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Archive for the ‘Biology’ Category

At the recent Genomic Standards Consortium (GSC) workshop, George Garrity led discussions to review and produce a final version of the MIGS/MIMS checklist that will be included in the MIGS paper to be published in Nature Biotechnology in February 2008.

The revised version of the MIGS/MIMS checklist, together with comments recorded during the GSC workshop, are available via the GSC wiki at:

http://gensc.org/gc_wiki/index.php/MIGS_Checklist_Proofs

The MIGS/MIMS checklist document is available directly at:

http://gensc.sourceforge.net/docs/migsmims/

Nature Biotechnology Journal home page:

http://www.nature.com/nbt/index.html

Nature Biotechnology invited the scientific community to comment on the MIGS paper prior to publication. The community consultation page http://www.nature.com/nbt/consult/index.ht includes a link to the version of the MIGS paper made available for the community consultation:

Towards richer descriptions of our collection of genomes and metagenomes: the “Minimum Information about a Genome Sequence” (MIGS) specification (PDF 45K)

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The GSC will present a poster at the Genomics and Society meeting, to be held in London on 25-26th October 2007.

The event will feature lectures, debates, workshops and exhibitions, on the past, present and future roles of genomics in society. More information on the meeting is available on the dedicated web site: http://www.genomicsandsociety.org/

If you plan to attend the meeting, please send a note to curator@ceh.ac.uk.

 

genomics and society network logo

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The Genomic Standards Consortium held a Birds of a Feather meeting at ISMB/ECCB 2007.

There were three presentations, and a discussion led by Robert Stevens. Presentation slides can be downloaded from the GSC wiki:

Presentation Slides

* Tatiana Tatusov slides

* Dawn Field slides

* Lynette Hirschman slides

We mostly discussed how to achieve wider community involvement. In particular we discussed the fact that a group of us worked quite extensively at ISMB on the development of an ontology for the georeferencing of biological samples and records.

Environmental Ontology workshop

Related to this, the GSC is co-sponsor of an Environmental Ontology (EnvO) workshop to be held on August 29-31 2007 where the ontology obo file (called geo.obo) will be further reviewed. The agenda for the EnvO meeting is available on the GSC wiki and further details will be publishing shortly.

http://darwin.nerc-oxford.ac.uk/gc_wiki/index.php/EnvO_Workshop

Geo.obo file from Michael Ashburner

Michael Ashburner sent out an email on June 29th 2007 regarding the geo.obo file. A copy of the email and file attachments have been uploaded to the GSC wiki.

http://darwin.nerc-oxford.ac.uk/gc_wiki/index.php/Michael_ashburner_email

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A meeting report summarizing the proceedings of the “eGenomics: Cataloguing our Complete Genome Collection III” workshop held September 11–13, 2006, at the National Institute for Environmental eScience (NIEeS), Cambridge, United Kingdom, is now available:

download meeting report

Comparative and Functional Genomics
Volume 2007 (2007), Article ID 47304, 7 pages
doi:10.1155/2007/47304

Meeting Report

eGenomics: Cataloguing Our Complete Genome Collection III

Dawn Field, George Garrity, Tanya Gray, Jeremy Selengut, Peter Sterk, Nick Thomson, Tatiana Tatusova, Guy Cochrane, Frank Oliver Glöckner, Renzo Kottmann, Allyson L. Lister, Yoshio Tateno, and Robert Vaughan

This 3rd workshop of the Genomic Standards Consortium was divided into two parts. The first half of the three-day workshop was dedicated to reviewing the genomic diversity of our current and future genome and metagenome collection, and exploring linkages to a series of existing projects through formal presentations. The second half was dedicated to strategic discussions. Outcomes of the workshop include a revised “Minimum Information about a Genome Sequence” (MIGS) specification (v1.1), consensus on a variety of features to be added to the Genome Catalogue (GCat), agreement by several researchers to adopt MIGS for imminent genome publications, and an agreement by the EBI and NCBI to input their genome collections into GCat for the purpose of quantifying the amount of optional data already available (e.g., for geographic location coordinates) and working towards a single, global list of all public genomes and metagenomes.

http://www.hindawi.com/GetArticle.aspx?doi=10.1155/2007/47304

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Presentation slides from the 4th GSC Workshop held on 6-8th June 2007 at NIEeS in Cambridge, are now available from the NIEeS archive

NIEeS

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James Watson, co-discoverer of the DNA double helix and developer of the Human Genome Project, was presented with the DNA sequence data from his personal genome at Baylor College of Medicine in Houston on May 31st 2007.

Photos of the event are on flickr: photos

From the press release:

The $1 million, two-month project is a collaboration of 454 Life Sciences and the BCM Human Genome Sequencing Center, said Dr. Richard Gibbs, director of the HGSC and a scientific advisor to the Connecticut-based company. The announcement, aside from its meaning to Watson, is significant because it demonstrates that it will be possible in the future to sequence anyone’s genome – a goal toward which many sequencing firms are working. The time and cost will decrease as the technology improves.

A report on the project and a commentary on its ethical implications are scheduled to appear in the near future. The raw sequencing data was released today to the publicly available resource called GenBank National Center for Biotechnology Information Trace Archive

http://www.ncbi.nlm.nih.gov/Traces/trace.cgi

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The 4th Genomic Standards Consortium Workshop will be held next week, 6-8th June, 2007 at the National Institute for Environmental e-Science (NIEeS), Cambridge.

As at previous workshops there will be a mix of talks and discussion sessions, although this year the talks will be shorter and more focused on progress made towards GSC goals. There will be 6 sessions covering key topics of interest to the GSC.

There will be a special focus on progress to date, the development of MIMS, future implementation of MIGS/MIMS, CVs and ontologies for describing genomes and metagenomes, the need for a single, global list of genomes and metagenomes and the role of the GSC’s proposed Genomic Rosetta Stone.

The latest agenda is available on the GSC wiki. Workshop homepage on NIEeSweb site

Date: 6-8 June, 2007

Venue: National Institute for Environmental e-Science, Cambridge, UK

Organizers: Dawn Field, Tatiana Tatusova, Tanya Gray, George Garrity, and Frank Oliver Glöckner

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