Archive for the ‘ontology’ Category

Further to the 5th Genomic Standards Consortium (GSC) workshop, slides are available to download from the GSC wiki:

agenda and presentations


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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.


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.


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The Genomic Standards Consortium will be hosting a Birds of a Feather meeting at ISMB/ECCB 2007.

Date: Monday 23rd July 2007
Time: 12.15pm – 1.30pm
Room: see noticeboards

An open invitation :-
Meet members of the Genomic Standards Consortium
Learn about the activities of the Genomic Standards Consortium
Find out how to participate in the work of the Genomic Standards Consortium
Join in an open discussion

Meeting agenda:

* 12.30 – 12.40 : Introduction by Tatiana Tatusov
* 12.40 – 12.50 : Dawn Field – Overview of Genomic Standards Consortium (GSC) Activities
* 12.50 – 13.00 : Robert Stevens – Harnessing Ontologies to Describe Genomes
* 13.00 – 13.10 : Lynette Hirschman – Mining Metadata for Metagenomics
* 13.10 – 13.30 : Open Discussion


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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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EnvO (Environmental Ontology) is a collaboration between many individuals and groups interested in how we describe the environment.

The EnvO project homepage is currently under construction. Contact Norman Morrison for further details: morrison at cs.man.ac.uk.

The Genomic Standards Consortium will be helping to sponsor the first EnvO Workshop.

EnvO mailing list: https://lists.sourceforge.net/lists/listinfo/obo-envo

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