The digitization of natural history collections is revolutionizing the preservation and utilization of biological and geological specimens. These collections, encompassing diverse ecosystems and time periods, are invaluable for scientific research, education, and conservation. However, physical specimens face challenges such as degradation, limited accessibility, and logistical difficulties. Digitization addresses these issues by converting specimens into high-resolution digital formats, preserving their integrity and making them widely accessible. This presentation explores the development of a unified platform for the digital twins of natural history specimens, focusing on standardization, management, and accessibility of multimedia files. The platform aims to integrate various digitization efforts as the Distributed System of Scientific Collections (DiSSCo ERIC) in Europe. This initiative adheres to the FAIR principles (Findable, Accessible, Interoperable, and Reusable) to enhance research capabilities and interdisciplinary studies. Key components of the platform include: 1. Digitization Techniques: High-resolution imaging, 3D scanning, and photogrammetry are used to create digital twins of specimens. These techniques ensure comprehensive documentation and accessibility for scientific research. 2. Metadata: The Darwin Core and ABCD standards for biodiversity data are managed by the institution CMS and DICOM is used for high-resolution and 3D imaging data. Links between CMS and Multimedia server are achieved using UUID/permalinks. This ensures quality, consistency, and interoperability of data. 3. Multimedia File Management: The platform utilizes the Open Source ORTHANC server, which supports various multimedia formats and provides a RESTful API for integration with other systems. Custom plugins and viewers were adapted or developed to enhance the visualization and analysis of digital specimens. 4. Interdisciplinary Collaboration: By providing a unified structure, the platform facilitates large-scale data analysis including access by AI and fosters collaboration among researchers, educators, and the general public. The integration of digital technologies into natural history collections not only safeguards specimens but also democratizes access to data, enabling global research and education. The proposed platform represents a significant advancement in the field, promoting the preservation and utilization of natural history collections in the digital age using Open Sources technologies. The proposed platform can easily be reused in a CH context.
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RBINS Staff Publications 2025
For more than 10 years, thanks to funding provided by the Belgian Development Cooperation (DGD), the Belgian Clearing House Mechanism (CHM) team of the Convention on Biological Diversity (CBD), has been helping its partner countries in the South develop their national CHM networks. In 2003, the European Union adopted the PTK (Portal Toolkit): a Content Management System that allows to develop national CHM websites in Europe. The PTK is released under the Mozilla Public License. It is a free and open source software, that allows multi user-generated content. It includes collaborative tools managed through the Web, such as discussion forums, consultations and surveys. With the PTK, users can: • Mobilize networks of experts through a user-friendly content management system • Raise public awareness by uploading short films, photos and presentations • Communicate biodiversity by state-of-the-art mapping services using YAHOO backgrounds and Google Earth exports • Prepare for biodiversity reporting by using public content contribution, user discussion forum, public consultation tools, survey tools and syndication • Collaborate in technical and scientific projects with modern web standards • Connect biodiversity databases. Belgium has been using the PTK for its national CHM website (http://www.biodiv.be/) for 10 years. More than 30 countries in Africa use the PTK for their national websites (such as Benin, Madagascar, Morocco, etc.), see full list here (http://www.biodiv.be/cooperation/chm_coop/chm-partnering/part_country). The national website URLs are as follows: country code + .chm-cbd.net. For instance, for Niger, the URL is http://ne.chm-cbd.net. The Belgian CHM hosts the national CHM websites of its partner countries on its server and offers training courses for the development and maintenance of these websites. Distance learning manuals on the use of the PTK have been developed by the Belgian CHM team for the last 4 years. The manuals are developed both in English and French. They are available on a training website: http://training.biodiv.be/formationptk. This website is used for distance learning for our partners and for any other interested party but also for blended learning. Two weeks before a face-to-face training in a partner country, all future trainees are invited to: • surf their national CHM website; • read a basic manual that introduces the PTK and the CHM; • create a user account on the training website.
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Nearly every geological subdiscipline relies to some degree on regional geological knowledge. In the introductory section of most geological papers it is standard practice to provide regional geological background information. Stratigraphic terminology is often well defined while other disciplinary concepts rely, at least to some degree, on generally agreed definitions or hierarchical schemes, such as paleontological, structural or magmatic terminology. This, however, is much less the case for the regional geological building blocks. Their names are usually composed of a combination of a geographical locality and a geological term. A few examples from Belgium are Brabant Massif, Campine Basin, Stavelot-Venn Inlier, and Malmedy Graben. Most of these have in common that, although their importance is well recognised, their definitions are vague and sometimes even conflicting, in that their meaning may differ between contexts and authors. Even if their meaning has drifted or become less exact, as a result of their frequent historical use, they commonly remain in use today. This issue is not exclusive to Belgium, but seems to be an altogether historic and worldwide phenomenon. Recently within Europe there is a growing awareness of this issue, resulting in important but rather isolated efforts to better structure and define regional information (Hintersberger et al. 2017; Németh 2021; Le Bayon et al. 2022) which have been brought together through pan-European cooperation (GSEU – Horizon Europe 101075609). The central element that seems to encompass most geologic features, is the lithotectonic unit (a distinct unit based on its partly separate geological history; URI: http://inspire.ec.europa.eu/codelist/GeologicUnitTypeValue/lithotectonicUnit). Grabens, basins and inliers are examples of lithotectonic units. In order to define and describe these units more accurately, lithotectonic limits are introduced. These are planar features, such as faults and unconformities, that correspond to the geologic events that formed the lithotectonic unit (Piessens et al. 2024). All information is organised and linked in vocabularies (thesauri) that together not only adequately define each concept, but also determine the relations between them, placing them in space and geological time (Plašienka 1999). This outlines the core methodology, around which 2D and 3D multi-scale visualisations are built, annotations can be added, existing ontologies can be linked (such as the ICS Geological Time Scale Ontology; Cox and Richard, 2005) and newly developed extensions such as the Modified Wilson Cycle (Németh 2021). As such, the work at Belgian level is closely linked to the ongoing international developments. Making use of the ongoing developments at European level, Belgium was the first country to set up a lithotectonic working group that became operational in 2023. Its first goal is to provide a lithotectonic framework that describes a starting set of main geological units and limits in Belgium, according to emerging European standards (the work at European level is linked to the implementation of INSPIRE and 195 is in communication with the GeoSciML community), by the end of 2024. The working group meets approximately every 2 months, and organisationally resides under the National Commission for Stratigraphy in Belgium. The working group will soon be looking for additional experts (junior and senior) in its continuing effort to identify and define broad superstructures, detail the regional geology to the more local level, to tackle new types of lithotectonic elements, or better address parts of geological history. Potential candidates are encouraged to contact one of the authors or the NCS secretariat. Cox SJD, Richard SM (2005) A formal model for the geologic time scale and global stratotype section and point, compatible with geospatial information transfer standards. Geosphere 1:119. https://doi.org/10.1130/GES00022.1 Hintersberger E, Iglseder C, Schuster R, Huet B (2017) The new database “Tectonic Boundaries” at the Geological Survey of Austria. Jahrbuch der geologischen Bundesanstalt 157:195–207 Le Bayon B, Padel M, Baudin T, et al (2022) The geological-event reference system, a step towards geological data harmonization. BSGF - Earth Sci Bull 193:18. https://doi.org/10.1051/bsgf/2022017 Németh Z (2021) Lithotectonic units of the Western Carpathians: Suggestion of simple methodology for lithotectonic units defining, applicable for orogenic belts world-wide. Mineralia Slovaca 2:81–90 Piessens K, Walstra J, Willems A, Barros R (2024) Old concepts in a new semantic perspective: introducing a geotemporal approach to conceptual definitions in geology. Life Sciences Plašienka D (1999) Definition and correlation of tectonic units with a special reference to some Central Western Carpathian examples. Mineralia Slovaca 31:3–16
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