Updates from the Working Groups

Many of Pistoia's working groups will be starting 2011 by announcing deliverables from their work.  For complete details on Pistoia Alliance projects, visit www.pistoia.basecamphq.com/clients or for questions on any of the current working groups, email the This e-mail address is being protected from spambots. You need JavaScript enabled to view it . We are also building a new portfolio of projects comprising new phases of existing projects and entirely new initiatives. Send ideas to the Executive Director or This e-mail address is being protected from spambots. You need JavaScript enabled to view it , President of the Pistoia Alliance.

SESL

SESL is thrilled to announce that bioinformatics data from the EBI and literature content from the scientific publishing community (NPG, Elsevier, OUP, RSC) has been brokered! The project team is now testing the Phase 1 proof-of-concept implementation (view the report on the first prototype in Basecamp). The results will be assembled in January and reported by February 2011, and the team is on schedule to deliver the proof-of-concept demonstrator for public use by the end of Q1 2011.

Special thanks to the following members of the SESL team:

• EBI, which provided the technology infrastructure on which the SESL pilot runs and set up the all-important triple store
• Roche, Pfizer, AstraZeneca, and Unilever, which have found scientific users to execute the tests
• GSK, which is overseeing and directing the testing program
• RSC, Elsevier, and other publishers who have participated in prototype testing

The team is now considering the next phases of the project. The vision has long been to provide a fully functional scientific knowledge brokering system that would be commercially available to the scientific community. Achieving this will require the development of a new business model for the delivery of scientific information that will be equally attractive to consumers, scientific literature suppliers, bioinformatics database providers, and of course, to the commercial brokering service vendor. SESL is currently seeking funding to support consultancy work to interview stakeholders and propose business models that might prove attractive to all.

Regrettably, one of SESL's co-leads, Ian Harrow from Pfizer, will be stepping down from his leadership role at the beginning of 2011. Thanks Ian for all your hard work, skill, and commitment to getting this important project off the ground. Wendy Filsell of Unilever will continue in her role as a SESL co-lead, but the group is actively seeking a new co-leader, particularly one representing the scientific literature community.  

Sequence Services

Four companies/consortia accepted the Pistoia Alliance's invitation to provide proof-of-concept installations: Cognizant/Eagle Genomics, Constellation Technologies/Microsoft, Infosys and Thomson-Reuters. They are due to deliver their solutions for testing early in January 2011. An important piece of the testing-ethical hacks on the installations-will be conducted by AT&T.

The Sequence Services team is launching an "Innocentive" challenge with a prize of $15,000 to find the most efficient gene sequence data compression algorithm. Although disc space is quite cheap, and internet bandwidth is quite broad, NGS will generate massive data volumes. Any algorithm that can intelligently compress gene sequence data would rapidly realise a return on the investment prize money.

The project team continues to function well, ably lead by Simon Thornber of GSK. The Novartis team members have been rotated, and Novartis is now represented by Ralf Wahl. Cary O'Donnell and Claus Stie Kallesøe continue to represent AZ and Lundbeck respectively. The team is planning a project meeting for 1-2 March 2011, to review performance of the proof-of-concept installations, determine additional functionality needs, and consider other technology support needs. The Pistoia Alliance Workshop on next generation sequencing follows on 3 March 2011.  

ELN Query Services

Phase 3 of the ELN Query Standards project is about to be launched! This fall, the team delivered a draft XML-based query standard based on the user stories and requirements defined at the end of 2009. Such a standard is the kernel of this project.

In Phase 3, ELN vendors will exploit the XML query standard to construct "connectors" to their ELN databases. GGA Software Services-the software integrator retained to assist in earlier phases of the project-will build the GUI. GGA will also host a public-domain chemistry ELN data set to demonstrate the standard. Consumer companies will test the functionality of these connectors to the ELNs that they currently use. The team expects to complete Phase 3 in Q3 2011, and a demonstrator will run for six months after implementation to enable other interested parties to test the standard and its implementation.

Stakeholder buy-in for Phase 3 of the project is proceeding well--although more interest is always welcome. So far, AstraZeneca and GSK have committed financial support for Phase 3.  

Vocabulary Standards

The VSI Target Description project team spent the fall defining the project's scope. It agreed that its goal is to define and publish a standard, vocabulary-based methodology for querying the scientific literature and bioinformatics databases such that all hits-rather than a subset-are found against molecular drug target search criteria. The inherent challenge preventing all hits being returned is the plethora of synonyms, acronyms, and ambiguities that exist in current molecular drug target descriptions. The team has constructed a beta standard to test with varied examples and is currently drafting a paper that will clearly set out these challenges and opportunities.

In 2011, the team plans to seek funding from a variety of Pistoia Alliance members and other sympathetic companies-on the consumer side, in the academic domain, commercial information providers, and technology suppliers. Such funding will enable the team to employ an experienced (albeit part-time) project manager and retain a consultancy to interview key stakeholders, help crystalise the project's vision, and draft a report that will identify appropriate ways forward. This report will be instrumental in kicking-off the socialization of the business drivers associated with this project. An RFP will be drafted in early 2011, the preferred agency appointed in Q2, and the report disseminated publicly toward the end of this year.