTS Category

As the ChemSpider content and data mappings have continued to expand, the demands on our web services have increased dramatically. With the popularity of the site continuing to increase we anticipate even heavier usage of our web services. This is true for our involvement with the Open PHACTS project as well as from a number of software packages served up by analytical instrument vendors, especially in the mass spectrometry domain. Because of the increasing load on our systems, we have taken steps to prevent us from outgrowing our existing infrastructure and have implemented a new scalable, future-proof web services offering that your applications can rely upon.

Continual availability and business continuity for subscribers and academics

We have reinvented our web service infrastructure using Microsoft SQL Server replication technology in order to maintain multiple copies of the ChemSpider database. As a result all system resources are dedicated purely to web services with no background tasks running to affect the performance. Also, the databases are read-only which results in database lock contention being completely eliminated.

A standalone and scalable web service establishment for faster response times

The ChemSpider servers run on the VMWare virtualization platform which allows us to scale out the hardware by assigning more resources as required. In the future we can easily provide a consistently high-performance service even as usage further increases.

Over 1/4 million calls in the first 18 hours

Although ChemSpider web services are fast becoming a priority for us, we are still dedicated to ensuring the website experience is optimal. The changes we have implemented will reduce traffic to the website so you should already have noticed improvements in website performance and reliability.

Some examples of implementations of ChemSpider web service usage can be found here.

Access to the ChemSpider API is free to academic users; for commercial use please contact us at chemspider-at-rsc.org.

I am happy to announce that ChemSpider is a part of the Open PHACTS project. It is detailed in the following PDF file but can be summarized with the extract from the Wikipedia article I recently posted.

“Open PHACTS is an Innovative Medicines Initiative project aiming to deploy a highly innovative open standards, open access, semantic web approach to address key bottlenecks in small molecule drug discovery – disparate information sources, lack of standards and information overload. It will become an open, integrated and sustainable chemistry, biology and pharmacology knowledge resource for drug discovery. It will provide tools for a comprehensive platform of chemical, biological and pharmacological information, confederated from vast, distributed and variable data and information sources. This semantically enriched and fully interoperable platform will deliver information on small molecules and their pharmacological profiles, including pharmacokinetics and ADMET data as well as on biological targets and pathways. The proposed platform will be a widely accessible, open innovation platform that will serve EFPIA partners as well as biotech and academic drug-discovery for one of their core business activities: knowledge discovery and verification. Practicing drug-discovery scientists in both the public and the private sector will turn to this service to: – integrate data on target expression, biological pathways and pharmacology to identify the most productive points for therapeutic intervention – investigate the in vitro pharmacology and mode-of-action of novel targets to help develop screening assays for drug discovery programs – compare molecular interaction profiles to assess potential off-target effects and safety pharmacology – analyse chemical motifs against biological effects to deconvolute high content biology assays.

The Open PHACTS consortium comprises 23 European core partners, with leading experts in the fields of data mining, annotation, small molecule data storage and manipulation, target related bioinformatics, pathway annotation, protein structure analysis, massive daily in silico reasoning, chemical biology, and computational chemistry. These are: Pfizer, Universität Wien>, Technical University of Denmark, University of Hamburg, BioSolveIT GmBH, Consorci Mar Parc de Salut de Barcelona, Leiden University Medical Centre, Netherlands Bioinformatics Centre, Royal Society of Chemistry, Vrije Universiteit, Spanish National Cancer Research Centre, University of Manchester, Maastricht University, ACKnowledge, University of Santiago de Compostela, >Rheinische Friedrich-Wilhelms-Universität Bonn, AstraZeneca, GlaxoSmithKline, Laboratorios del Dr. Esteve, Novartis, Merck KGaA, Lundbeck, and Eli Lilly.”

The Open PHACTS website can be found here. There will be a lot more details about Open PHACTS in the next few months. Follow the conversation on Twitter here: http://twitter.com/#!/Open_PHACTS