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talk · Thursday 24 September · 15:18–⁠15:30 · SAL A

The More Extended, The More Open: Semantic Integration of 3D Natural Heritage Data into Biodiversity CMS

Yeeun Lee · Solutions for Research Collection Management Systems Challenges

Recording time 7:38:50–7:49:16Open on Vimeo ↗

Summaries and key moments are machine-produced. Check the recording for the speaker’s exact words.

The short versionTreating 3D specimen models as entry points in a knowledge graph that includes heritage context and digitisation paradata makes them reusable knowledge assets.

Overview

What this was about

Yeeun Lee argued that specimens bridge natural history and heritage, because they record biological evidence along with histories of collection, curation, research and exhibition. Existing services (GBIF, BHL, Smithsonian 3D, DiSSCo) cover parts of the task in separate systems, and 3D data are often low quality. The project combines AI-assisted photogrammetric 3D capture of specimens from seven institutions, sized from insects to large mammals, with a semantic model of data, metadata and paradata layers. The model is aligned with openDS, Dublin Core, Europeana and CIDOC CRM, and visualised in Neo4j as a knowledge graph of about 2,400 nodes and 3,600 relations. Example applications are CMS integration, recommendations and map-based views.

Why it matters. It links biodiversity and cultural heritage standards and argues for recording 3D production paradata, which matters as 3D specimens are used for exhibitions, citizen science and AI.

Key ideas

In the room

  • Specimens carry both natural history evidence and heritage value formed through human curation and interpretation.
  • Natural heritage information is distributed across institutions with differing quality, and 3D data are often low quality.
  • Photogrammetric 3D production in four stages: capture, multi-point imaging, registration and meshing, with setups adapted to specimen size.
  • The semantic model has three layers: data (nature, specimen, occurrence), metadata (heritage, resource) and paradata (project, institution, item).
  • It is aligned with openDS, Dublin Core, Europeana and CIDOC CRM via one-to-one mappings.
  • The Neo4j knowledge graph has about 2,400 nodes and 3,600 relations.
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Notable moments

In their words

Transcript

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Programme abstract

The More Extended, The More Open: Semantic Integration of 3D Natural Heritage Data into Biodiversity CMS

Yeeun Lee

Biodiversity platforms are evolving into 'Open Knowledge Spaces' connecting primary data, research, and exploration. While the Digital Extended Specimen (DES) framework integrates derivative data, current Collection Management Systems (CMS) using models like openDS limit the ability to accommodate the 3D complexity and broader utility of physical specimens.

Mobilizing biodiversity data beyond taxonomy-into exhibitions, citizen science, and AI-requires high-fidelity 3D resources. For these to act as reliable knowledge assets, an expanded schema must track 3D modeling paradata and 'utilization contexts' of how specimens are preserved and exhibited. Through the temporal dynamics of human curation, biological specimens transform from mere evidence into 'Natural Heritage' with socio-historical value.

This study proposes a 'Natural Historical Specimen (NHS)' data model based on 3D data from 320 natural heritage animal species in South Korea. To maximize interoperability, this schema integrates Darwin Core (DwC) for occurrences, Prov-O and MorphoSource for 3D digitization provenance, and CIDOC-CRM for institutional curation and exhibition contexts.

Mapping biological resources, digital objects, and utilization contexts ensures traceability from field collection to public engagement. We implemented an interactive dashboard using this model, enabling users to explore morphological attributes and historical trajectories via a Knowledge Graph. This study offers practical solutions for next-generation CMS, demonstrating that integrating DwC and CIDOC-CRM standards elevates 3D resources into hubs within global biodiversity networks.

Submitted to the conference programme before the talk, so the talk itself may differ.