GSC FAQ
From Genomic Standards Consortium
[edit] Frequently asked Questions about the GSC
[edit] What is the GSC?
About the GSC
[edit] What is the GSC mission?
Better descriptions of our collection of genomes and metagenomes: the GSC Mission
[edit] Frequently Asked Questions about MIGS
Below we answer the most frequently asked questions about MIGS, its development and usage.
[edit] What is MIGS?
• MIGS specifies a formal way to describe genomes and metagenomes in more detail than is currently captured in DDBJ/EMBL/Genbank documents. • The information in MIGS is intended to be used in comparative genomic analysis, provide a better understanding of the source of each genome, and enable us to put genomes and metagenomes into a temporal and geospatial context (when relevant) through the specification of geographic location and sampling date.
[edit] Do all genomes and metagenomes fall under the scope of MIGS?
Yes. MIGS has elements describing eukaryotic, bacterial/archaeal, plasmid, viral, and organellar genomes as well as metagenomes. Some of the core elements overlap between types of records while some are unique to one or more groups.
[edit] Who has driven the development of MIGS?
MIGS has been developed through a series of GSC workshops involving participants from DDBJ, EMBL, NCBI, EBI, JGI, Sanger, JVCI (formerly TIGR), MPI, CAMERA and a range of other research institutions.
[edit] Who should complete a MIGS report?
Authors of genome and metagenome publications should submit a report after submitting project information to DDBJ, EMBL or Genbank.
[edit] Is MIGS very time-consuming to complete?
MIGS is a short specification compared to most other ‘omic checklists (See http://mibbi.sf.net). This stems from three key facts. • MIGS is an extension of the data already captured by DBBJ/EMBL/Genbank to describe genomes and metagenomes and is designed to be complementary to these authoritative sources of metadata. The INSDC Genome project database will contain essential administrative information, and identifiers like taxids, and a genome project identifier (PID). • MIGS was intentionally designed to be ‘minimal’ for the purpose of promoting adoption. • Genomic sequencing experiments, unlike transcriptomic, proteomic or metabolomic investigations, are ‘state-independent’ (a genome sequence is ‘stable’ with respect to cellular state or environmental factors). In contrast, metagenomic experiments are far more dependent on the exact sampling strategy and specific habitat of a given community, thus necessitating the development of MIMS to capture additional measures that define habitat (e.g. salinity, pH, temperature).
[edit] How can I get a unique identifier for my submission for use in my publication?
The Genomes Online Database (http://www.genomesonline.org/) is the recognized authority for issuing GCat Identifiers for Eukaryotes, Bacteria and Archaea and metagenomes. The Genome Catalogue will issue identifiers for other genomes.
[edit] Can I submit MIGS-compliant information online?
Yes. The GSC has developed a portal called the “Genome Catalogue” that has been useful in prototyping the MIGS specification. MIGS-compliant information can be submitted through user friendly web forms with drop down menus for the selection of appropriate terms and batch uploading functions are being developed (http://gensc.sf.net).
[edit] Are sample reports available?
Yes, the Genome Catalogue contains a collection of MIGS-compliant reports and examples are given in Supplementary Table 1 of the MIGS publication (Field et al, 2008).
[edit] How would I report the existence of MIGS-compliant data in my publication?
MIGS-compliant information could be reported as a Supplementary Table in a publication. Far more beneficial to the wider community would be to submit this information to the Genome Catalogue and report the GCat identifier and the URL of this database.
[edit] How can I get involved in the GSC/provide feedback into the development of MIGS?
The GSC has an open call for participation. Further information can be found at http://gensc.sf.net.
[edit] What is GCDML?
[edit] What is the Genomic Rosetta Stone?
[edit] How is the GSC participating in ontology development?
The GSC recognizes the importance of using shared, agreed upon terms for the completion of MIGS/MIMS reports and for creating any extensions in GCDML. The MIGS specification is tagged with a set of ontologies that are expected to be used. The Genome Catalogue currently supports term capture and ontology support will be a future functionality.
[edit] What is the EnvO Project?
http://www.environmentontology.org
The GSC is a founding member of the EnvO Project.
[edit] What is OBI?
The GSC is a member of the Ontology for Biomedical Investigation (OBI) initiative.
