Developing standards for the microbial dark matter

The 17th workshop of the Genomics Standards Consortium and the Genomes to Secondary metabolites workshop


In the last few years, we have witnessed large efforts to sequence much of the uncultured microbial diversity on Earth, employing various new technologies. Some focus on single cell approaches, while others focus on improved methods of assembling complete or partial genomes directly from the metagenomic data. There is a common theme in these approaches —an urgent need to establish common data standards.

Founded in 2005, the Genomic Standards Consortium (GSC) is an international organization that promotes the standardization of  genomes and metagenome descriptions, and the exchange and integration of genomic data. It is only by creating more robust metadata that we will actually be able to understand this growing “big” data.

The consortium started with the task of establishing standards for genomic and metagenomics data, which evolved to what is now termed the “Minimum Information about any Sequence” (MIxS) standard. The success of this project led to the development and implementation of several more projects, all aiming to implement standards in Biodiversity and Bioinformatics.

The 17th workshop of the Genomics Standards Consortium (GSC-17) will take place at the Department of Energy, Joint Genome Institute in Walnut Creek, California, USA, on May 4-6, 2015. In an effort to support the understanding and analysis of the uncultured microbial life, the theme of this workshop is ‘Standards for the Microbial Dark Matter’.

GSC-17 is organized around 8 sessions:

  1. Biodiversity
  2. Single cell standards
  3. Genomes Extracted from Metagenomes (GEM) standards
  4. M5 Standards
  5. Pangenome Standards
  6. Biosynthetic Clusters (BC) standards
  7. Ontology on Microbial Phenotypes (MP)
  8. MixS Standards

GSC-17 will be followed by a two-day workshop on Genomes to Secondary Metabolites. The goal of this workshop is to discuss the available standards, databases and methods to support end-to-end discovery of novel secondary metabolites. This will include mining genomic data for the discovery of Secondary Metabolite (SM) gene clusters, expression, metabolic profiling, and testing for bioactivity. The workshop will have the following four sessions:

  1. Mining genomes to discover gene clusters involved in secondary metabolism
  2. Standards and Databases
  3. Chemoinformatics
  4. End-to-end pipelines

Discussions at the end of sessions are aimed at establishing both near-term and long-term objectives for informatics systems in the field. We encourage you to look at the conference website to explore the full list of speakers and topics.



Amye Kenall

Journal Development Manager at BioMed Central
Amye Kenall

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