Biodiversity Information Science and Standards :
Conference Abstract
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Corresponding author: Elisabeth Hüllbusch (elisabeth.huellbusch@bfn.de), Anton Güntsch (a.guentsch@bo.berlin)
Received: 29 Aug 2024 | Published: 30 Aug 2024
© 2024 Elisabeth Hüllbusch, Anton Güntsch, Katja Luther, Rudolf May, Andreas Müller, Falko Riemenschneider, Gerhard Ludwig
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Hüllbusch E, Güntsch A, Luther K, May R, Müller A, Riemenschneider F, Ludwig G (2024) A Concept-Aware API for the Taxonomic Checklist Infrastructure in Germany. Biodiversity Information Science and Standards 8: e135846. https://doi.org/10.3897/biss.8.135846
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Biological data refer to taxa (e.g., species) or to populations (e.g., all individuals of a taxon in a region). Scientific names of organisms are commonly used as identifiers for those data, e.g., in databases. However, scientific names are assigned (linked) to taxonomic concepts, which very often change over time or space, e.g., when a species name refers to
Examples of concept relationships between taxa. The circles in column "Illustration" represent two taxa (red circle = taxon a, white circle = taxon b). The square symbolizes all taxa of one checklist (red square = all taxa of checklist a, white square = all taxa of checklist b).
From a user perspective, however, there are hardly any interfaces that can be used to effectively access taxonomic concepts and their relationships, for example to semantically annotate research data with name references. The German Federal Agency for Nature Conservation (BfN) and the National Research Data Infrastructure NFDI4Biodiversity have cooperatively developed an API (Application Programming Interface) for accessing available German species checklists, where taxonomic concept relationships between checklist versions can flexibly be queried and integrated into other systems. The query for scientific names includes a similarity search and initially returns the taxa with matching names. In a subsequent query, hierarchies, synonyms and the concept relationships to name usages in other checklist versions are output (e.g., congruence, inclusion, pro-parte-inclusion, interference, exclusion, and total exclusion).
From this output, it is possible to recognize, in particular, to which taxa an assignment of information is problematic.
The API is currently in the testing phase and is used in the context of NFDI4Biodiversity for the annotation and integration of research data.
taxonomic concepts, taxa, taxon names, annotation
Elisabeth Hüllbusch
SPNHC TDWG 2024
The development of the API was funded by the German Research Foundation DFG under the grant agreement number 442032008 (NFDI4Biodiversity).