Putting Molecules on the Map
From Genomic Standards Consortium
[edit] Putting Molecules on the Map
At the heart of the MIGS specification is a call for all genomes and metagenomes to be reported with geographic location (lat/long). We were therefore very pleased to see a Nature Editorial calling for ALL biological samples to be tagged with lat/long. We responded with a Nature Correspondence to underscore our collaborative interest in seeing all molecules (in particular genomes, metagenomes and phylogenetic markers like 16S/18S ribosomal RNA genes) placed into a geospatial framework. Location of isolation is increasingly of relevance as an informative piece of contextual data for the interpretation of collections of sequences.
The original Editorial can be found here: http://www.nature.com/nature/journal/v453/n7191/full/453002a.html
Our response is here (see bottom of article for all signatories including the GSC): http://www.nature.com/nature/journal/v453/n7198/full/453978b.html
Both pieces are available as free content and can be accessed without a subscription to Nature.
[edit] Affiliations of all Signatories on Nature Correspondence
The full list of signatory affiliations are given below.
Dawn Field
NERC Centre for Ecology and Hydrology, Mansfield Rd Oxford OX1 3SR, UK.
Norman Morrison
School of Computer Science, University of Manchester, Manchester M13 9PL, UK and the NERC Environmental Bioinformatics Centre, Oxford Centre for Ecology and Hydrology, Oxford OX1 3SR, UK.
Frank Oliver Gloeckner and Renzo Kottmann
Microbial Genomics Group, Max Planck Institute for Marine Microbiology and Jacobs University Bremen, Bremen 28359 Germany.
Guy Cochrane and Robert Vaughan
European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
George Garrity and James Cole
Michigan State University, East Lansing, Michigan, 48824, USA
Lynette Hirschman
Information Technology Center, The MITRE Corporation, Bedford, Massachusetts, 01730, USA
Lynn Schriml
Institute for Genome Sciences and Department of Epidemiology and Preventive Medicine, University of Maryland School of Medicine, 685 West Baltimore Street, Baltimore, Maryland 21201, USA.
Ilene Mizrachi and Scott Federhen
National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, Maryland 20894, USA
Yoshio Tateno
Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka 411-8540, Japan.
David Schindel and Scott Miller
Smithsonian Institution, Washington, DC, 20013-7012, USA
Paul Hebert, Sujeevan Ratnasingham, Robert Hanner
Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G2W1, Canada
Linda Amaral-Zettler and Mitchell Sogin
Josephine Bay Paul Center, Marine Biological Laboratory, 7 MBL Street Woods Hole MA 02543, USA
Michael Ashburner
Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK.
Suzanna Lewis
Genomics Group, Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA.
Barry Smith
Department of Philosophy and New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, 701 Ellicott Street, Buffalo,New York 14203, USA.
Genomic Standards Consortium (GSC) http://gensc.org
International Nucleotide Sequence Database Collaboration (INSDC) http://insdc.org
The Consortium for the Barcode of Life (CBOL)http://www.barcoding.si.edu/
The International Census of Marine Microbes (ICoMM)http://icomm.mbl.edu/
The Environment Ontology Consortium (EnvO) http://environmentontology.org
[edit] Databases containing molecules and latitude/longitude and maps
Increasingly, molecules are being put on the map. Here are some examples. Please feel free to add more.
EMBL Access to data via map
"In 2005 International Nucleotide Sequence Database Collaboration introduced new lat_lon (latitude-longitude) qualifier that allows to describe precisely where the sequenced specimen was collected. The data collected so far can now be seen plotted on the world map."
URL: http://www3.ebi.ac.uk/Services/EMBLWorld/EMBLWorld.pl
and Geographic-BLAST available at http://www.megx.net/mm/genomes_mapserver-1.0/geoblast.php
