Information on the Concept Web Alliance is being continued on the site of the Netherlands BioInformatics Centre (NBIC). The functionality there is somewhat different than this Conceptweblog, and comments or contributions should be sent to velterop[at]conceptweballiance[dot]org, stating clearly that you wish them to be published on the CWA pages. We reserve the right not to publish contributions or comments, but will motivate such a decision.
Several of the Working Groups have now set out their ‘stall’ on the MyExperiment scientific collaboration platform. Those interested in participating should register in MyExperiment and request membership of the group(s) they want to join for the discussion. Groups that have not yet done so are invited to create a Group on MyExperiment as well.
For animals there was agreement earlier, but now there is agreement for a system of ‘barcodes’ to identify plant species. See the article in Scientific American.
For most working groups a Chair has now been confirmed and those groups are ready to start their activities (see the tab Groups). Anybody who wants to participate in the capacity of either a Member or a Reviewer, or just an Observer, is most welcome. They should take up contact with the respective Chair, via the email address firstname.lastname@example.org.
Physician and geneticist Francis Collins was nominated by President Barack Obama on 8 July as the next director of the National Institutes of Health (NIH).
The University of Manchester and the European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI) have launched a major new e-science resource for biologists – which could accelerate research into treatments for H1N1 flu and cancer: Biocatalogue.org. See the full news release on the web site of the University of Manchester.
Jeanene Swanson in Genome Technology, July/August 2009
“Biobanking is changing rapidly, and it’s in no small part due to the demands of systems biology. Many [large-scale biobanks] are also adding clinical annotation, genetic data, and increasingly genomic, proteomic, and other ‘omics’ information.”
“Because biobanks not only collect and store specimens, but serve as a library of sorts for researchers wishing to work with these samples, they have many requirements.”
“The goal, says Jennifer Harris at the Norwegian Institute of Public Health in Oslo, is to develop a common infrastructure that encourages sharing in order to make high-throughput work possible. “Getting the most out of the data will require a certain amount of sharing and data release,” she says.”
(From GenomeWeb News, 1 July 2009)
The body focused on enhancing Europe’s biobanking potential for research purposes has completed a review of over 300 biobanks and now will move on to the next phase of its efforts to develop a prototype for an international system.
The Biobanking and Biomolecular Resources Research Infrastructure, or BBMRI, aims to provide a Europe-wide collection of samples of biomedical quality. Currently, the research infrastructure includes 51 participating institutions and 190 associated organizations, representing 30 EU and associated countries. In the upcoming prototype development phase, the project partners hope to close “a potential gap between the planning and implementation phases of the project, to be functional by the end of 2010.”
This preparatory phase of the BBMRI program has been funded with €5 million ($7.1 million) by the EU’s Seventh Framework Program.
(From: GenomeWeb News, 29 June 2009)
The US Senate will consider a bill that would require that researchers funded by a number of government agencies submit electronic versions of their papers within six months after they have been published in peer-reviewed journals.
The legislation, which was introduced yesterday, is similar to the open access policy already in place at the National Institutes of Health, and would apply to federal agencies with annual extramural research budgets of $100 million.
The new bill, the Federal Research Public Access Act, introduced by Senator Joseph Lieberman (I – Conn.) and co-sponsored by Sen. John Cornyn (R – Texas), will require that researchers funded totally or partially by the agency submit the electronic copy of their manuscripts, which will be preserved in a digital repository and available for public access. Each agency affected by the law would either maintain its own repository or select a suitable one that permits free public access, interoperability, and long-term preservation.
The policy would not apply to materials such as lab notes, preliminary data analyses, author notes, phone logs, or other information used in the manuscript.
It would cover the research funded by the Department of Energy; Department of Health and Human Services; National Science Foundation; Department of Agriculture; Department of Commerce; Department of Defense; Department of Education; Department of Homeland Security; Department of Transportation; Environmental Protection Agency; and the National Aeronautics and Space Administration.
Recap of CWA goals and ambitions:
- CWA is to focus initially on the Life Sciences.
- CWA will largely build on existing institutions as a not-for-profit organization with tax-exempt status in all regions. It will be organized in such a way as to allow for funding to be routed through the CWA to its partners and other contract research collaborators.
- CWA aims at forming an ever-growing Scientific Alliance starting with the faculty already committed after the inaugural meeting.
- A specific task group has been formed to discuss strategies to grow the Scientific Alliance and propose strategies for maintaining and growing scientific credibility.
- CWA will mainly serve as a coordinating and administrative body to further the stated goals.
- CWA will have a Steering Committee elected by participating Founding Members and an Executive Committee with a mandate from the steering committee to run daily operations.
- CWA aims at having minimally one physical location in each continent, preferably, and where possible, associated with a leading university or organization that is also a Founding Member.
- Founding and Associate member organizations (the latter are organizations joining CWA after its initial establishment) will be allowed to grant eligible faculty members a formal CWA affiliation in addition to their university or institution affiliations.
- The Steering Committee may, at its discretion, also grant formal affiliation to individual scientists whose home institution is not a CWA member.
- A dedicated set of working groups (and sub tasks groups) has been formed.
Road map and operational process
During its inaugural meeting CWA core group members decided to delegate preparation and execution of next steps to the Executive Committee under supervision of the Steering Committee. An inventory has been produced of all activities in need of attention and discussion. Based upon that inventory approximately 20 task groups have been formed, grouped in 3 major categories:
Category 1: organizational and operational
1.3 Organizational structure
1.4 Legal and licensing
1.5 Capacity building
1.6 Commercialization / valorization
1.7 Sustainability / public fundraising
Category 2: Scientific and Technical
2.1 Content capture
2.2 Tool development
2.3 Storage and maintenance
2.4 Unifies persistent ID
2.5 Quality control
2.6 Triple model / format
2.7 Attribution (micro- and nano-credits)
2.8 Content acquisition
2.9 Triple Browser/reasoning
2.10 Multilingual issues
Category 3: Strategy/Advocacy
3.1 Scientific credibility
3.4 Conference 2010
For each category and task group, time lines, deliverables and milestones have been proposed and the Executive Committee has been put in charge of managing the process with a final delivery date of December 31, 2009. Chairs of these groups (selected from initial signatories who have expressed an interest in actively participating) have been invited and they will be responsible for both timing and deliverables of their task group. The process will be that a number of task group (virtual) meetings are held, resulting in a proposal per task group, each of which will be “peer reviewed” by experts before it is delivered to the Executive Committee. The Executive Committee will summarize all proposals and present them to the Steering Committee for guidance, approval and execution. It is expected that the first of these task group meetings will be held imminently.
The working group commercialization and valorization is tasked with delivering a plan (due September 2009) on how to build up the ‘trusted party’ role of CWA towards the public as well as the private sector, while building the structure and partnerships to serve commercial users with realizable services based on the ‘triple store’ to contribute to the long term sustainability of CWA.