A lab-centric, workflow-based data management system for environmental DNA research
The adoption of environmental DNA approaches as a standard tool for biodiversity monitoring leads to the increase in the number of eDNA-based species occurrence records; however, considerable disparity remains in the nature and quality of associated information, much of it unpublished and/or poorly...
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| Format: | Article |
| Language: | English |
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Pensoft Publishers
2024-03-01
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| Series: | Research Ideas and Outcomes |
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| Online Access: | https://riojournal.com/article/120483/download/pdf/ |
| _version_ | 1827572325999968256 |
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| author | Alex Borisenko Robert Young Robert Hanner |
| author_facet | Alex Borisenko Robert Young Robert Hanner |
| author_sort | Alex Borisenko |
| collection | DOAJ |
| description | The adoption of environmental DNA approaches as a standard tool for biodiversity monitoring leads to the increase in the number of eDNA-based species occurrence records; however, considerable disparity remains in the nature and quality of associated information, much of it unpublished and/or poorly parametrised. A robust system for tracking biological materials from their point of origin through laboratory analyses is required to connect inferred taxon occurrences with analytical history and provenance data. The bulk of eDNA research is currently driven by small-scale operations where the tasks of digitisation, organisation and cross-referencing field records with laboratory analytical data and biomaterial sample location, are often performed manually and disconnected.We present an integrative, full-stack data management solution that provides a structured ontological concept, a minimalist data schema for eDNA research and a software application prototype designed to facilitate real-time digitisation, parsing, annotation and archival of eDNA data. The system tracks the provenance and analytical history of biological samples through a structured hierarchy of events, linked with associated digital file attachment archives, such as images and raw sequence files, and with inferred taxonomic occurrence records. The data entry process is compartmentalised and incorporated into the corresponding stages of standard operations used in fieldwork, biological collection management and laboratory analysis. Resulting data records can be integrated into various output formats required for large-scale analytics, publication and/or submission to global data aggregators. The prototype is implemented on the Microsoft 365 platform as a relational database (Access) linked to cloud-based data tables (SharePoint) and a set of associated data conversion spreadsheets (Excel). The system is designed primarily around the data management needs of small research labs; however, it is scalable to larger institutions and inter-institutional academic networks. |
| first_indexed | 2024-04-24T16:29:10Z |
| format | Article |
| id | doaj.art-5e0dadaf64a14b5eab0af9ceb05f06cf |
| institution | Directory Open Access Journal |
| issn | 2367-7163 |
| language | English |
| last_indexed | 2024-04-24T16:29:10Z |
| publishDate | 2024-03-01 |
| publisher | Pensoft Publishers |
| record_format | Article |
| series | Research Ideas and Outcomes |
| spelling | doaj.art-5e0dadaf64a14b5eab0af9ceb05f06cf2024-03-30T07:33:07ZengPensoft PublishersResearch Ideas and Outcomes2367-71632024-03-011013910.3897/rio.10.e120483120483A lab-centric, workflow-based data management system for environmental DNA researchAlex Borisenko0Robert Young1Robert Hanner2Biodetics Data SolutionsUniversity of GuelphUniversity of GuelphThe adoption of environmental DNA approaches as a standard tool for biodiversity monitoring leads to the increase in the number of eDNA-based species occurrence records; however, considerable disparity remains in the nature and quality of associated information, much of it unpublished and/or poorly parametrised. A robust system for tracking biological materials from their point of origin through laboratory analyses is required to connect inferred taxon occurrences with analytical history and provenance data. The bulk of eDNA research is currently driven by small-scale operations where the tasks of digitisation, organisation and cross-referencing field records with laboratory analytical data and biomaterial sample location, are often performed manually and disconnected.We present an integrative, full-stack data management solution that provides a structured ontological concept, a minimalist data schema for eDNA research and a software application prototype designed to facilitate real-time digitisation, parsing, annotation and archival of eDNA data. The system tracks the provenance and analytical history of biological samples through a structured hierarchy of events, linked with associated digital file attachment archives, such as images and raw sequence files, and with inferred taxonomic occurrence records. The data entry process is compartmentalised and incorporated into the corresponding stages of standard operations used in fieldwork, biological collection management and laboratory analysis. Resulting data records can be integrated into various output formats required for large-scale analytics, publication and/or submission to global data aggregators. The prototype is implemented on the Microsoft 365 platform as a relational database (Access) linked to cloud-based data tables (SharePoint) and a set of associated data conversion spreadsheets (Excel). The system is designed primarily around the data management needs of small research labs; however, it is scalable to larger institutions and inter-institutional academic networks.https://riojournal.com/article/120483/download/pdf/eDNAdatabaseMicrosoft 365AccessSharePoint |
| spellingShingle | Alex Borisenko Robert Young Robert Hanner A lab-centric, workflow-based data management system for environmental DNA research Research Ideas and Outcomes eDNA database Microsoft 365 Access SharePoint |
| title | A lab-centric, workflow-based data management system for environmental DNA research |
| title_full | A lab-centric, workflow-based data management system for environmental DNA research |
| title_fullStr | A lab-centric, workflow-based data management system for environmental DNA research |
| title_full_unstemmed | A lab-centric, workflow-based data management system for environmental DNA research |
| title_short | A lab-centric, workflow-based data management system for environmental DNA research |
| title_sort | lab centric workflow based data management system for environmental dna research |
| topic | eDNA database Microsoft 365 Access SharePoint |
| url | https://riojournal.com/article/120483/download/pdf/ |
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