Ensuring Adherence to Standards in Experiment-Related Metadata Entered Via Spreadsheets
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arXiv
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| Autori principali: | , , , , , , , |
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| Natura: | Preprint |
| Pubblicazione: |
2024
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| _version_ | 1866917099015766016 |
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| author | O'Connor, Martin J. Hardi, Josef Martínez-Romero, Marcos Somasundaram, Sowmya Honick, Brendan Fisher, Stephen A. Pillai, Ajay Musen, Mark A. |
| author_facet | O'Connor, Martin J. Hardi, Josef Martínez-Romero, Marcos Somasundaram, Sowmya Honick, Brendan Fisher, Stephen A. Pillai, Ajay Musen, Mark A. |
| contents | Scientists increasingly recognize the importance of providing rich, standards-adherent metadata to describe their experimental results. Despite the availability of sophisticated tools to assist in the process of data annotation, investigators generally seem to prefer to use spreadsheets when supplying metadata, despite the limitations of spreadsheets in ensuring metadata consistency and compliance with formal specifications. In this paper, we describe an end-to-end approach that supports spreadsheet-based entry of metadata, while ensuring rigorous adherence to community-based metadata standards and providing quality control. Our methods employ several key components, including customizable templates that represent metadata standards and that can inform the spreadsheets that investigators use to author metadata, controlled terminologies and ontologies for defining metadata values that can be accessed directly from a spreadsheet, and an interactive Web-based tool that allows users to rapidly identify and fix errors in their spreadsheet-based metadata. We demonstrate how this approach is being deployed in a biomedical consortium known as HuBMAP to define and collect metadata about a wide range of biological assays. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2409_08897 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Ensuring Adherence to Standards in Experiment-Related Metadata Entered Via Spreadsheets O'Connor, Martin J. Hardi, Josef Martínez-Romero, Marcos Somasundaram, Sowmya Honick, Brendan Fisher, Stephen A. Pillai, Ajay Musen, Mark A. Digital Libraries Scientists increasingly recognize the importance of providing rich, standards-adherent metadata to describe their experimental results. Despite the availability of sophisticated tools to assist in the process of data annotation, investigators generally seem to prefer to use spreadsheets when supplying metadata, despite the limitations of spreadsheets in ensuring metadata consistency and compliance with formal specifications. In this paper, we describe an end-to-end approach that supports spreadsheet-based entry of metadata, while ensuring rigorous adherence to community-based metadata standards and providing quality control. Our methods employ several key components, including customizable templates that represent metadata standards and that can inform the spreadsheets that investigators use to author metadata, controlled terminologies and ontologies for defining metadata values that can be accessed directly from a spreadsheet, and an interactive Web-based tool that allows users to rapidly identify and fix errors in their spreadsheet-based metadata. We demonstrate how this approach is being deployed in a biomedical consortium known as HuBMAP to define and collect metadata about a wide range of biological assays. |
| title | Ensuring Adherence to Standards in Experiment-Related Metadata Entered Via Spreadsheets |
| topic | Digital Libraries |
| url | https://arxiv.org/abs/2409.08897 |