English
 
User Manual Privacy Policy Disclaimer Contact us
  Advanced SearchBrowse

Item

ITEM ACTIONSEXPORT

Released

Journal Article

MetaBar - a tool for consistent contextual data acquisition and standards compliant submission

MPS-Authors
/persons/resource/persons210435

Hankeln,  W.
Microbial Genomics Group, Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Max Planck Society;

/persons/resource/persons210306

Buttigieg,  P. L.
HGF MPG Joint Research Group for Deep Sea Ecology & Technology, Max Planck Institute for Marine Microbiology, Max Planck Society;

/persons/resource/persons210370

Fink,  D.
Department of Symbiosis, Max Planck Institute for Marine Microbiology, Max Planck Society;

/persons/resource/persons210538

Kottmann,  R.
Microbial Genomics Group, Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Max Planck Society;

/persons/resource/persons210890

Yilmaz,  P.
Microbial Genomics Group, Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Max Planck Society;

/persons/resource/persons210403

Glöckner,  F. O.
Microbial Genomics Group, Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Max Planck Society;

External Ressource
No external resources are shared
Fulltext (public)

Hankeln10.pdf
(Publisher version), 2MB

Supplementary Material (public)
There is no public supplementary material available
Citation

Hankeln, W., Buttigieg, P. L., Fink, D., Kottmann, R., Yilmaz, P., & Glöckner, F. O. (2010). MetaBar - a tool for consistent contextual data acquisition and standards compliant submission. BMC Bioinformatics, 11, 1-8.


Cite as: http://hdl.handle.net/21.11116/0000-0001-CB0A-0
Abstract
Background: Environmental sequence datasets are increasing at an exponential rate; however, the vast majority of them lack appropriate descriptors like sampling location, time and depth/altitude: generally referred to as metadata or contextual data. The consistent capture and structured submission of these data is crucial for integrated data analysis and ecosystems modeling. The application MetaBar has been developed, to support consistent contextual data acquisition. Results: MetaBar is a spreadsheet and web-based software tool designed to assist users in the consistent acquisition, electronic storage, and submission of contextual data associated to their samples. A preconfigured Microsoft Excel spreadsheet is used to initiate structured contextual data storage in the field or laboratory. Each sample is given a unique identifier and at any stage the sheets can be uploaded to the MetaBar database server. To label samples, identifiers can be printed as barcodes. An intuitive web interface provides quick access to the contextual data in the MetaBar database as well as user and project management capabilities. Export functions facilitate contextual and sequence data submission to the International Nucleotide Sequence Database Collaboration (INSDC), comprising of the DNA DataBase of Japan (DDBJ), the European Molecular Biology Laboratory database (EMBL) and GenBank. MetaBar requests and stores contextual data in compliance to the Genomic Standards Consortium specifications. The MetaBar open source code base for local installation is available under the GNU General Public License version 3 (GNU GPL3). Conclusion: The MetaBar software supports the typical workflow from data acquisition and field-sampling to contextual data enriched sequence submission to an INSDC database. The integration with the megx.net marine Ecological Genomics database and portal facilitates georeferenced data integration and metadata-based comparisons of sampling sites as well as interactive data visualization. The ample export functionalities and the INSDC submission support enable exchange of data across disciplines and safeguarding contextual data.