Cargando…
*-DCC: A platform to collect, annotate, and explore a large variety of sequencing experiments
BACKGROUND: Over the past few years the variety of experimental designs and protocols for sequencing experiments increased greatly. To ensure the wide usability of the produced data beyond an individual project, rich and systematic annotation of the underlying experiments is crucial. FINDINGS: We fi...
Autores principales: | , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2020
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7069921/ https://www.ncbi.nlm.nih.gov/pubmed/32170312 http://dx.doi.org/10.1093/gigascience/giaa024 |
_version_ | 1783505866891198464 |
---|---|
author | Hörtenhuber, Matthias Mukarram, Abdul K Stoiber, Marcus H Brown, James B Daub, Carsten O |
author_facet | Hörtenhuber, Matthias Mukarram, Abdul K Stoiber, Marcus H Brown, James B Daub, Carsten O |
author_sort | Hörtenhuber, Matthias |
collection | PubMed |
description | BACKGROUND: Over the past few years the variety of experimental designs and protocols for sequencing experiments increased greatly. To ensure the wide usability of the produced data beyond an individual project, rich and systematic annotation of the underlying experiments is crucial. FINDINGS: We first developed an annotation structure that captures the overall experimental design as well as the relevant details of the steps from the biological sample to the library preparation, the sequencing procedure, and the sequencing and processed files. Through various design features, such as controlled vocabularies and different field requirements, we ensured a high annotation quality, comparability, and ease of annotation. The structure can be easily adapted to a large variety of species. We then implemented the annotation strategy in a user-hosted web platform with data import, query, and export functionality. CONCLUSIONS: We present here an annotation structure and user-hosted platform for sequencing experiment data, suitable for lab-internal documentation, collaborations, and large-scale annotation efforts. |
format | Online Article Text |
id | pubmed-7069921 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-70699212020-03-18 *-DCC: A platform to collect, annotate, and explore a large variety of sequencing experiments Hörtenhuber, Matthias Mukarram, Abdul K Stoiber, Marcus H Brown, James B Daub, Carsten O Gigascience Research BACKGROUND: Over the past few years the variety of experimental designs and protocols for sequencing experiments increased greatly. To ensure the wide usability of the produced data beyond an individual project, rich and systematic annotation of the underlying experiments is crucial. FINDINGS: We first developed an annotation structure that captures the overall experimental design as well as the relevant details of the steps from the biological sample to the library preparation, the sequencing procedure, and the sequencing and processed files. Through various design features, such as controlled vocabularies and different field requirements, we ensured a high annotation quality, comparability, and ease of annotation. The structure can be easily adapted to a large variety of species. We then implemented the annotation strategy in a user-hosted web platform with data import, query, and export functionality. CONCLUSIONS: We present here an annotation structure and user-hosted platform for sequencing experiment data, suitable for lab-internal documentation, collaborations, and large-scale annotation efforts. Oxford University Press 2020-03-14 /pmc/articles/PMC7069921/ /pubmed/32170312 http://dx.doi.org/10.1093/gigascience/giaa024 Text en © The Author(s) 2020. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Hörtenhuber, Matthias Mukarram, Abdul K Stoiber, Marcus H Brown, James B Daub, Carsten O *-DCC: A platform to collect, annotate, and explore a large variety of sequencing experiments |
title | *-DCC: A platform to collect, annotate, and explore a large variety of sequencing experiments |
title_full | *-DCC: A platform to collect, annotate, and explore a large variety of sequencing experiments |
title_fullStr | *-DCC: A platform to collect, annotate, and explore a large variety of sequencing experiments |
title_full_unstemmed | *-DCC: A platform to collect, annotate, and explore a large variety of sequencing experiments |
title_short | *-DCC: A platform to collect, annotate, and explore a large variety of sequencing experiments |
title_sort | *-dcc: a platform to collect, annotate, and explore a large variety of sequencing experiments |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7069921/ https://www.ncbi.nlm.nih.gov/pubmed/32170312 http://dx.doi.org/10.1093/gigascience/giaa024 |
work_keys_str_mv | AT hortenhubermatthias dccaplatformtocollectannotateandexplorealargevarietyofsequencingexperiments AT mukarramabdulk dccaplatformtocollectannotateandexplorealargevarietyofsequencingexperiments AT stoibermarcush dccaplatformtocollectannotateandexplorealargevarietyofsequencingexperiments AT brownjamesb dccaplatformtocollectannotateandexplorealargevarietyofsequencingexperiments AT daubcarsteno dccaplatformtocollectannotateandexplorealargevarietyofsequencingexperiments |