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

Abstract

This report summarizes the proceedings of the 6th and 7th workshops of the Genomic Standards Consortium (GSC), held back-to-back in 2008. GSC 6 focused on furthering the activities of GSC working groups, GSC 7 focused on outreach to the wider community. GSC 6 was held October 10-14, 2008 at the European Bioinformatics Institute, Cambridge, United Kingdom and included a two-day workshop focused on the refinement of the Genomic Contextual Data Markup Language (GCDML). GSC 7 was held as the opening day of the International Congress on Metagenomics 2008 in San Diego California. Major achievements of these combined meetings included an agreement from the International Nucleotide Sequence Database Consortium (INSDC) to create a “MIGS” keyword for capturing ”Minimum Information about a Genome Sequence” compliant information within INSDC (DDBJ/EMBL /Genbank) records, launch of GCDML 1.0, MIGS compliance of the first set of “Genomic Encyclopedia of Bacteria and Archaea” project genomes, approval of a proposal to extend MIGS to 16S rRNA sequences within a “Minimum Information about an Environmental Sequence”, finalization of plans for the GSC eJournal, “Standards in Genomic Sciences” (SIGS), and the formation of a GSC Board. Subsequently, the GSC has been awarded a Research Co-ordination Network (RCN4GSC) grant from the National Science Foundation, held the first SIGS workshop and launched the journal. The GSC will also be hosting outreach workshops at both ISMB 2009 and PSB 2010 focused on “Metagenomics, Metadata and MetaAnalysis” (M3). Further information about the GSC and its range of activities can be found at http://gensc.org, including videos of all the presentations at GSC 7.

IMG: the integrated microbial genomes database and comparative analysis system

“…Scientists can submit their private genome data sets into IMG ER (using password protected access) prior to their public release either with their original annotations or with annotations generated by IMG's annotation pipeline (18). Since August 2009, close to 750 private genomes have been reviewed and curated using IMG/ER.…”

Improving Microbial Genome Annotations in an Integrated Database Context

“…IMG helps the users to identify such genes and gene families by integrating the data from different annotation sources. IMG’s annotation process [16] attempts to assign every protein-coding gene to three types of sequence-similarity based protein classifications: COG, Pfam and TIGRfam, as well as the models collected in the integrated database InterPro [17]. These protein classifications have been generated using different approaches, and protein families carry more or less extensive manually curated functional descriptions; as a result, the information provided by them is only partially redundant.…”

“…On the other hand, since both systems are based on a seed set of genes with manual assignments performed using additional refinement criteria, such as orthology detection and synteny, they often provide finer granularity of functional annotations than those generated by COGs and Pfams. Protein assignments to KO terms and FIGfams are imported from the corresponding resources using identifier- or protein sequence-based mapping, and in the case of KEGG Orthology native annotations are supplemented by additional assignments of IMG proteins to KO terms using the methodology described in [16].…”

“…Each IMG term is functionally coherent and is not required to contain sequences that share similarity. Subsequently the IMG terms are propagated using strict sequence similarity thresholds [16] and are inspected by expert curators. IMG terms are further connected to entities describing transformations of various metabolites and macromolecules called IMG reactions and IMG pathways , as described below.…”

“…Each IMG reaction is associated with one or more IMG terms, which can participate in the reaction as catalysts, or as substrates and products (e.g., proteolytic cleavage of an inactive precursor producing a mature enzyme). During the genome annotation process, genes in the genome are assigned to IMG terms using a standard operating functional procedure [16]. Briefly, a gene is assigned to an IMG term if it has at least five homologs in the IMG database with >50% identity and at least two of these five homologs have an IMG term assigned, and the alignment length of the pairwise comparison should be >70% of the length of both the query and target proteins.…”