Updates from the Working Groups

The Alliance currently has four active working groups, with several more projects planned or proposed.  For a full list of projects, visit https://pistoia.basecamphq.com/clients. For more information on these Working Groups please contact the Pistoia Executive Director at This e-mail address is being protected from spambots. You need JavaScript enabled to view it .

SESL

Born and eponymously named at the Semantically Enriched Scientific Literature (SESL) conference in March 2009, SESL's aim is to explore the feasibility of an Amazon.com-like "brokering service" that scientists can use to rapidly gather information on disease-causing genes. Rather than requiring scientists to "pull" information from currently available but often disconnected databases and literature sources, the service envisioned by the SESL team will "push" appropriate information to scientists based on a single query.

SESL's members Ian Harrow [Pfizer], Wendy Filsell [Unilever], Dietrich Rebholz Schuhmann  and Jo McEntyre [EBI], Mike Braxenthaler [Roche], Ian Stott [Unilever], and Jabe Wilson [Elsevier] represent research organizations, academic service providers, and major scientific publishers. They launched the project in January 2010 with Wendy Filsell and Ian Harrow as project leads. SESL secured funding (AstraZeneca, GSK, Pfizer, and Roche) to support FTEs from academia (EBI) to serve as "technical staff" for the project. SESL has published a technical specification and launched a pilot this summer; testing is scheduled for completion in November. SESL plans to release a public prototype demonstrating the feasibility of the technology in Q1 2011.

The SESL project team will meet next on Oct. 7 at EBI, Hinxton, Cambridge. SESL members will also be presenting at:

• The 8th Annual Pharmaceutical 2010 Technology IT Congress Oxford Global, Sept. 15-16, London (Ian Harrow)
• The International Conference on Trends for Scientific Information Professional (ICIC), October 24-27, Vienna (Ian Harrow)

Sequence Services

The sequence services project emerged from the biology domain in February 2010. It aims to define and document an externally hosted service where organizations can securely store and mine both in-house derived gene/sequence information as well as the public domain gene databases. Currently, pharmaceutical companies must build and maintain their own workflows and associated infrastructure to search both public and private gene repositories effectively. The working group anticipates that subscribing companies could reduce individual infrastructure management costs by about 50%. Such a state-of-the-art, securely-managed service would leave subscribers well positioned to meet future challenges in gene data management, including the very significant compute and application demands associated with next-generation sequencing.

Simon Thornber (GSK) serves as project lead along with working group colleagues Cary O'Donnell (AZ), Monica Arenz & Quan Yang (Novartis), and Claus Stie Kallesøe (Lundbeck). The group has gathered the user requirements and categorized them into "functional requirements" (e.g. sequence searching algorithms, plasmid mapping) and "non-functional requirements (e.g. security, performance, service levels, business charging models, disaster recovery and liability).

Five companies/consortia (Cognizant/Eagle Genomics, Constellation Technologies/Microsoft, GenomeQuest, Infosys and Thomson-Reuters) have been selected to provide proof of concept installations, and funding has been raised to finance these test installations. Project development will continue through 2010, and testing will commence in Q1 2011.

ELN Query Services

Pistoia's oldest active working group aims to define a common standard that would enable scientists to use the same query across any and multiple electronic laboratory notebooks (ELNs). Such a standard would make it easier for scientists to search and extract data from ELNs, greatly increasing the value of experimental data in research organizations.

Richard Bolton (GSK) GSK leads the team that comprises both consumer and provider companies.  The members are David Drake and Kevin Higgins (AZ), Carol McNab (BMS), Andrew Lemon (Edge), Steve Trudel and John Duncan (Pfizer), Jim Barstow and Mike Wilson (Symyx), and Uwe Geissler.

The group has published a draft of user stories that defined the scope of the challenge. An RFP for a technology vendor to produce the query standard was produced in Q1 2010. The group selected GGA Software Services, who are developing an XML-based methodology for inputting queries and outputting search results. Vendors, some of whom are active members of the group, will need to build an API that can interpret these input and output standards. The resulting interface will benefit all stakeholders by:

• Increasing the functionality and overall value and performance of ELNs
• Lowering the cost of ELN implementation and support
• Freeing vendors to focus on providing innovation in the engine of their ELNs

This Pistoia project opens up exciting opportunities for information aggregators to new added-value services.

Vocabulary Standards Initiative: Molecular Drug Target Reporting Standard

In Dec 2009, Pistoia Alliance sponsored a Vocabulary Standards workshop in Boston to foster collaboration & discussion with a wide range of groups (Pistoia members and other organisations) involved in vocabulary standards and information delivery and exploitation workflows. Out of this meeting came a number of ideas for future working groups and of these ideas, Molecular Drug Target Reporting has just started as a Working Group run by Lee Harland (Pfizer) and Chris Larminie (GSK).

There is currently no universal standard for describing a molecular drug target within structured content and this impacts consumers in a number of ways. These include the inability to navigate, find and exploit information on a core pharmaceutical entity and the inability to use the same standard to connect internal & external data. This undermines the efforts of information providers to make data more accessible, causes potential search findings to be missed and as such, reduces the value of their products.

This project will increase the knowledge of industry/provider experiences dealing with these challenging concepts to increase definition and thereby access for all. There will be more on this project in our forthcoming Pistoia updates and newsletters.

Translational Services Domain - Start up

We have begun to plan the creation of the Translational Services Domain and of possible working groups supporting this key area of information and services. We are building a team to help drive this domain and are also looking for others to help develop potential project ideas. If you can help, please contact Nick Lynch or John Wise! We will come back to this topic in our next newsletter.