GCDML Workshop
The GSC 6 workshop opened with a two day GCDML workshop at which GCDML version v1.0 was presented and discussed in depth by about 20 attendees. The workshop, led by Renzo Kottmann (MPI-Bremen), was designed to inform developers within the GSC of the design and construction of GCDML with the goal of accelerating its adoption and extending its content. The workshop included sessions on how to create and edit genome reports using GCDML markup in an XML Editor. Examples of 30 marine phage genomes marked up in GCDML by Melissa Beth Duhaime (MPI-Bremen) were used to illustrate the creation and maintenance of GCDML instances.
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. Participants agreed to create a community-led requirements document describing an ideal future solution. It was agreed that, at a minimum, the Genome Catalogue should be:
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Funded (a long-term endeavor that can not be done on a voluntary basis)
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Based on GCDML
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Underpinned by a rich, user-friendly tool kit
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Shared by the GSC
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Designed to give credit to all contributors
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Expressed in XML using GCDML syntax
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Web services based (supporting the automated exchange of content)
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Serve as the international GCAT identifier authority (for Genome Catalogue entries)
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Comprehensive (containing reports for all taxa and metagenomes)
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Ontology-supportive
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Able to maintain all versions of GCDML schemas used to curate metadata
The workshop closed with agreement that the focus for 2009 should be curation of MIGS/MIMS metadata for key sets of genomes. Peter Sterk is now leading this effort.
GSC 6: Main Meeting
The GCDML workshop provided an excellent foundation for the main meeting, which was structured into six sessions held over three days. The first day of this meeting was spent reviewing ongoing GSC activities and developments since the GSC 5 workshop [1]. The “Minimum Information about a (Meta) Genome Sequence” (MIGS) appeared in print in June 2008 [2]. A special issue of OMICS was published as a result of GSC 5 [3] containing roadmap papers on core GSC activities including: GCDML [4], the Genomic Rosetta Stone mapping of genomic identifiers [5], Habitat-Lite [6]and the GSC eJournal [7,8]. These roadmaps place the GSC firmly in Phase II, which will center on implementation in aid of the adoption of the MIGS specification [2] now that the GSC has built it and presented to the community in Phase I of the evolution of the GSC. As done previously, the final day was dedicated to the development of the next leg of the GSC strategy.
The full agenda of the workshop, which was attended by more than 40 invited participants, is available on line and included a line-up of excellent speakers and talks. Only the major highlights of the meeting are covered in this brief overview and include:
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INSDC agreement (Guy Cochrane, EMBL, Ilene Mizrachi and Scott Federhan, NCBI) to take forward a proposal to allow the GSC create a reserved keyword “MIGS” for inclusion in INSDC submission files following the precedent set previously by the CBoL (the Consortium for Barcodes of Life) This proposal was approved at the INSDC annual meeting in May 2009
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Discussion of the MIGS checklist (Nikos Kyrpides, DOE Joint Genome Institute) and finalization of MIGS information for the first 60 genomes to be published by the “Genomic Ency-clopedia of Bacteria and Archaea” project
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Approval of a proposal (Frank Oliver Glöckner, MPI-Bremen) to extend MIGS/MIMS to ribosomal RNA that will be defined by a newly developed “Minimum Information about an Environmental Sequence”. This will be a major focus of GSC 8.
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Agreement to name the GSC eJournal Standards in Genomic Sciences (SIGS) and recruitment of editors (George Garrity, Michigan State University)
Key actions and designated project leads agreed to by the group included:
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Development of MIGS/MIMS content in coming months and publication of requirements for a GSC Genome Catalogue (Peter Sterk).
Incorporation of a MIGS keyword into INSDC records (Peter Sterk, Guy Cochrane and Nikos Kyrpides)
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Compilation of MIGS 2.1, with the view that the checklist would be maintained as a function of SIGS (Peter Sterk).
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Improvement of the GSC wiki content (Dawn Field, Peter Sterk and Renzo Kottmann).
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Initiation of publication of SIGS, including recruitment of authors, editors and reviewers (George Garrity)
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Further engagement of the broader community through a Special Interest Group workshop at the Intelligent Systems in Molecular Biology (ISMB 2009) conference (Iddo Friedberg)