PSB 2010

PSB Workshop: Metagenomics, Metadata and Metaanalysis (m3)

Call for Participation and Abstracts

The m3 workshop will build directly on the past seven Genomic Standards Consortium (GSC) workshops and on the Special Interest Group (SIG) workshop by the same name that the GSC is hosting at ISMB 2009. The GSC 7 workshop was held at the International Congress of Metagenomics 2008 conference, a highly successful annual meeting in its third year hosted by the CAMERA project in San Diego, California. To date, the GSC has published two special issues of the journal OMICS involving over 150 co-authors. The GSC's "Minimum Information about a (Meta) Genome Sequence" (MIGS) specification was published in Nature Biotechnology (Field et al 2008). The GSC Wiki provides further information about the Genomic Standards Consortium and its activities in the area of standards for the capture of genome/metagenome sequences.

The m3 workshop will focus on comparative studies of (meta) genomes that bring these sequences into "context" (i.e., by geolocation, habitat, organism phenotype, etc). For example, a seminal paper, illustrating the power of this approach, has just been published in PNAS (Gianoulisa et al, 2009). It reports a study aimed at elucidating the relationships between metabolic pathways and environmental parameters in microbial communities using the data and metadata from the Global Ocean Survey (GOS), an earlier landmark paper in the history of the field of metagenomics (Rusch et al, 2007). The kick-off of the Human Microbiome Project and the resulting data sets will open enormous new possibilities for integration and analysis of metagenomic data sets in context.

The agenda of the m3 workshop will be designed to cover the growing intersection of science and standards. The workshop will combine invited talks, talks selected from abstract submissions to this call, and a panel discussion to give a "voice" to the community. Building such community-driven consensus, in the form of standards that support and accelerate scientific discovery in biology, is of growing importance. This is especially true given the rapid growth of experimental data, most notably including both genomic and metagenomic sequences.

Aims and Goals:

Our goal is to attract experimentalists and computational researchers making "next-generation" use of contextual metadata. We solicit abstract submissions describing comparative (meta) genomic studies that demonstrate the power of using contextual data curated (e.g. habitat or host) and measured (e.g. geographic location, salinity, temperature, or pH) in comparative metagenomic studies of large numbers of samples. Likewise, studies describing new approaches, tools, databases, standards, ontologies or substantial new sets of curated metadata that aid in the integration and inter-operability of disparate datasets will be welcomed. We will also aim to attract research focused on capture and organization of metadata, for example through text-mining and ontology development, that enables new understanding of the interaction of organisms in their ecological context.

1. Nikos Kyrpides (DOE JGI) with his GOLD database and extensive work in the fields of genomics, metagenomics and most recently on the Human Microbiome.
2. Victor Markowitz (LNBL) responsible for the Human Microbiome Project-specific version of IMG/M and the collection of HMP specific metadata in the HMP Project Catalog.
3. Guy Cochrane (EMBL), head of the EMBL nucleotide database and the European Short Read Archive and responsible for the INSDC practices regarding metadata, submission of metadata to the INSDC (including the MIGS structured comments) and linking of molecular information with organismal information.
4. Susanna Sansone (EBI) is a leading member of the standards development community to provide an overview of standards activities including the work of the MIBBI consortium in harmonizing checklists in omics, the Ontology of Biomedical Investigations (OBI) and the ISATab initiative, aimed at develop a tabular format for global omics data exchange.
5. Owen White (U of Maryland) is PI of the newly established Digital Analysis and Curation Centre (DACC) for the Human Microbiome Project. He has been focused on issues of standardization including the need for Standard Operating Procedures and adequate metadata.