Feeds:
Posts
Comments

Archive for April, 2007

The latest release of the Genomic Standards Consortium Genome Catalogue is now available:

http://gensc.sf.net

Features are described in the
GSC wiki

Read Full Post »

The current GSC publication list:

The MIGS manuscript: The Nature Biotech community consultation concluded April 19th, 2007. Decision by NBT pending.

Nature Biotech

GSC Meeting Reports

  • Dawn Field, George Garrity, Tanya Gray, Jeremy Selengut, Peter Sterk, Nick Thomson, Tatiana Tatusova, Guy Cochrane, Frank Oliver Glockner, Renzo Kottmann, Allyson L. Lister, Yoshio Tateno, and Robert Vaughan. (2007) Meeting Report: eGenomics: Cataloguing Our Complete Genome Collection III. Comparative and Functional Genomics: A journal of integrative biology (2006) June, Vol. 10, No. 2: 100 -104.

PDF – Uncorrected proof Journal PubMed

  • Field D, Morrison N, Selengut J, Sterk P. Meeting Report: eGenomics: Cataloguing Our Complete Genome Collection II. OMICS: A journal of integrative biology (2006) June, Vol. 10, No. 2: 100 -104.

PDF Journal PubMed

  • Field D, Garrity G, Morrison N, Selengut J, Sterk P, Thomson N, Tatusova T. Meeting Report: eGenomics: Cataloguing our Complete Genome Collection. Comparative and Functional Genomics (2006) 6: 363-368.

PDF Journal

 

Special Issue of OMICS

Papers from the special issue of OMICS (http://www.liebertonline.com/toc/omi/10/2) on data standards that emerged from the 2nd and 1st GSC workshops:

  • Field D, Sansone S-A. A special issue on Omic data standards. OMICS: A journal of integrative biology (2006) June, Vol. 10, No. 2: 84 -93

PDF Journal PubMed

  • Morrison N, Cochrane G, Faruque N, Tatusova T, Tateno Y, Hancock D, and Field D. The concept of Sample in Omics Technology. OMICS: A journal of integrative biology (2006) June, Vol. 10, No. 2: 127 -137 .

PDF PubMed

OMICS Journal

Related papers: standardization of genomic databases

  • Jeffrey L. Boore. Requirements and Standards for Organelle Genome Databases. OMICS: A Journal of Integrative Biology (2006) June, Vol. 10, No. 2 : 119 -126.

PDF Journal PubMed

  • Guy Cochrane, Kirsty Bates, Rolf Apweiler, Yoshio Tateno, Jun Mashima, Takehide Kosuge, Ilene Karsch Mizrachi, Susan Schafer, Michael Fetchko. Evidence Standards in Experimental and Inferential INSDC Third Party Annotation Data. OMICS: A Journal of Integrative Biology (2006) June, 2006, Vol. 10, No. 2: 105-113.

PDF Journal PubMed

  • Peter Sterk, Paul J. Kersey, Rolf Apweiler. Genome Reviews: Standardizing Content and Representation of Information about Complete Genomes OMICS: A Journal of Integrative Biology (2006) June, 2006, Vol. 10, No. 2: 114-118.

PDF Journal PubMed

 

Development of Ontologies relevant to the description of genomes and metagenomes

  • Whetzel P.L, Brinkman R.R, Causton H.C, Fan L, Field D, Fostel J, Fragaso G, Gray T, Heiskanen M, Hernandez-Boussard T, Morrison N, Parkinson H, Rocca-Serra P, Sansone S-A, Schober D, Smith B, Stevens R, Stoeckert Jnr C.J, Taylor C, White J, Wood A, and the FuGO Working Group. Development of FuGO: An Ontology for Functional Genomics Investigations. OMICS: A journal of integrative biology (2006) June, Vol. 10, No. 2: 199 -204.

PDF Journal PubMed

Initial Proposal for MIGS

  • Field D, & Hughes J. Cataloguing our current genome collection. Microbiology (2005) 151, 1016-1019.

PDF Journal PubMed

  • The review paper that led to the above call for MIGS: Martiny, J.B.H. and D. Field. Ecological perspectives on the sequenced genome collection. (2005) Ecology Letters 8: 1334-1345.

PDF Journal

See the GSC wiki for the latest publications list: http://darwin.nerc-oxford.ac.uk/gc_wiki/index.php/GSC_Publications

Read Full Post »

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

Read Full Post »

 GSC logo

A new mashup function has been added to the Genome Catalogue that combines content from sites including NCBI Genome Project, PubMed, Flickr and even YouTube video!

You can either enter your own search term, or else link to the Query the Web page from one of the genome reports contained in the Genome Catalogue.

Here is an example query for Streptococcus:

http://darwin.nox.ac.uk/gsc/gcat/mashup?query=Streptococcus

Read Full Post »

The rhesus macaque monkey (Macaca mulatta) genome was described in the 13th April issue of Science Magazine.

Genome report for Macaca mulatta:

http://darwin.nox.ac.uk/gsc/ gcat/report/002485_GCAT/html

Genome wiki page:

http://darwin.nerc-oxford.ac.uk/gc_wiki/index.php/ /gcat/report/002485_GCAT/html

Genome mashup for macaque genome:

http://darwin.nox.ac.uk/gsc/gcat /mashup?query=macaque%20genome,  returned the following three videos from YouTube:

Macaque Genome video part I

Read Full Post »