Meeting Report: The Fifth Genomic Standards Consortium (GSC) Workshop

Abstract

This meeting report summarizes the proceedings of the fifth Genomic Standards Consortium (GSC) workshop held December 12-14, 2007, at the European Bioinformatics Institute (EBI), Cambridge, UK. This fifth workshop served as a milestone event in the evolution of the GSC (launched in September 2005); the key outcome of the workshop was the finalization of a stable version of the MIGS specification (v2.0) for publication. This accomplishment enables, and also in some cases necessitates, downstream activities, which are described in the multiauthor, consensus-driven articles in this special issue of OMICS produced as a direct result of the workshop. This report briefly summarizes the workshop and overviews the special issue. In particular, it aims to explain how the various GSC-led projects are working together to help this community achieve its stated mission of further standardizing the descriptions of genomes and metagenomes and implementing improved mechanisms of data exchange and integration to enable more accurate comparative analyses. Further information about the GSC and its range of activities can be found at http://gensc.org.

Toward an Online Repository of Standard Operating Procedures (SOPs) for (Meta)genomic Annotation

“…The need for SOPs describing the genome annotation processes was highlighted at the fifth workshop of the Genomic Standards Consortium (Field et al, 2008a(Field et al, , 2008b. In its capacity as an organization to promote standards that increase the richness and usability of genomic datasets (Field et al, 2008a), the GSC advocates that SOPs for genome annotation become more routinely used, as a way to increase transparency and quality of the annotation process.…”

Metagenomics, paratransgenesis and the Anopheles microbiome: a portrait of the geographical distribution of the anopheline microbiota based on a meta-analysis of reported taxa

“…When designing experiments that encompass metagenomic data generation, it is imperative to consider factors such as sampling techniques, DNA/RNA extraction protocols, sequencing platforms, assembly, taxonomic binning and gene annotation tools, statistical analysis and data/meta-data sharing formats (Wommack et al 2008, Tanenbaum et al 2010, Wooley et al 2010, Thomas et al 2012). The availability of standardised procedures (Field et al 2008, Tanenbaum et al 2010) and platforms for data storage and sharing are increasingly important to ensure that the output of individual projects can be assessed, shared and compared (Thomas et al 2012). …”

Meeting Report from the Genomic Standards Consortium (GSC) Workshops 6 and 7

“…Discussions of GCDML and the vision of MIGS/MIMS compliance by the community in the near future led to renewed interest in building the GSC Genome Catalogue [1]. A comprehensive catalogue could act as a central hub of information accessible by web services and linked to core databases maintained by participating GSC organizations, many of which already collect, or soon will collect MIGS/MIMS metadata.…”

“…The Genomic Standards Consortium (GSC) is an initiative working towards richer descriptions of our collection of genomes and metagenomes through the development of standards and tools for supporting compliance and exchange of contextual information [1]. Established in September 2005, this international community includes representatives from the International Nucleotide Sequence Database Collaboration (INSDC), major genome sequencing centers, bioinformatics centers and a range of research institutions.…”