GOs Network GSC Project

GOs Network GSC project proposal April 2012

Project Title: The Genomic Observatories (GOs) Network

Project Lead: Neil Davies (Berkeley) and Dawn Field (CEH, U Oxford)

Initial Team members:  See authors of: Sequencing data: A genomic network to monitor Earth. Nature 2012, 481:145 (60+ authors).  Also, see the GOs Community of Scientists (GOsCOS) membership page for those who have signed up to the GOs Network’s Founding Charter.

Elevator pitch:  A global network of premier research sites working to generate genomic observations that are well contextualized and compliant with global data standards. To coordinate a set of long-term, place-based, DNA-centric programs that quantify biotic interactions in an ecosystem and develop models of biodiversity to predict the quality and distribution of ecosystem services.

Project Summary: In order to preserve Earth’s life support systems and promote sustainable development, we need a better understanding of the human-environment interaction. The GOs Network addresses this by applying cutting-edge genomic technologies to observe the flux of genetic variation — the Earth’s “biocode” — across human and natural ecosystems. We link these genetic data to other biophysical and socioeconomic data and integrate the resulting information in predictive models. These models aim to map the quality and distribution of biodiversity and the ecosystem services it provides under various scenarios of human activity.

When it comes to applying the power of the genomics revolution to large-scale biodiversity and ecological studies, we as a community, should begin to focus on sites of long-term research interest. The primary benefit of an increased focus on ‘DNA centric’, ‘place-based’ research is the potential to quantify the complete set of interactions between living organisms in a particular environment (ecosystem) from microbes to large multicellular organisms.

The GOs Network is a collaboration of research sites pioneering genomic research and embedded in, and cutting across, several ecological and biodiversity science networks. GOs will be selected based on their rich histories of data collection with long-term commitments to future research across a broad range of disciplines.  The GOs Network will launch sub-projects (that could also be under GSC) such as a GOs Portal, the Minimum Information for a GO (MIGO), and the Biocode Commons (software that supports genomic observations from collection through analysis).

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?).  There is currently no formal organization of sites of long-term scientific research doing significant genomic work – we aim to link up these sites and the networks they are embedded in to promote best practice, share experiences and solve common bottlenecks in analysis of data.  Collaboration between such important sites will also open up new opportunities for the coordination of large-scale projects across sites.

There is obvious synergy with the GSC’s GBWG which provides (and will continue to provide) input to GOs in terms of genomic standards and cross-domain standard interoperability (notably with LTER and TDWG).  GOs provide use-cases for standards development, including interoperability of standards across scientific domains.  As significantly, GOs also engage scientists and other stakeholders to provide showcases of what is possible when genomic and other standards are fully deployed and implemented.

How does this project fit into GSC’s mission statement (might also expand it)?  Genomic Observatories of the future are perhaps our best chance to capture highly contextualized, long-term (time series) genomic data.  The data from GOs should be GSC compliant.  Describing GOs and their data in a consistent manner will help close the loop between sampling, contextual information and well-annotated genomic information in the public domain.

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).  We (Neil and Dawn) formally presented this the GOs Network concept at GSC 12, organized a session on GOs at GSC 13 and made an open call for additional GO sites to come forward.  We plan to follow up at GSC 14 which has a focus on GOs.

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).  The GOs Network is already far larger (60+ people) than a traditional working group and we’d like to bring the entire activity under the umbrella of the GSC as the GSC continues to grow.  The Network largely consists of those representing sites, networks of sites that might include GOs, and related projects.  The GOs Network will aim to nucleate a range of working groups and these will be open to participation.

How do you wish to further engage the GSC (recruit members to project, get consultation, link to other GSC projects, etc)? We wish to bring this site-based research community into the GSC to promote interactions with the major sequencing/bioinformatics centres in GSC, researchers, encourage use of GOs data for GSC case studies, and facilitate adoption of standards across GOs.

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 (http://genomicobservatories.org), but would create a link in the GSC website to this external site.

What other resources might you like from what the GSC can offer (mailing lists, etc)? All available – likely a mailing list to start with.

What kind of timeline are you working to for building consensus, releasing a first version etc? We are looking for help/funding to help get this project off the ground.  GSC 14 will be the formal launch of the GOs Network.

What resources will be required for completion (funding, manpower, etc.)? (This question is just to give an idea about the size of the project).  We are currently seeking funding for the GOs Network (to support meetings of sites/networks, ideally in a GSC context, but also something in smaller more focused meetings.

What are your current plans for publishing/promoting the project?  We have expended significant effort since summer 2012 in pulling this community together and we will continue to promote the concept. We have just submitted a paper to the GSC 13 special issue of GigaScience.

References or relevant websites (for further reading): GOs Network: http://www.genomicobservatories.org and citations listed.