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Megx.net: integrated database resource for marine ecological genomics

R. Kottmann, I. Kostadinov, M. B. Duhaime, P. L. Buttigieg, P. Yilmaz, W. Hankeln, J. Waldmann, F. O. Glockner
2009 Nucleic Acids Research  
ACKNOWLEDGEMENTS We would like to acknowledge Timmy Schweer, Thierry Lombardot, Magdalena Golden and Laura Sandrine for their valuable input to megx.net, as well as David E.  ...  Todd for redesigning the web page.  ...  NEW DATABASE STRUCTURE AND CONTENT The Microbial Ecological Genomics DataBase (MegDB), the backbone of megx.net, is a centralized database based on the PostgreSQL database management system.  ... 
doi:10.1093/nar/gkp918 pmid:19858098 pmcid:PMC2808895 fatcat:3rmqab7tqzffzhighlpgp6fwba

Megx.net--database resources for marine ecological genomics

T. Lombardot
2006 Nucleic Acids Research  
These integrative databases and webserver will help researchers to generate a better understanding of the functioning of marine ecosystems. All resources are freely accessible at http://www.megx.net.  ...  We introduce Megx.net, a set of databases and tools that handle genomic and metagenomic sequences in their environmental contexts.  ...  ACKNOWLEDGEMENTS We thank the Max Planck Society for initial funding and the EU Sixth Framework Programme (FP6-NEST) for providing financial support for further development of the Genomes Mapserver (contract  ... 
doi:10.1093/nar/gkj070 pmid:16381894 pmcid:PMC1347433 fatcat:zws2dhbd5bejzeleapcewv55nq

Enriching public descriptions of marine phages using the Genomic Standards Consortium MIGS standard

Melissa Beth Duhaime, Renzo Kottmann, Dawn Field, Frank Oliver Glöckner
2011 Standards in Genomic Sciences  
The Genomic Standards Consortium (GSC) has developed the "Minimum Information about Genome/Metagenome Sequences (MIGS/MIMS)" checklist for the description of genomes and here we annotate all 30 publicly  ...  available marine bacteriophage sequences to the MIGS standard.  ...  Having such environmental data easily accessible and integrated with sequenced entities via GCDML reports allows for a rapid, automated "first pass" evaluation of environmental/ecological clusters and  ... 
doi:10.4056/sigs.621069 pmid:21677864 pmcid:PMC3111985 fatcat:l35i7jzkobenzjtecddurphw4u

The MAR databases: development and implementation of databases specific for marine metagenomics

Terje Klemetsen, Inge A Raknes, Juan Fu, Alexander Agafonov, Sudhagar V Balasundaram, Giacomo Tartari, Espen Robertsen, Nils P Willassen
2017 Nucleic Acids Research  
While MarRef is a database for completely sequenced marine prokaryotic genomes, which represent a marine prokaryote reference genome database, MarDB includes all incomplete sequenced prokaryotic genomes  ...  We introduce the marine databases; MarRef, MarDB and MarCat (https://mmp.sfb.uit.no/databases/), which are publicly available resources that promote marine research and innovation.  ...  ACKNOWLEDGEMENTS We thank all the experts who contributed to the MMP database annotations from their field of expertise, especially ELIXIR EXCELERATE WP6 partners.  ... 
doi:10.1093/nar/gkx1036 pmid:29106641 pmcid:PMC5753341 fatcat:wgg4tz754zcebam7dvtoddoawm

The environment ontology: contextualising biological and biomedical entities

Pier Buttigieg, Norman Morrison, Barry Smith, Christopher J Mungall, Suzanna E Lewis
2013 Journal of Biomedical Semantics  
As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors  ...  The Environment Ontology (ENVO; www.environmentontology.org) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science  ...  For example, the Marine Ecological GenomiX portal (Megx.net; [41] ) offers a manual annotation of a portion of the genome collection using classes from Habitat-Lite [42, 43] , a proper subset of ENVO  ... 
doi:10.1186/2041-1480-4-43 pmid:24330602 pmcid:PMC3904460 fatcat:boxqxyq2pnen3nzboofx2dvsd4

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 (+1 others)
2007 Comparative and Functional Genomics  
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.  ...  (www.metafunctions.org) that integrates genomic information with habitat parameters, and described the design and use of the Megx.net database [10] .  ... 
doi:10.1155/2007/47304 fatcat:ukz5zp7njjdw5os65arn2q2efy

Meeting Report from the Genomic Standards Consortium (GSC) Workshop 9

Tanja Davidsen, Ramana Madupu, Peter Sterk, Dawn Field, George Garrity, Jack Gilbert, Frank Oliver Glöckner, Lynette Hirschman, Eugene Kolker, Renzo Kottmann, Nikos Kyrpides, Folker Meyer (+4 others)
2010 Standards in Genomic Sciences  
It included sessions on Standards in Genomic Sciences, the open access journal of the GSC, building standards for genome annotation, the M5 platform for next-generation collaborative computational infrastructures  ...  This report summarizes the proceedings of the 9th workshop of the Genomic Standards Consortium (GSC), held at the J. Craig Venter Institute, Rockville, MD, USA.  ...  Lynette Hirschman has also been supported in part by NSF IIS 0844419: SGER for Utility and Usability of Text Mining for Biological Curation. We offer many thanks to our hosts at the J.  ... 
doi:10.4056/sigs.1353455 pmid:21304722 pmcid:PMC3035308 fatcat:gxlecmfcynhbri764staw4ante

Exploring research frontiers in microbiology: the challenge of metagenomics in soil microbiology

Stefano Mocali, Anna Benedetti
2010 Research in Microbiology  
Metagenomics, the study of the entire genome of soil biota, currently represents a powerful tool for assessing the diversity of complex microbial communities, providing access to a number of new species  ...  In this paper, the onset of new high-throughput metagenomic approaches and new perspectives in soil microbial ecology and data handling are discussed.  ...  /megan Algorithm which supports comparison of multiple and large datasets Megx.net http://www.megx.net Database tools for analysis of Marine Metagenomics MetaGene http://metagene.cb.k.u-tokyo.ac.jp  ... 
doi:10.1016/j.resmic.2010.04.010 pmid:20452420 fatcat:qhyocb2brnh5zpcm3dgeatbxdu

Towards an Integrated Biodiversity and Ecological Research Data Management and Archiving Platform: The German Federation for the Curation of Biological Data (GFBio)

Michael Diepenbroek, Frank Oliver Glöckner, Peter Grobe, Anton Güntsch, Robert Huber, Birgitta König-Ries, Ivaylo Kostadinov, Jens Nieschulze, Bernhard Seeger, Robert Tolksdorf, Dagmar Triebel
2014 Jahrestagung der Gesellschaft für Informatik  
Its data management is characterized by integration and is particularly challenging due to the large volume and tremendous heterogeneity of the data.  ...  Stephan Frickenhaus, Christoph Häuser, Thomas Hickler, Jens Kattge, Heike Neuroth, Jörg Overmann, Jens Schumacher, Johann Wägele, Christian Wirth, Ramin Yahyapour) and everyone else involved in GFBio for  ...  The Megx.net portal 7 integrates microbial genomic and environmental data based on georeferencing.  ... 
dblp:conf/gi/DiepenbroekGGGHKKNSTT14 fatcat:njes2auh35ezboikw5ueu2s2l4

GenGIS: A geospatial information system for genomic data

D. H. Parks, M. Porter, S. Churcher, S. Wang, C. Blouin, J. Whalley, S. Brooks, R. G. Beiko
2009 Genome Research  
The development of GenGIS has been supported by Genome Atlantic, the Natural Sciences and Engineering Research Council of Canada, the Canada Foundation for Innovation, and the Dalhousie Faculty of Computer  ...  Acknowledgments We thank Harman Clair, Norman MacDonald, and Gregory Smolyn for assistance with the development of GenGIS.  ...  Existing tools such as megx.net (Lombardot et al. 2006) and Micro-Mar (Pushker et al. 2005) integrate marine microbial data with environmental variables and a world map, and the aforementioned geophylogeny  ... 
doi:10.1101/gr.095612.109 pmid:19635847 pmcid:PMC2765287 fatcat:6zmsoeul6jhvth5spckjmc47wa

A Primer on Metagenomics

John C. Wooley, Adam Godzik, Iddo Friedberg, Philip E. Bourne
2010 PLoS Computational Biology  
Metagenomics is a discipline that enables the genomic study of uncultured microorganisms.  ...  In cultured microbes, the genomic data come from a single clone, making sequence assembly and annotation tractable.  ...  Acknowledgments We would like to thank Linda Amaral-Zettler, Yanay Ofran, Daniel Huson, Jack Gilbert, Mufit Ozden, Frank Oliver Glöckner, and Renzo Kottmann for their critique and input.  ... 
doi:10.1371/journal.pcbi.1000667 pmid:20195499 pmcid:PMC2829047 fatcat:ykwqb3r4preo7is4vcqlk2caey

Assessing the Polysaccharide Degradation Potential in Marine Microbial Genomes and Metagenomes [article]

Sixing Huang, Universität Bremen, Universität Bremen, Rudolf Amann
2020
This doctoral project focuses on CAZyme distributions in marine genomic and metagenomic studies with a focus on the MIMAS (Microbial Interactions in Marine Systems) Project and a sediment sample from the  ...  This limits not only our interpretation of the 'omics (in particular metagenomic) data and understanding of marine ecosystems, but it also keeps us from utilizing this vast enzyme repertoire for biotechnological  ...  Acknowledgements We thank Tobin J Hammer for fruitful discussions and proof reading of the paper.  ... 
doi:10.26092/elib/44 fatcat:qfdecrkxavcotn7kjtrbkuhjhi

The Gut Microbiome In Healthy And Severely Malnourished Humans

Tanya Yatsunenko
2011
Finally, I characterized assembly of gut microbiomes in a cohort of Malawian twins concordant for healthy status and twins discordant for severe forms of malnutrition (kwashiorkor or marasmus).  ...  I found that the fecal microbiota and microbiome are stable within each co-twin even in the face of ecologic invasion with a popular commercial fermented diary product.  ...  Acknowledgements acKnoWLedGments We thank our collaborators for their helpful suggestions on features, documentation and the manuscript, and our funding agencies for their commitment to open-source software  ... 
doi:10.7936/k7n58jdw fatcat:cofism3k4belpctinyexb6egoy