Standards in Genomic Sciences (2010) 3:225-231 DOI:10.4056/sigs.1423520 Meeting Report from the Genomic Standards Consortium (GSC) Workshop 10 Elizabeth Glass1, Folker Meyer1,2, Jack A Gilbert1,3, Dawn Field4, Sarah Hunter5, Renzo Kottmann6, Nikos Kyrpides7, Susanna Sansone8, Lynn Schriml9, Peter Sterk10, Owen White9 and John Wooley11 1 Argonne National Laboratory, Argonne, IL USA 2 Computation Institute, University of Chicago, Chicago, IL USA 3 Department of Ecology and Evolution, University of Chicago, Chicago, IL USA, 4 Centre for Ecology & Hydrology, Oxfordshire, UK 5 European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Insti- tute (EBI), Hinxton, Cambridge UK 6 Microbial Genomics Group, Max Planck Institute for Marine Microbiology and Jacobs University Bremen, Bremen, Germany 7 DOE Joint Genome Institute, Walnut Creek, CA, USA 8 University of Oxford, Oxford e-Research Centre, Oxford, UK 9 Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD USA 10 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge UK 11 University of California San Diego, La Jolla, CA USA *Corresponding Author: Dawn Field This report summarizes the proceedings of the 10th workshop of the Genomic Standards Consortium (GSC), held at Argonne National Laboratory, IL, USA. It was the second GSC workshop to have open registration and attracted over 60 participants who worked together to progress the full range of projects ongoing within the GSC. Overall, the primary focus of the workshop was on advancing the M5 platform for next-generation collaborative computa- tional infrastructures. Other key outcomes included the formation of a GSC working group focused on MIGS/MIMS/MIENS compliance using the ISA software suite and the formal launch of the GSC Developer Working Group. Further information about the GSC and its range of activities can be found at http://gensc.org/. Introduction The Genomic Standards Consortium (GSC) formed Sequence (MIMS) and an ENvironmental Sequence in 2005 to tackle the challenge of working as a (MIENS) [3,4]. community towards improving the quantity and Currently, the GSC exists as an open-member in- quality of contextual data made accessible for ge- ternational community consisting of 100+ biolo- nomes and metagenomes [1]. The GSC works to- gists, bioinformaticians and computer scientists wards its goal through the creation, maintenance that includes representatives from EMBL, EMBL- and adoption of a range of standards and colla- EBI, DDBJ, NCBI and major sequencing centers borative projects. In 2008, the GSC also expanded including BGI, JCVI, JGI, and the Wellcome Trust its scope to include the description of marker gene Sanger Institute (WTSI). In addition to the core sequences (i.e. ribosomal genes) [2]. Now, the GSC work of the GSC on the development of minimal has created three Minimum Information checklists information checklists [3,4] the GSC is also work- to cover contextual data for genomes, metage- ing towards adoption of these standards, including nomes and marker genes: Minimum Information the launch of this journal, Standards in Genomic about a Genome Sequence (MIGS), a Metagenome Sciences (SIGS) [5]. Implementation and adoption The Genomic Standards Consortium Glass et al. projects include the Genomic Contextual Data Following this overview, Phillipe Rocca-Serra Markup Language (an XML data format to support and Eamonn Maguire (University of Oxford) GSC minimal standards) [6], the Genomic Rosetta gave more detailed presentations on the actual Stone (a resolving service for top-level genome use of the tools. Key outcomes of the discussions and metagenome project information from differ- that followed included agreement to formalize an ent resources) [7] and Habitat-Lite (a lightweight ISA working group within the GSC as part of its ecological ontology) [8]. The GSC is now working compliance activities. on how to cope with the large quantities of meta- genomic data in the form of the M5 project [9], the GSC Board meeting focus of this workshop. The GSC established a board in April 2009 whose The GSC builds consensus through the hosting members have been selected from representatives meetings and working groups. The GSC 10 work- within the wider community most active in driv- shop was held on the campus of Argonne National ing GSC activities. The Board currently has 21 Laboratory (ANL), which occupies 1,500 beautiful, members and a set of standing committees. Mem- wooded acres, about 25 miles southwest of Chica- bership in GSC standing committees is currently go and surrounded by the Waterfall Glen Forest defined by participation and the Board welcomes Preserve. ANL is one of the leading federally anyone from the wider community that would like funded research and development centers in the to join a standing committee. This Board meeting US, and maintains a core metagenomics research covered a range of topics, but focused primarily on group and sequencing facility. The workshop con- how to continue the formalization of the GSC. Key sisted of three focused working group meetings outcomes include a decision to aim for two meet- and two days of open sessions with presentations, ings a year, one of which is to be an open registra- discussions and break out groups. tion meeting designed to engage with the wider community (April time) and one smaller meeting The ISA software suite workshop focused specifically on progressing GSC projects. The GSC meeting started on Oct 4th with a work- shop dedicated to the use of the ISA software GSC Developer Meeting suite. While several key groups already interested In the afternoon the first face-face meeting of the in working with these tools formed the core of the GSC’s Developer working group took place. Renzo meeting, the event was open to all and attendance Kottmann, (Max Planck Institute for Marine was very high. The scope of this workshop was to Microbiology, Bremen) chair of this session and provide an overview of the ISA Infrastructure tool the Developer group, first described the goals of kit and discuss how it can be used within the GSC the group and progress to date and then opened to promote compliance with MIGS/MIMS/MIENS. the floor for discussion. The discussion allowed This meeting was organized by Susanna-Assunta everyone to introduce himself or herself in person, Sansone and Dawn Field. To start, Susanna San- give updates on their particular activities and sone (University of Oxford) gave an overview of therefore set the stage for the rest of GSC 10. The the software suite and its role in data sharing. The meeting was very well attended and the introduc- Investigation/Study/Assay (ISA) tools ( [10]; ) of- tions attested to the wide range of adoption activi- fer a way to capture MIGS/MIMS/MIENS com- ties ongoing in the community. The role of this pliant metadata as well as metadata describing a group is to push forward GSC projects on a tech- range of other types of investigations. The ISA nical level, and GSC contributions to other stan- tools are freely available as a desktop software dardization projects, through technical discus- suite, targeted to curators and experimentalists, sions of the best solutions for implementation and and empowers users by enabling better access to work with adopters towards implementation of minimum information checklists and ontologies. GSC standards. The GSC developer group was de- This can be used to describe studies employing fined as an intersection between all the other GSC one or a combination of technologies and to sub- working groups. The main goal was achieved: the mit that metadata to suitable public repositories, members got to meet each other and talk at including the European Nucleotide Archive (ENA; length, and several new members joined. The genomics), PRIDE (proteomics) and ArrayExpress group will communicate mainly via the newly es- (transcriptomics). tablished mailing list. Additionally, the RCN4GSC http://standardsingenomics.org 226 GSC Workshop 10 grant finances monthly teleconference calls. The ture Digital Biology Foundation, Susanna San- membership is defined by participation so new sone described the role of the GSC as a founding members are encouraged to consider joining the community in the BioSharing forum, and Norman web page of the GSC Developer group is in the GSC Morrison described progress towards the forma- wiki. tion of the Biodiversity working group within the GSC. Formal Opening of GSC 10 and Keynote talk on the Microbial Earth project The formal start of GSC 10 came with the evening Session II: Adoption of GSC recommended mixer followed by a Keynote talk on Microbial standards Earth by Nikos Kyrpides (DOE Joint Genome The second morning session gave the floor to Institute). The Microbial Earth project aims to speakers from a variety of adoption activities, and generate a comprehensive genome catalog of all was chaired by Nikos Kyrpides, Renzo Kott- the bacterial and archaeal type strains, currently mann, and Dawn Field formally introduced the estimated to be nearly 9,000 strains. It builds on work of the developers group. David Aanensen the hundreds of stains currently being completed (Imperial College, London) talked about com- within the Genomic Encylopedia of Bacteria and pliance with GSC standards through SMART Archaea project (GEBA) [11]. As the GEBA project phones. Specifically, David gave an overview of his demonstrates, we have only begun to scratch the Epicollect system [12]. James Cole (Michigan diversity of microbial life and genome sequences State University) talked about efforts by the RDP are the ideal foundation for a wide range of down- project to support submission of MIENS compliant stream studies, including metagenomic studies of data and Philippe Rocca-Serra talked about con- the environment. Kyrpides emphasized that cost figurations to the ISA software tools to suport of DNA sequencing is no longer the bottleneck in MIGS/MIMS/MIENS compliance and the use of realizing this dream for microbiology, and that ontologies.