Onedata4Sci: Life-science experimental datasets management
system

ROŠINEC, Adrián, Tomáš SVOBODA, Tomáš RAČEK, Josef HANDL, Jozef SABO, Aleš KŘENEK and Radka SVOBODOVÁ. Onedata4Sci: Life-science experimental datasets management system. In 3D-BioInfo | ISCB 3D-SIG | ELIXIR Czech Republic Structural Bioinformatics. 2023.

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TY  - CONF
ID  - 2340017
AU  - Rošinec, Adrián - Svoboda, Tomáš - Raček, Tomáš - Handl, Josef - Sabo, Jozef - Křenek, Aleš - Svobodová, Radka
PY  - 2023
TI  - Onedata4Sci: Life-science experimental datasets management system
KW  - datasets management;FAIR principles;life-science data;Onedata
UR  - https://www.conftool.com/3d-bio-2023/index.php?page=browseSessions&presentations=show&abstracts=show&search=Onedata4Sci
N2  - In many scientific disciplines, especially life-sciences, expensive equipment is shared nowadays (like cryoEM devices, optical microscopes, …). The users – scientists request specific experiments from facilities, which perform the experiments on their behalf. The outcome of such an experiment is a dataset, which can get quite large in many cases (tens of gigabytes to terabytes). Data are then processed in order to draw scientific conclusions from their interpretation, and the results are published. However, today more and more emphasis is being placed on sharing the primary data itself - not only for the purpose of verification of scientific findings, but also for the re-use of the dataset to be used in future research. Automatic/manual annotation with appropriate metadata, storage or archiving of the dataset, assignment of DOIs, and subsequent publication of the dataset in disciplinary metadata catalogues or data repositories are necessary. To address these challenges, we design and develop a system Onedata4Sci, that automates acquiring, sharing, and publishing of data produced by specialized scientific devices. The proposed solution automatically makes experimental data available to the scientific community in a predefined way. It is particularly useful for on-the-fly processing in local or distant data centers, real-time analysis, or archiving to permanent storage according to defined quality of service (e.g., data distribution). The solution includes a web-based system that can be used to manage emerging datasets and annotate them with metadata (automatically extracted from the data produced by the instruments or manually entered by users according to defined templates). The system makes it easy to automate the individual steps of dataset preparation, checking compliance with FAIR principles, and publishing the dataset to the scientific community. The development of the system is guided by FAIR principles and national EOSC-CZ activities.
ER  -

Basic information
Original name	Onedata4Sci: Life-science experimental datasets management system
Authors	ROŠINEC, Adrián, Tomáš SVOBODA, Tomáš RAČEK, Josef HANDL, Jozef SABO, Aleš KŘENEK and Radka SVOBODOVÁ.
Edition	3D-BioInfo \| ISCB 3D-SIG \| ELIXIR Czech Republic Structural Bioinformatics, 2023.

Other information
Original language	English
Type of outcome	Conference abstract
Country of publisher	Czech Republic
Confidentiality degree	is not subject to a state or trade secret
WWW	URL
Organization unit	Faculty of Science
Keywords in English	datasets management;FAIR principles;life-science data;Onedata
Tags	International impact
Changed by	Changed by: Mgr. Ing. Tomáš Svoboda, učo 323969. Changed: 16/11/2023 12:34.

Abstract

In many scientific disciplines, especially life-sciences, expensive equipment is shared nowadays (like cryoEM devices, optical microscopes, …). The users – scientists request specific experiments from facilities, which perform the experiments on their behalf. The outcome of such an experiment is a dataset, which can get quite large in many cases (tens of gigabytes to terabytes). Data are then processed in order to draw scientific conclusions from their interpretation, and the results are published. However, today more and more emphasis is being placed on sharing the primary data itself - not only for the purpose of verification of scientific findings, but also for the re-use of the dataset to be used in future research. Automatic/manual annotation with appropriate metadata, storage or archiving of the dataset, assignment of DOIs, and subsequent publication of the dataset in disciplinary metadata catalogues or data repositories are necessary. To address these challenges, we design and develop a system Onedata4Sci, that automates acquiring, sharing, and publishing of data produced by specialized scientific devices. The proposed solution automatically makes experimental data available to the scientific community in a predefined way. It is particularly useful for on-the-fly processing in local or distant data centers, real-time analysis, or archiving to permanent storage according to defined quality of service (e.g., data distribution). The solution includes a web-based system that can be used to manage emerging datasets and annotate them with metadata (automatically extracted from the data produced by the instruments or manually entered by users according to defined templates). The system makes it easy to automate the individual steps of dataset preparation, checking compliance with FAIR principles, and publishing the dataset to the scientific community. The development of the system is guided by FAIR principles and national EOSC-CZ activities.

Links
744R1/2023, interní kód MU	Name: Portálové řešení pro správu a zpracování life-science datových sad a jejich metadat ukládaných v systému Onedata
744R1/2023, interní kód MU	Investor: CESNET

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Onedata4Sci: Life-science experimental datasets management system

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