GSC projects
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[edit] A Portal into all GSC Projects
This page should serve as a portal into all of the ongoing GSC projects. Following the 5th GSC workshop, we've established a set of workspaces for each project. These workspaces help identify the key people leading each working group and the individuals involved and will lead into the complete set of information for that page (project homepage). In particular, for the projects described in the special issue of OMICS these pages contain Supplementary information cited in the papers. All of the pages are designed to aid in the collection of feedback from the community.
[edit] The GSC Roadmap - how it all fits together
The most current GSC Roadmap Publication is found in the 5th GSC workshop report in the special issue of OMICS: PROOFS
An overview of GSC activities is also found in Wikipedia: http://en.wikipedia.org/wiki/Genomic_Standards_Consortium
[edit] GSC projects
The GSC is developing a variety of consensus-driven, community-level projects which are summarized below.
[edit] MIGS/MIMS
- Short Description: Defining the scope of the "Minimum Information about a Genome Sequence" (MIGS) checklist (applies equally to metagenomes which are extended by MIMS)
- Publication: Free content in Nature Biotechnology
[edit] GCDML
- Short Description: The report outlines the Genomic Contextual Data Markup Language (GCDML) which is a core project of the Genomic Standards Consortium (GSC) that implements the “Minimum Information about a Genome Sequence” (MIGS) specification and its extension, the “Minimum Information about a Metagenome Sequence” (MIMS).
- Roadmap Publication: Pubmed
[edit] EML-GCDML
- Short Description: Linkages with NSF's LTERs (EML-GCDML): This report outlines the steps that the Long Term Ecological Research Network is taking towards adopting the standards proposed by the Genomics Standards Consortium.
- Roadmap Publication: PubMed
[edit] Genomic Rosetta Stone (GRS)
- Short Description: A collaboration between many genomic/metagenomic databases to map local identifiers to create a way to navigate through all databases to find information about genomes/metagenomes
- Roadmap Publication: Pubmed
[edit] Habitat-Lite
- Short Description: Habitat-Lite aims to provide a short list of high-level terms describing habitats that is tailored to describing genomes/metagenomes and related molecules (like 16S). It draws its terms from the Environment Ontology.
- Roadmap Publication: PubMed
[edit] SOP Repository
- Short Description: A call for a Central Repository for Standard Operating Procedures (SOPs):
- Roadmap Publication: Pubmed
[edit] GSC Genome Catalogue
- Short Description:The GSC is developing a beta repository for holding MIGS/MIMS compliant data.
[edit] GenCat
- Short Description: The GSC's Genome Catalogue is run by a piece of software called GenCat.
[edit] Putting Molecules on the Map
At the heart of the MIGS specification is a call for geospatial information for all relevant genomes and metagenomes...
[edit] A standards compliant OpenAccess Journal for the GSC
The GSC has received funding through George Garrity at Michigan State University to launch an Open Access eJournal.
[edit] Projects in which the GSC is a member community
The GSC aims to learn from other communities through indirect and direct interactions whenever possible. The GSC is formally a part of the following much large communities/projects.
[edit] Checklists (Scope)
[edit] MINSEQE
- Involvment: GSC is a participating community
- MINISEQE Homepage: http://www.mged.org/minseqe/
- Workshop: http://gensc.wordpress.com/2008/04/03/feedback-request-on-minseqe/
As an output of discussions at the recent MGED-organized UHTS standardization workshop (in Berkeley, March 17-18, 2008), a new Minimum Information checklist is being developed called MINSEQE
[edit] MIBBI
- Involvment: GSC is a participating community
- MIBBI Homepage: http://mibbi.sf.net
- Publication: "Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project." Pubmed
MIBBI offers a common portal to Minimum Information checklists; to act as a ‘one-stop shop’ for those exploring the range of extant projects, foster collaborative development and ultimately promote gradual integration.
[edit] Formats (Syntax)
[edit] ISA-Tab
"Investigation, Study, Assay tab-delimited format (ISA-TAB) is a general purpose framework with which to communicate both metadata (i.e., contact details, sample characteristics, technologies used, etc.) and data from experiments employing (meta)genomics-, transcriptomics-, proteomics- and metabol/nomics-based (hereafter referred as "omics-based" experiments) and conventional technologies."
[edit] Ontologies (semantics)
[edit] OBI
- Involvment: GSC is a participating community
- OBI homepage: http://obi-ontology.org/page/Main_Page
- Publication: See previous FuGO paper GSC Publications and NBT publication on OO Foundry Pubmed
The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of life-science and clinical investigations.
[edit] ENVO
- Involvment: GSC is a participating community and has cofunded workshops
- See: Habitat-Lite is a GSC Case study for EnvO
- EnvO Homepage: http://environmentontology.org
We see the new Environment Ontology (EnvO) bringing similar benefits to those that can already be achieved with the Gene Ontology (GO); through consistent annotation grounded in an ontological framework, we hope to facilitate the semantic retrieval of any biological record anchored to EnvO. For example, those contained in sequence databases, omic data repositories, tissue banks and museum collections.
