Genomic Standards Consortium

The Genomic Standards Consortium (GSC) is an open-membership working body formed in September 2005. The aim of the GSC is making genomic data discoverable. The GSC enables genomic data integration, discovery and comparison through international community-driven standards.

This project is maintained by GenomicsStandardsConsortium

Genomic Standards Consortium

Micro B3

Micro B3 GSC project proposal April 2012

Project Title: The Micro B3 (Biodiversity, Bioinformatics, Biotechnology) project and the Ocean Sampling Day (OSD) initiative

Project Coordinator: Frank Oliver Glöckner (Jacobs University Bremen)

Team members: 32 partners see (from GSC this includes Renzo Kottmann, Guy Cochrane, Sarah Hunter, Dawn Field, Pelin Yilmaz)

Elevator pitch (20 – 50 words): The large scale integrated project Micro B3 which stands for marine microbial Biodiversity, Bioinformatics and Biotechnology will develop new technologies and leverage capacities and standards for data analysis and integration in ecosystems biology. It will use the data for biotechnological applications and work towards a sustainable legal framework for intellectual property management.

Project Summary The EU 7FP project Micro B3 (Biodiversity, Bioinformatics, Biotechnology) will develop innovative bioinformatic approaches and a legal framework to make large-scale data on marine viral, bacterial, archaeal and protists genomes and metagenomes accessible for marine ecosystems biology and to define new targets for biotechnological applications. Micro B3 will build upon a highly interdisciplinary consortium of 32 academic and industrial partners comprising world-leading experts in bioinformatics, computer science, biology, ecology, oceanography, bioprospecting and biotechnology, as well as legal aspects.

Micro B3 is based on a strong user- and data basis from ongoing European sampling campaigns to long-term ecological research sites. For the first time a strong link between oceanographic and molecular microbial research will be established to integrate global marine data with research on microbial biodiversity and functions. The Micro B3 Information System will provide innovative open source software for data-processing, -integration, -visualisation, and -accessibility. Interoperability will be the key for seamless data transfer of sequence and contextual data to public repositories.

Micro B3 will allow taking full advantage of current sequencing technologies to efficiently exploit large-scale sequence data in an environmental context. Micro B3 will create integrated knowledge to inform marine ecosystems biology and modeling. Moreover, it will facilitate detecting candidate genes to be explored by targeted laboratory experiments for biotechnology and for assigning potential functions to unknown genes. Micro B3 will develop clear IP agreements for the protection and sustainable use of pre-competitive microbial genetic resources and their exploitation in high potential commercial applications. To underline the translational character of Micro B3, outreach and training activities for diverse stakeholders are planned as well as an Ocean Sampling Day to transparently make project results accessible and gain valuable user feedback.

What will this project aim to contribute to the GSC? On a very high level: Micro B3 wants to create bioinformatics capacity which supports, implements, develops GSC standards from sampling to analysis, so that with OSD Micro B3 can practically demonstrate the value of GSC standards for science.

Which existing projects, if any, does this one replace/complement/subsume? Explain briefly why an extra project is needed/justified (what gap does it fill?) So far there was no structured approach to bring together the biodiversity, oceanography, biotechnology and bioinformatics communities to follow an integrated approach to make data interoperable for data exchange and integration. Furthermore, the global Ocean Sampling Day (OSD) provides the first concerted approach to define a standardized baseline of marine microbial diversity.

How does this project fit into GSC’s mission statement (might also expand it)? Micro B3 will implement and further develop GSC standards which is a prerequisite for success of the Ocean Sampling Day ( Workpackage 4 ( headed by Guy Cochrane, is dedicated to work on Standards and Interoperability which is crucial for large scale data integration.

Have you spoken about the project already within GSC? (on a call, at a formal GSC meeting, would like to request time to present at a future meeting). Yes. When the application was written up in 2010 the outline of Micro B3 was formally presented on GSC 10 (Argonne National Lab, USA). Permission was asked of the Board to bring Micro B3 under the GSC if funded. This was discussed again at GSC 12 after the project was funded.

Will you start a GSC working group (how far along are you?)? If not, why not (i.e. subgroup within developers group, existing external community, etc). I think this is not necessary because most of the issues we need in Micro B3 are already covered by the existing GSC working groups like Biodiversity, MIxS and Developer Group. We plan to work in collaboration with existing and upcoming GSC efforts, like the Genomic Observatories.

How do you wish to further engage the GSC (recruit members to project, get consultation, link to other GSC projects, etc)? Key members of the GSC like Dawn Field, Guy Cochrane, Pelin Yilmaz and Renzo Kottmann are already engaged in the project as WP leaders. Solid links to Neil Davies/Dawn Field and the Genomic Observatories are established.

Do you already have a website or do you wish to create a home page for the project in the GSC website (GSC maintains an open wiki at present, all working groups have a page)? We already have a website see and

What other resources might you like from what the GSC can offer (mailing lists, etc)? All available. A GSC support letter might be helpful for upcoming grant applications.

What kind of timeline are you working to for building consensus, releasing a first version etc? Ocean Sampling Day will take place on 21. June 2014 where all standards and protocols need to be in place.

What resources will be required for completion (funding, manpower, etc.)? Funding of the project is already granted. Start of the project was 01. January 2012 with a duration of 4 years. No additional funding is required.

What are your current plans for publishing/promoting the project? Website, press releases, publications, flyers, factsheets, videos

References or relevant websites (for further reading):