The Microbial Antarctic Resource System: Integrating discoverability and preservation of environmentally-annotated microbial 'omics data
Microbial organisms - including Archaea, Bacteria and unicellular Eukaryota - collectively dominate the Earth in terms of bio- and functional diversity. Their study, often constrained by technology, has strongly benefited from the recent advancements in high-throughput DNA sequencing techniques. The...
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ftzenodo:oai:zenodo.org:3340247 2023-06-06T11:44:22+02:00 The Microbial Antarctic Resource System: Integrating discoverability and preservation of environmentally-annotated microbial 'omics data Sweetlove, Maxime Gan, Yi Ming Murray, Alison Van de Putte, Anton 2019-07-10 https://zenodo.org/record/3340247 https://doi.org/10.3897/biss.3.37499 unknown Pensoft Publishers https://zenodo.org/communities/biosyslit https://zenodo.org/record/3340247 https://doi.org/10.3897/biss.3.37499 oai:zenodo.org:3340247 info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/legalcode Biodiversity Information Science and Standards 3 e37499 data archiving Antarctica microorganisms Bacteria Archaea Eukaryota MIxS DarwinCore info:eu-repo/semantics/article publication-article 2019 ftzenodo https://doi.org/10.3897/biss.3.37499 2023-04-13T23:04:02Z Microbial organisms - including Archaea, Bacteria and unicellular Eukaryota - collectively dominate the Earth in terms of bio- and functional diversity. Their study, often constrained by technology, has strongly benefited from the recent advancements in high-throughput DNA sequencing techniques. The vast amounts of microbial data generated in the wake of these developments, however, remains severely underrepresented on open access biodiversity data repositories (e.g. the Global Biodiversity Information Facility; GBIF). Moreover, when sequencing data has been made publicly available, is often poorly annotated with metadata and environmental variables, making it difficult to find or query. Therefore, the microbial Antarctic Resource System (mARS) aims to fill this lacuna by documenting and geo-referencing microbial datasets and linking the sequence data in the International Nucleotide Sequence Database Collaboration (INSDC) repositories with the associated environmental measurements on mARS, which is aimed to be interoperable with both INSDC and GBIF. This way, mARS helps to preserve environmental data and the metadata that is crucial for the correct processing and interpretation of sequence data, while it also connects researchers via its webportal to the existing wealth of molecular information, and allows these datasets to be more effectively accessed. Given the general complexity of microbial ecological datasets, mARS needs to operate between different data archiving standards, such as MIxS (see https://press3.mcs.anl.gov/gensc/mixs/), which is oriented towards DNA sequence data, and the biodiversity-based DarwinCore standard. Currently, mARS tries to address the challenges of integrating microbial data with these existing systems as well as connecting with the communities behind them, by documenting the datasets on GBIF's extensions or investigate the feasibility of routinely processing raw sequence data into occurrence datasets using the open computing facilities offered by the European Molecular Biology ... Article in Journal/Newspaper Antarc* Antarctic Antarctica Zenodo Antarctic Biodiversity Information Science and Standards 3 |
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data archiving Antarctica microorganisms Bacteria Archaea Eukaryota MIxS DarwinCore |
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data archiving Antarctica microorganisms Bacteria Archaea Eukaryota MIxS DarwinCore Sweetlove, Maxime Gan, Yi Ming Murray, Alison Van de Putte, Anton The Microbial Antarctic Resource System: Integrating discoverability and preservation of environmentally-annotated microbial 'omics data |
topic_facet |
data archiving Antarctica microorganisms Bacteria Archaea Eukaryota MIxS DarwinCore |
description |
Microbial organisms - including Archaea, Bacteria and unicellular Eukaryota - collectively dominate the Earth in terms of bio- and functional diversity. Their study, often constrained by technology, has strongly benefited from the recent advancements in high-throughput DNA sequencing techniques. The vast amounts of microbial data generated in the wake of these developments, however, remains severely underrepresented on open access biodiversity data repositories (e.g. the Global Biodiversity Information Facility; GBIF). Moreover, when sequencing data has been made publicly available, is often poorly annotated with metadata and environmental variables, making it difficult to find or query. Therefore, the microbial Antarctic Resource System (mARS) aims to fill this lacuna by documenting and geo-referencing microbial datasets and linking the sequence data in the International Nucleotide Sequence Database Collaboration (INSDC) repositories with the associated environmental measurements on mARS, which is aimed to be interoperable with both INSDC and GBIF. This way, mARS helps to preserve environmental data and the metadata that is crucial for the correct processing and interpretation of sequence data, while it also connects researchers via its webportal to the existing wealth of molecular information, and allows these datasets to be more effectively accessed. Given the general complexity of microbial ecological datasets, mARS needs to operate between different data archiving standards, such as MIxS (see https://press3.mcs.anl.gov/gensc/mixs/), which is oriented towards DNA sequence data, and the biodiversity-based DarwinCore standard. Currently, mARS tries to address the challenges of integrating microbial data with these existing systems as well as connecting with the communities behind them, by documenting the datasets on GBIF's extensions or investigate the feasibility of routinely processing raw sequence data into occurrence datasets using the open computing facilities offered by the European Molecular Biology ... |
format |
Article in Journal/Newspaper |
author |
Sweetlove, Maxime Gan, Yi Ming Murray, Alison Van de Putte, Anton |
author_facet |
Sweetlove, Maxime Gan, Yi Ming Murray, Alison Van de Putte, Anton |
author_sort |
Sweetlove, Maxime |
title |
The Microbial Antarctic Resource System: Integrating discoverability and preservation of environmentally-annotated microbial 'omics data |
title_short |
The Microbial Antarctic Resource System: Integrating discoverability and preservation of environmentally-annotated microbial 'omics data |
title_full |
The Microbial Antarctic Resource System: Integrating discoverability and preservation of environmentally-annotated microbial 'omics data |
title_fullStr |
The Microbial Antarctic Resource System: Integrating discoverability and preservation of environmentally-annotated microbial 'omics data |
title_full_unstemmed |
The Microbial Antarctic Resource System: Integrating discoverability and preservation of environmentally-annotated microbial 'omics data |
title_sort |
microbial antarctic resource system: integrating discoverability and preservation of environmentally-annotated microbial 'omics data |
publisher |
Pensoft Publishers |
publishDate |
2019 |
url |
https://zenodo.org/record/3340247 https://doi.org/10.3897/biss.3.37499 |
geographic |
Antarctic |
geographic_facet |
Antarctic |
genre |
Antarc* Antarctic Antarctica |
genre_facet |
Antarc* Antarctic Antarctica |
op_source |
Biodiversity Information Science and Standards 3 e37499 |
op_relation |
https://zenodo.org/communities/biosyslit https://zenodo.org/record/3340247 https://doi.org/10.3897/biss.3.37499 oai:zenodo.org:3340247 |
op_rights |
info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/legalcode |
op_doi |
https://doi.org/10.3897/biss.3.37499 |
container_title |
Biodiversity Information Science and Standards |
container_volume |
3 |
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1767960774256361472 |