Applying Systems Biology to Benefit Human Health forum: topic
This is a public forum
Establishing a Consortium
Adriano Henney
Tuesday, 04 November 2008 18:32 UTC
Over recent years funding of Systems Biology has increased significantly, with a number of countries also investing in a variety of national initiatives to boost skills in this discipline. Much of the effort, however, is fragmented and lacks standardisation. Delivering a comprehensive, integrated systems biology toolbox that can be applied consistently to the challenges of modern medicine and drug discovery is a complex, “big science” project, comparable to, but more challenging than other major biological endeavours undertaken in the last 20 years. Arguably, if it is ever to reach its full potential and deliver genuine impact, this challenge demands the establishment of a consortium to coordinate effort and establish agreed standards. Views on the feasibility of this proposal and how to it could be achieved are invited.
-
Replies
-
Dear Adriano,
I agree completely to your opinion that a standardisation consortium needs to be established. But this demand is not only true for systems biology demands but also for metabolic pathway data and any data created from experiments. There are in principle at least two requirements: i) standardisation of experimental conditions (very hard aim) and ii) standardization of data reporting in a way that e.g. all the functional enzyme data are comprehensive, comparable and reliable. This needs the change of the current publication practice and also the support from (writing) scientists and journals.
There is already an initiative active which established the so-called MIBBI at the EBI. MIBBI aims at assembling all the existing “check list” standardization groups under one roof as a one-stop -shop site if one is interested in standards.
One of the participants of this project is STRENDA. The STRENDA group (www.strenda.org) has just agreed to the latest version of checklists for reporting enzymology data which have been adopted recently by JBC.
So, it becomes clear that such consortia as you mentioned are already existing but obviously they are not visible very well.
Carsten -
There are clearly different levels of consortia to be discussed. For the time being, the most urgent issue is the standardization for the collection and reporting of data. Not only this requires the coordinate effort of scientists and a change in the requirements for publication, but also a change in the requirements of the funding and regulatory agencies.
For example, there is a major initiative called European Initiative for Innovative medicines funded by the EU and supported by Pharma industries to enhance the competitiveness of life science research in Europe. One of the programs is dedicated to informatics and data storage. However it is not clear how much of the data generated by the single consortia working on different disease areas will be actually generated according to generally accepted standards and stored in a retrievable way (the problem of storing biological data in their context is in general challenging) [I will invite a colleague to comment with his first hand experience in a FP7 program]. Funding agencies (using taxpayers money) should require standards for data collection and retrieval before funding consortia. Another example could come from regulatory agencies requesting Pharma companies to generate and submit data according to well-defined standards (this applies mainly to safety data and predictive toxicology).
In summary, on the one hand scientists and journals are realizing the changes needed for systems biology to succeed, on the other hand the adoption of changes could be accelerated if funding and regulatory agencies could see the benefit of making available high quality data to be used after the lifespan of projects. The final goal of building a mathematical model as repository of knowledge relies on the ability to have good data repositories. -
Dear Adriano / forum members,
Here I suggest possible initial actions to support the creation of the proposed consortium
1. The definition of general criteria for consortium membership could be a starting point, independently of funding mechanisms or specific tasks within this initiative. Or at least criteria to accept expressions of interest of participation from individuals and/or organisations.
2. Perhaps we could start listing funding sources (scientific funding organisations and national / international programmes?) that could potentially support coordination activities or at least specific actions to support consortium establishment.
3. As part of the initial coordination actions I agree that we should continue identifying ongoing initiatives (e.g. community-based standards) that the proposed consortium should take into account.
Cheers,
Francisco.
-
