The Experts below are selected from a list of 5385 Experts worldwide ranked by ideXlab platform
Frank Oliver Glockner - One of the best experts on this subject based on the ideXlab platform.
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identification of habitat specific biomes of aquatic fungal communities using a comprehensive nearly full length 18s rrna Dataset enriched with Contextual Data
PLOS ONE, 2015Co-Authors: Katrin Panzer, Pelin Yilmaz, Michael Weis, Lothar Reich, Michael Richter, Jutta Wiese, Rolf Schmaljohann, Antje Labes, Johannes F Imhoff, Frank Oliver GlocknerAbstract:Molecular diversity surveys have demonstrated that aquatic fungi are highly diverse, and that they play fundamental ecological roles in aquatic systems. Unfortunately, comparative studies of aquatic fungal communities are few and far between, due to the scarcity of adequate Datasets. We combined all publicly available fungal 18S ribosomal RNA (rRNA) gene sequences with new sequence Data from a marine fungi culture collection. We further enriched this Dataset by adding validated Contextual Data. Specifically, we included Data on the habitat type of the samples assigning fungal taxa to ten different habitat categories. This Dataset has been created with the intention to serve as a valuable reference Dataset for aquatic fungi including a phylogenetic reference tree. The combined Data enabled us to infer fungal community patterns in aquatic systems. Pairwise habitat comparisons showed significant phylogenetic differences, indicating that habitat strongly affects fungal community structure. Fungal taxonomic composition differed considerably even on phylum and class level. Freshwater fungal assemblage was most different from all other habitat types and was dominated by basal fungal lineages. For most communities, phylogenetic signals indicated clustering of sequences suggesting that environmental factors were the main drivers of fungal community structure, rather than species competition. Thus, the diversification process of aquatic fungi must be highly clade specific in some cases.The combined Data enabled us to infer fungal community patterns in aquatic systems. Pairwise habitat comparisons showed significant phylogenetic differences, indicating that habitat strongly affects fungal community structure. Fungal taxonomic composition differed considerably even on phylum and class level. Freshwater fungal assemblage was most different from all other habitat types and was dominated by basal fungal lineages. For most communities, phylogenetic signals indicated clustering of sequences suggesting that environmental factors were the main drivers of fungal community structure, rather than species competition. Thus, the diversification process of aquatic fungi must be highly clade specific in some cases.
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cdinfusion submission ready on line integration of sequence and Contextual Data
PLOS ONE, 2011Co-Authors: Wolfgang Hankeln, Renzo Kottmann, Pelin Yilmaz, Pier Luigi Buttigieg, Norma Johanna Wendel, Jan Gerken, Jost Waldmann, Ivaylo Kostadinov, Frank Oliver GlocknerAbstract:State of the art (DNA) sequencing methods applied in “Omics” studies grant insight into the ‘blueprints’ of organisms from all domains of life. Sequencing is carried out around the globe and the Data is submitted to the public repositories of the International Nucleotide Sequence Database Collaboration. However, the context in which these studies are conducted often gets lost, because experimental Data, as well as information about the environment are rarely submitted along with the sequence Data. If these Contextual or metaData are missing, key opportunities of comparison and analysis across studies and habitats are hampered or even impossible. To address this problem, the Genomic Standards Consortium (GSC) promotes checklists and standards to better describe our sequence Data collection and to promote the capturing, exchange and integration of sequence Data with Contextual Data. In a recent community effort the GSC has developed a series of recommendations for Contextual Data that should be submitted along with sequence Data. To support the scientific community to significantly enhance the quality and quantity of Contextual Data in the public sequence Data repositories, specialized software tools are needed. In this work we present CDinFusion, a web-based tool to integrate Contextual and sequence Data in (Multi)FASTA format prior to submission. The tool is open source and available under the Lesser GNU Public License 3. A public installation is hosted and maintained at the Max Planck Institute for Marine Microbiology at http://www.megx.net/cdinfusion. The tool may also be installed locally using the open source code available at http://code.google.com/p/cdinfusion.
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CDinFusion – Submission-Ready, On-Line Integration of Sequence and Contextual Data
PLOS ONE, 2011Co-Authors: Wolfgang Hankeln, Renzo Kottmann, Pelin Yilmaz, Pier Luigi Buttigieg, Norma Johanna Wendel, Jan Gerken, Jost Waldmann, Ivaylo Kostadinov, Frank Oliver GlocknerAbstract:State of the art (DNA) sequencing methods applied in “Omics” studies grant insight into the ‘blueprints’ of organisms from all domains of life. Sequencing is carried out around the globe and the Data is submitted to the public repositories of the International Nucleotide Sequence Database Collaboration. However, the context in which these studies are conducted often gets lost, because experimental Data, as well as information about the environment are rarely submitted along with the sequence Data. If these Contextual or metaData are missing, key opportunities of comparison and analysis across studies and habitats are hampered or even impossible. To address this problem, the Genomic Standards Consortium (GSC) promotes checklists and standards to better describe our sequence Data collection and to promote the capturing, exchange and integration of sequence Data with Contextual Data. In a recent community effort the GSC has developed a series of recommendations for Contextual Data that should be submitted along with sequence Data. To support the scientific community to significantly enhance the quality and quantity of Contextual Data in the public sequence Data repositories, specialized software tools are needed. In this work we present CDinFusion, a web-based tool to integrate Contextual and sequence Data in (Multi)FASTA format prior to submission. The tool is open source and available under the Lesser GNU Public License 3. A public installation is hosted and maintained at the Max Planck Institute for Marine Microbiology at http://www.megx.net/cdinfusion. The tool may also be installed locally using the open source code available at http://code.google.com/p/cdinfusion.
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metabar a tool for consistent Contextual Data acquisition and standards compliant submission
BMC Bioinformatics, 2010Co-Authors: Wolfgang Hankeln, Renzo Kottmann, Pelin Yilmaz, Pier Luigi Buttigieg, Frank Oliver Glockner, Dennis FinkAbstract: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.
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MetaBar - a tool for consistent Contextual Data acquisition and standards compliant submission.
BMC bioinformatics, 2010Co-Authors: Wolfgang Hankeln, Renzo Kottmann, Pelin Yilmaz, Pier Luigi Buttigieg, Dennis Fink, Frank Oliver GlocknerAbstract: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.\n\nRESULTS: 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).\n\nCONCLUSION: 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.
Pelin Yilmaz - One of the best experts on this subject based on the ideXlab platform.
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plant specimen Contextual Data consensus
GigaScience, 2016Co-Authors: Petra Ten Hoopen, Ramona Walls, Ethalinda K S Cannon, Guy Cochrane, James R Cole, Anjanette Johnston, Ilene Karschmizrachi, Pelin YilmazAbstract:: The Compliance and Interoperability Working Group of the Genomic Standards Consortium facilitates the establishment of a community of experts and the development of recommendations to describe genomic Data and associated information. Here we present our ongoing conation to harmonise the reporting of Contextual plant specimen Data associated with genomics and functional genomics. This commentary summarises the current state of our plant sample Contextual Data harmonisation efforts to engage a broad plant science community.
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identification of habitat specific biomes of aquatic fungal communities using a comprehensive nearly full length 18s rrna Dataset enriched with Contextual Data
PLOS ONE, 2015Co-Authors: Katrin Panzer, Pelin Yilmaz, Michael Weis, Lothar Reich, Michael Richter, Jutta Wiese, Rolf Schmaljohann, Antje Labes, Johannes F Imhoff, Frank Oliver GlocknerAbstract:Molecular diversity surveys have demonstrated that aquatic fungi are highly diverse, and that they play fundamental ecological roles in aquatic systems. Unfortunately, comparative studies of aquatic fungal communities are few and far between, due to the scarcity of adequate Datasets. We combined all publicly available fungal 18S ribosomal RNA (rRNA) gene sequences with new sequence Data from a marine fungi culture collection. We further enriched this Dataset by adding validated Contextual Data. Specifically, we included Data on the habitat type of the samples assigning fungal taxa to ten different habitat categories. This Dataset has been created with the intention to serve as a valuable reference Dataset for aquatic fungi including a phylogenetic reference tree. The combined Data enabled us to infer fungal community patterns in aquatic systems. Pairwise habitat comparisons showed significant phylogenetic differences, indicating that habitat strongly affects fungal community structure. Fungal taxonomic composition differed considerably even on phylum and class level. Freshwater fungal assemblage was most different from all other habitat types and was dominated by basal fungal lineages. For most communities, phylogenetic signals indicated clustering of sequences suggesting that environmental factors were the main drivers of fungal community structure, rather than species competition. Thus, the diversification process of aquatic fungi must be highly clade specific in some cases.The combined Data enabled us to infer fungal community patterns in aquatic systems. Pairwise habitat comparisons showed significant phylogenetic differences, indicating that habitat strongly affects fungal community structure. Fungal taxonomic composition differed considerably even on phylum and class level. Freshwater fungal assemblage was most different from all other habitat types and was dominated by basal fungal lineages. For most communities, phylogenetic signals indicated clustering of sequences suggesting that environmental factors were the main drivers of fungal community structure, rather than species competition. Thus, the diversification process of aquatic fungi must be highly clade specific in some cases.
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cdinfusion submission ready on line integration of sequence and Contextual Data
PLOS ONE, 2011Co-Authors: Wolfgang Hankeln, Renzo Kottmann, Pelin Yilmaz, Pier Luigi Buttigieg, Norma Johanna Wendel, Jan Gerken, Jost Waldmann, Ivaylo Kostadinov, Frank Oliver GlocknerAbstract:State of the art (DNA) sequencing methods applied in “Omics” studies grant insight into the ‘blueprints’ of organisms from all domains of life. Sequencing is carried out around the globe and the Data is submitted to the public repositories of the International Nucleotide Sequence Database Collaboration. However, the context in which these studies are conducted often gets lost, because experimental Data, as well as information about the environment are rarely submitted along with the sequence Data. If these Contextual or metaData are missing, key opportunities of comparison and analysis across studies and habitats are hampered or even impossible. To address this problem, the Genomic Standards Consortium (GSC) promotes checklists and standards to better describe our sequence Data collection and to promote the capturing, exchange and integration of sequence Data with Contextual Data. In a recent community effort the GSC has developed a series of recommendations for Contextual Data that should be submitted along with sequence Data. To support the scientific community to significantly enhance the quality and quantity of Contextual Data in the public sequence Data repositories, specialized software tools are needed. In this work we present CDinFusion, a web-based tool to integrate Contextual and sequence Data in (Multi)FASTA format prior to submission. The tool is open source and available under the Lesser GNU Public License 3. A public installation is hosted and maintained at the Max Planck Institute for Marine Microbiology at http://www.megx.net/cdinfusion. The tool may also be installed locally using the open source code available at http://code.google.com/p/cdinfusion.
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CDinFusion – Submission-Ready, On-Line Integration of Sequence and Contextual Data
PLOS ONE, 2011Co-Authors: Wolfgang Hankeln, Renzo Kottmann, Pelin Yilmaz, Pier Luigi Buttigieg, Norma Johanna Wendel, Jan Gerken, Jost Waldmann, Ivaylo Kostadinov, Frank Oliver GlocknerAbstract:State of the art (DNA) sequencing methods applied in “Omics” studies grant insight into the ‘blueprints’ of organisms from all domains of life. Sequencing is carried out around the globe and the Data is submitted to the public repositories of the International Nucleotide Sequence Database Collaboration. However, the context in which these studies are conducted often gets lost, because experimental Data, as well as information about the environment are rarely submitted along with the sequence Data. If these Contextual or metaData are missing, key opportunities of comparison and analysis across studies and habitats are hampered or even impossible. To address this problem, the Genomic Standards Consortium (GSC) promotes checklists and standards to better describe our sequence Data collection and to promote the capturing, exchange and integration of sequence Data with Contextual Data. In a recent community effort the GSC has developed a series of recommendations for Contextual Data that should be submitted along with sequence Data. To support the scientific community to significantly enhance the quality and quantity of Contextual Data in the public sequence Data repositories, specialized software tools are needed. In this work we present CDinFusion, a web-based tool to integrate Contextual and sequence Data in (Multi)FASTA format prior to submission. The tool is open source and available under the Lesser GNU Public License 3. A public installation is hosted and maintained at the Max Planck Institute for Marine Microbiology at http://www.megx.net/cdinfusion. The tool may also be installed locally using the open source code available at http://code.google.com/p/cdinfusion.
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metabar a tool for consistent Contextual Data acquisition and standards compliant submission
BMC Bioinformatics, 2010Co-Authors: Wolfgang Hankeln, Renzo Kottmann, Pelin Yilmaz, Pier Luigi Buttigieg, Frank Oliver Glockner, Dennis FinkAbstract: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.
Renzo Kottmann - One of the best experts on this subject based on the ideXlab platform.
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cdinfusion submission ready on line integration of sequence and Contextual Data
PLOS ONE, 2011Co-Authors: Wolfgang Hankeln, Renzo Kottmann, Pelin Yilmaz, Pier Luigi Buttigieg, Norma Johanna Wendel, Jan Gerken, Jost Waldmann, Ivaylo Kostadinov, Frank Oliver GlocknerAbstract:State of the art (DNA) sequencing methods applied in “Omics” studies grant insight into the ‘blueprints’ of organisms from all domains of life. Sequencing is carried out around the globe and the Data is submitted to the public repositories of the International Nucleotide Sequence Database Collaboration. However, the context in which these studies are conducted often gets lost, because experimental Data, as well as information about the environment are rarely submitted along with the sequence Data. If these Contextual or metaData are missing, key opportunities of comparison and analysis across studies and habitats are hampered or even impossible. To address this problem, the Genomic Standards Consortium (GSC) promotes checklists and standards to better describe our sequence Data collection and to promote the capturing, exchange and integration of sequence Data with Contextual Data. In a recent community effort the GSC has developed a series of recommendations for Contextual Data that should be submitted along with sequence Data. To support the scientific community to significantly enhance the quality and quantity of Contextual Data in the public sequence Data repositories, specialized software tools are needed. In this work we present CDinFusion, a web-based tool to integrate Contextual and sequence Data in (Multi)FASTA format prior to submission. The tool is open source and available under the Lesser GNU Public License 3. A public installation is hosted and maintained at the Max Planck Institute for Marine Microbiology at http://www.megx.net/cdinfusion. The tool may also be installed locally using the open source code available at http://code.google.com/p/cdinfusion.
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CDinFusion – Submission-Ready, On-Line Integration of Sequence and Contextual Data
PLOS ONE, 2011Co-Authors: Wolfgang Hankeln, Renzo Kottmann, Pelin Yilmaz, Pier Luigi Buttigieg, Norma Johanna Wendel, Jan Gerken, Jost Waldmann, Ivaylo Kostadinov, Frank Oliver GlocknerAbstract:State of the art (DNA) sequencing methods applied in “Omics” studies grant insight into the ‘blueprints’ of organisms from all domains of life. Sequencing is carried out around the globe and the Data is submitted to the public repositories of the International Nucleotide Sequence Database Collaboration. However, the context in which these studies are conducted often gets lost, because experimental Data, as well as information about the environment are rarely submitted along with the sequence Data. If these Contextual or metaData are missing, key opportunities of comparison and analysis across studies and habitats are hampered or even impossible. To address this problem, the Genomic Standards Consortium (GSC) promotes checklists and standards to better describe our sequence Data collection and to promote the capturing, exchange and integration of sequence Data with Contextual Data. In a recent community effort the GSC has developed a series of recommendations for Contextual Data that should be submitted along with sequence Data. To support the scientific community to significantly enhance the quality and quantity of Contextual Data in the public sequence Data repositories, specialized software tools are needed. In this work we present CDinFusion, a web-based tool to integrate Contextual and sequence Data in (Multi)FASTA format prior to submission. The tool is open source and available under the Lesser GNU Public License 3. A public installation is hosted and maintained at the Max Planck Institute for Marine Microbiology at http://www.megx.net/cdinfusion. The tool may also be installed locally using the open source code available at http://code.google.com/p/cdinfusion.
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metabar a tool for consistent Contextual Data acquisition and standards compliant submission
BMC Bioinformatics, 2010Co-Authors: Wolfgang Hankeln, Renzo Kottmann, Pelin Yilmaz, Pier Luigi Buttigieg, Frank Oliver Glockner, Dennis FinkAbstract: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.
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MetaBar - a tool for consistent Contextual Data acquisition and standards compliant submission.
BMC bioinformatics, 2010Co-Authors: Wolfgang Hankeln, Renzo Kottmann, Pelin Yilmaz, Pier Luigi Buttigieg, Dennis Fink, Frank Oliver GlocknerAbstract: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.\n\nRESULTS: 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).\n\nCONCLUSION: 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.
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a standard migs mims compliant xml schema toward the development of the genomic Contextual Data markup language gcdml
Omics A Journal of Integrative Biology, 2008Co-Authors: Renzo Kottmann, Tanya Gray, Sean Murphy, Leonid Kagan, Saul Kravitz, Thierry Lombardot, Dawn Field, Frank Oliver GlocknerAbstract:The Genomic Contextual Data Markup Language (GCDML) is a core project of the Genomic Standards Consortium (GSC) that implements the “Minimum Information about a Genome Sequence” (MIGS) specification and its extension, the “Minimum Information about a Metagenome Sequence” (MIMS). GCDML is an XML Schema for generating MIGS/MIMS compliant reports for Data entry, exchange, and storage. When mature, this sample-centric, strongly-typed schema will provide a diverse set of descriptors for describing the exact origin and processing of a biological sample, from sampling to sequencing, and subsequent analysis. Here we describe the need for such a project, outline design principles required to support the project, and make an open call for participation in defining the future content of GCDML. GCDML is freely available, and can be downloaded, along with documentation, from the GSC Web site (http://gensc.org).
Wolfgang Hankeln - One of the best experts on this subject based on the ideXlab platform.
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cdinfusion submission ready on line integration of sequence and Contextual Data
PLOS ONE, 2011Co-Authors: Wolfgang Hankeln, Renzo Kottmann, Pelin Yilmaz, Pier Luigi Buttigieg, Norma Johanna Wendel, Jan Gerken, Jost Waldmann, Ivaylo Kostadinov, Frank Oliver GlocknerAbstract:State of the art (DNA) sequencing methods applied in “Omics” studies grant insight into the ‘blueprints’ of organisms from all domains of life. Sequencing is carried out around the globe and the Data is submitted to the public repositories of the International Nucleotide Sequence Database Collaboration. However, the context in which these studies are conducted often gets lost, because experimental Data, as well as information about the environment are rarely submitted along with the sequence Data. If these Contextual or metaData are missing, key opportunities of comparison and analysis across studies and habitats are hampered or even impossible. To address this problem, the Genomic Standards Consortium (GSC) promotes checklists and standards to better describe our sequence Data collection and to promote the capturing, exchange and integration of sequence Data with Contextual Data. In a recent community effort the GSC has developed a series of recommendations for Contextual Data that should be submitted along with sequence Data. To support the scientific community to significantly enhance the quality and quantity of Contextual Data in the public sequence Data repositories, specialized software tools are needed. In this work we present CDinFusion, a web-based tool to integrate Contextual and sequence Data in (Multi)FASTA format prior to submission. The tool is open source and available under the Lesser GNU Public License 3. A public installation is hosted and maintained at the Max Planck Institute for Marine Microbiology at http://www.megx.net/cdinfusion. The tool may also be installed locally using the open source code available at http://code.google.com/p/cdinfusion.
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CDinFusion – Submission-Ready, On-Line Integration of Sequence and Contextual Data
PLOS ONE, 2011Co-Authors: Wolfgang Hankeln, Renzo Kottmann, Pelin Yilmaz, Pier Luigi Buttigieg, Norma Johanna Wendel, Jan Gerken, Jost Waldmann, Ivaylo Kostadinov, Frank Oliver GlocknerAbstract:State of the art (DNA) sequencing methods applied in “Omics” studies grant insight into the ‘blueprints’ of organisms from all domains of life. Sequencing is carried out around the globe and the Data is submitted to the public repositories of the International Nucleotide Sequence Database Collaboration. However, the context in which these studies are conducted often gets lost, because experimental Data, as well as information about the environment are rarely submitted along with the sequence Data. If these Contextual or metaData are missing, key opportunities of comparison and analysis across studies and habitats are hampered or even impossible. To address this problem, the Genomic Standards Consortium (GSC) promotes checklists and standards to better describe our sequence Data collection and to promote the capturing, exchange and integration of sequence Data with Contextual Data. In a recent community effort the GSC has developed a series of recommendations for Contextual Data that should be submitted along with sequence Data. To support the scientific community to significantly enhance the quality and quantity of Contextual Data in the public sequence Data repositories, specialized software tools are needed. In this work we present CDinFusion, a web-based tool to integrate Contextual and sequence Data in (Multi)FASTA format prior to submission. The tool is open source and available under the Lesser GNU Public License 3. A public installation is hosted and maintained at the Max Planck Institute for Marine Microbiology at http://www.megx.net/cdinfusion. The tool may also be installed locally using the open source code available at http://code.google.com/p/cdinfusion.
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metabar a tool for consistent Contextual Data acquisition and standards compliant submission
BMC Bioinformatics, 2010Co-Authors: Wolfgang Hankeln, Renzo Kottmann, Pelin Yilmaz, Pier Luigi Buttigieg, Frank Oliver Glockner, Dennis FinkAbstract: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.
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MetaBar - a tool for consistent Contextual Data acquisition and standards compliant submission.
BMC bioinformatics, 2010Co-Authors: Wolfgang Hankeln, Renzo Kottmann, Pelin Yilmaz, Pier Luigi Buttigieg, Dennis Fink, Frank Oliver GlocknerAbstract: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.\n\nRESULTS: 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).\n\nCONCLUSION: 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.
Pier Luigi Buttigieg - One of the best experts on this subject based on the ideXlab platform.
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cdinfusion submission ready on line integration of sequence and Contextual Data
PLOS ONE, 2011Co-Authors: Wolfgang Hankeln, Renzo Kottmann, Pelin Yilmaz, Pier Luigi Buttigieg, Norma Johanna Wendel, Jan Gerken, Jost Waldmann, Ivaylo Kostadinov, Frank Oliver GlocknerAbstract:State of the art (DNA) sequencing methods applied in “Omics” studies grant insight into the ‘blueprints’ of organisms from all domains of life. Sequencing is carried out around the globe and the Data is submitted to the public repositories of the International Nucleotide Sequence Database Collaboration. However, the context in which these studies are conducted often gets lost, because experimental Data, as well as information about the environment are rarely submitted along with the sequence Data. If these Contextual or metaData are missing, key opportunities of comparison and analysis across studies and habitats are hampered or even impossible. To address this problem, the Genomic Standards Consortium (GSC) promotes checklists and standards to better describe our sequence Data collection and to promote the capturing, exchange and integration of sequence Data with Contextual Data. In a recent community effort the GSC has developed a series of recommendations for Contextual Data that should be submitted along with sequence Data. To support the scientific community to significantly enhance the quality and quantity of Contextual Data in the public sequence Data repositories, specialized software tools are needed. In this work we present CDinFusion, a web-based tool to integrate Contextual and sequence Data in (Multi)FASTA format prior to submission. The tool is open source and available under the Lesser GNU Public License 3. A public installation is hosted and maintained at the Max Planck Institute for Marine Microbiology at http://www.megx.net/cdinfusion. The tool may also be installed locally using the open source code available at http://code.google.com/p/cdinfusion.
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CDinFusion – Submission-Ready, On-Line Integration of Sequence and Contextual Data
PLOS ONE, 2011Co-Authors: Wolfgang Hankeln, Renzo Kottmann, Pelin Yilmaz, Pier Luigi Buttigieg, Norma Johanna Wendel, Jan Gerken, Jost Waldmann, Ivaylo Kostadinov, Frank Oliver GlocknerAbstract:State of the art (DNA) sequencing methods applied in “Omics” studies grant insight into the ‘blueprints’ of organisms from all domains of life. Sequencing is carried out around the globe and the Data is submitted to the public repositories of the International Nucleotide Sequence Database Collaboration. However, the context in which these studies are conducted often gets lost, because experimental Data, as well as information about the environment are rarely submitted along with the sequence Data. If these Contextual or metaData are missing, key opportunities of comparison and analysis across studies and habitats are hampered or even impossible. To address this problem, the Genomic Standards Consortium (GSC) promotes checklists and standards to better describe our sequence Data collection and to promote the capturing, exchange and integration of sequence Data with Contextual Data. In a recent community effort the GSC has developed a series of recommendations for Contextual Data that should be submitted along with sequence Data. To support the scientific community to significantly enhance the quality and quantity of Contextual Data in the public sequence Data repositories, specialized software tools are needed. In this work we present CDinFusion, a web-based tool to integrate Contextual and sequence Data in (Multi)FASTA format prior to submission. The tool is open source and available under the Lesser GNU Public License 3. A public installation is hosted and maintained at the Max Planck Institute for Marine Microbiology at http://www.megx.net/cdinfusion. The tool may also be installed locally using the open source code available at http://code.google.com/p/cdinfusion.
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metabar a tool for consistent Contextual Data acquisition and standards compliant submission
BMC Bioinformatics, 2010Co-Authors: Wolfgang Hankeln, Renzo Kottmann, Pelin Yilmaz, Pier Luigi Buttigieg, Frank Oliver Glockner, Dennis FinkAbstract: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.
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MetaBar - a tool for consistent Contextual Data acquisition and standards compliant submission.
BMC bioinformatics, 2010Co-Authors: Wolfgang Hankeln, Renzo Kottmann, Pelin Yilmaz, Pier Luigi Buttigieg, Dennis Fink, Frank Oliver GlocknerAbstract: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.\n\nRESULTS: 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).\n\nCONCLUSION: 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.