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The relational modeling of hierarchical data in biodiversity databases
1Department of Biology Education & Herbarium collections (PRC), Faculty of Science, Charles University, Viničná 7, Praha 128 00, Czech Republic.
Database : the Journal of Biological Databases and Curation
|October 10, 2024
Summary
Most biodiversity databases lack formal taxon hierarchy structures, hindering data usability. The Closure Table model is ideal but rarely implemented, despite its suitability for relational databases and ontologies.
Area of Science:
- Biodiversity Informatics
- Database Management
- Taxonomy
Background:
- Taxon hierarchy modeling is crucial for unifying biodiversity data.
- Existing biodiversity databases vary in their handling and presentation of hierarchical data.
- Formalized data structures are essential for robust data analysis and integration.
Purpose of the Study:
- To compare 25 biodiversity databases based on their taxon hierarchy modeling capabilities.
- To identify prevalent data structures used for representing taxonomic relationships.
- To assess the availability and suitability of hierarchical data structures for researchers.
Main Methods:
- Analysis of database documentation and demo installations.
- Examination of data structures using R packages.
- Review of public interfaces for databases lacking other documentation.
Main Results:
- Twelve out of 25 databases (nearly half) lacked formalized taxon hierarchy data structures.
- The Adjacency List model, storing only parent IDs, is the most common but least effective method.
- The Closure Table model, suitable for relational databases and ontologies, is sporadically used.
Conclusions:
- Current biodiversity databases pay insufficient attention to modeling and providing taxon hierarchy data structures.
- The lack of formalized hierarchy hinders data usability and integration for researchers.
- Adoption of the Closure Table model is recommended for improved biodiversity data management.
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