Biodiversity Information Science and Standards :
Conference Abstract
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Corresponding author: Christian Bölling (christian.boelling@mfn.berlin)
Received: 14 Sep 2021 | Published: 14 Sep 2021
This is an open access article distributed under the terms of the CC0 Public Domain Dedication.
Citation:
Bölling C, Bilkhu S, Gendreau C, Glöckler F, Macklin J, Shorthouse D (2021) Robust Integration of Biodiversity Data by Process- and State-based Representation of Object Histories and Modular Application Architecture. Biodiversity Information Science and Standards 5: e75178. https://doi.org/10.3897/biss.5.75178
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Biodiversity data is obtained by a variety of methodological approaches—including observation surveys, environmental sampling and biological object collection—employing diverse sample processing protocols and data transformations. While complete and accurate accounts of these data-generating processes are important to enable integration and informed reuse of data, the structure and content of published biodiversity data currently are often shaped by specific application goals. For example, data publishers that export specimen-based data from collection management systems for inclusion in aggregations like those in the Global Biodiversity Information Facility (GBIF) must frequently relax their internal models and produce unnatural joins to fit GBIF’s occurrences-based data structure. Third-party assertions over these aggregated data therefore assume the risk of irreproducibility or concept drift.
Here we introduce process- and state-based representation of object histories as the main organizing principle for data about specimens and samples in Digital Information System for Natural History Data (DINA,
(A) Concept schema for interconnected object histories (example). (B) Corresponding abstract concept schema of sequences of processes (triangles) and objects in particular states (circles) before and after processes. Processes give rise to new objects, object states and data items about objects and processes. Processes in the context of collection management will usually consist of separable sub-processes (e.g., different steps in a preservation protocol). Objects can be an aggregate of other objects (e.g., a lot of biological specimens and the preparation container as a composite object originating from a preparation process).
We argue that using object histories as main conceptual modeling paradigm in DINA offers the generality required to accommodate a diverse, open set of use cases in biodiversity data representation, yet also offers the versatility to serve as basis for use-case specific data aggregation and presentation. Specifically, a representation based on object histories provides
The approach is designed to be embedded in DINA’s modular application architecture, so that information on object histories can be accessed via corresponding APIs either through its own interfaces (Fig.
In DINA's modular software, architecture modules communicate with other modules through standard application programming interfaces (APIs) as do browser or machine users when interacting with the system.
Application programming integration of the DINA system with the Catalogue of Life (Checklist Bank) to anchor scientific names in determinations, Open Street Maps to anchor place names in georeferences, and with the GBIF registry to publish occurrences and sampling event core data sets.
In this contribution to the symposium, DINA's object histories as a main organizing principle for collection object data will be discussed and the utility of using it in the context of modular application architecture, data federation, and data integration in projects like BiCIKL will be illustrated.
collection management, biodiversity knowledge graph, DINA
Christian Bölling
TDWG 2021