bianchini88/monitoring_sra-samples_EBIsearch: Monitoring the submission to ENA/SRA of sample data from Norwegian institutions
The purpose of this code is to monitor the submissions of Norwegian sequencing data to domain repositories. This is achieved by querying the "sra-samples" endpoint of EBI search , containing metadata of the samples deposited in the Sequence Read Archive (SRA) which is also synchronised wit...
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ftzenodo:oai:zenodo.org:10948339 2024-09-15T18:39:26+00:00 bianchini88/monitoring_sra-samples_EBIsearch: Monitoring the submission to ENA/SRA of sample data from Norwegian institutions Federico Bianchini 2024-04-09 https://doi.org/10.5281/zenodo.10948339 unknown Zenodo https://github.com/bianchini88/monitoring_sra-samples_EBIsearch/tree/v1.0.0 https://zenodo.org/communities/elixir-no https://doi.org/10.5281/zenodo.10948338 https://doi.org/10.5281/zenodo.10948339 oai:zenodo.org:10948339 info:eu-repo/semantics/openAccess MIT License https://opensource.org/licenses/MIT monitoring Data submission annotation and curation info:eu-repo/semantics/other 2024 ftzenodo https://doi.org/10.5281/zenodo.1094833910.5281/zenodo.10948338 2024-07-26T14:40:40Z The purpose of this code is to monitor the submissions of Norwegian sequencing data to domain repositories. This is achieved by querying the "sra-samples" endpoint of EBI search , containing metadata of the samples deposited in the Sequence Read Archive (SRA) which is also synchronised with the European Nucleotide Archive (ENA) as part of the International Nucleotide Sequence Data Collaboration (INSDC) . The code performs a query based on the country name Norway. Note that this identifies all the samples collected in Norway, not necessarily by Norwegian institutions or organisations. Extensive filtering is used to isolate the relevant data due to the lack of standardisation across the centres' names. The results are then plotted in two graphs, one for the BOTT (Bergen, Oslo, Trondheim, and Tromsø) universities and one for the Norwegian Institute of Public Health (NIPH) (Norwegian: Folkehelseinstituttet; FHI). A non-updated reference for these plots is available in the /plots4reference folder. Powered by EBI Search. Other/Unknown Material Tromsø Zenodo |
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monitoring Data submission annotation and curation |
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monitoring Data submission annotation and curation Federico Bianchini bianchini88/monitoring_sra-samples_EBIsearch: Monitoring the submission to ENA/SRA of sample data from Norwegian institutions |
topic_facet |
monitoring Data submission annotation and curation |
description |
The purpose of this code is to monitor the submissions of Norwegian sequencing data to domain repositories. This is achieved by querying the "sra-samples" endpoint of EBI search , containing metadata of the samples deposited in the Sequence Read Archive (SRA) which is also synchronised with the European Nucleotide Archive (ENA) as part of the International Nucleotide Sequence Data Collaboration (INSDC) . The code performs a query based on the country name Norway. Note that this identifies all the samples collected in Norway, not necessarily by Norwegian institutions or organisations. Extensive filtering is used to isolate the relevant data due to the lack of standardisation across the centres' names. The results are then plotted in two graphs, one for the BOTT (Bergen, Oslo, Trondheim, and Tromsø) universities and one for the Norwegian Institute of Public Health (NIPH) (Norwegian: Folkehelseinstituttet; FHI). A non-updated reference for these plots is available in the /plots4reference folder. Powered by EBI Search. |
format |
Other/Unknown Material |
author |
Federico Bianchini |
author_facet |
Federico Bianchini |
author_sort |
Federico Bianchini |
title |
bianchini88/monitoring_sra-samples_EBIsearch: Monitoring the submission to ENA/SRA of sample data from Norwegian institutions |
title_short |
bianchini88/monitoring_sra-samples_EBIsearch: Monitoring the submission to ENA/SRA of sample data from Norwegian institutions |
title_full |
bianchini88/monitoring_sra-samples_EBIsearch: Monitoring the submission to ENA/SRA of sample data from Norwegian institutions |
title_fullStr |
bianchini88/monitoring_sra-samples_EBIsearch: Monitoring the submission to ENA/SRA of sample data from Norwegian institutions |
title_full_unstemmed |
bianchini88/monitoring_sra-samples_EBIsearch: Monitoring the submission to ENA/SRA of sample data from Norwegian institutions |
title_sort |
bianchini88/monitoring_sra-samples_ebisearch: monitoring the submission to ena/sra of sample data from norwegian institutions |
publisher |
Zenodo |
publishDate |
2024 |
url |
https://doi.org/10.5281/zenodo.10948339 |
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Tromsø |
genre_facet |
Tromsø |
op_relation |
https://github.com/bianchini88/monitoring_sra-samples_EBIsearch/tree/v1.0.0 https://zenodo.org/communities/elixir-no https://doi.org/10.5281/zenodo.10948338 https://doi.org/10.5281/zenodo.10948339 oai:zenodo.org:10948339 |
op_rights |
info:eu-repo/semantics/openAccess MIT License https://opensource.org/licenses/MIT |
op_doi |
https://doi.org/10.5281/zenodo.1094833910.5281/zenodo.10948338 |
_version_ |
1810483803176566784 |