Workshop 01|2023

Speaker: Pia Stieger, Head of SwissCollNet, SCNAT

Speaker: Holger Frick, Head of Life Sciences & Invertebrates curator, Natural History Museum Basel

Summary:

Verbatim data on collections labels are hardly standardised. But they can be translated to extra fields that follow standards and help humans and computers to find, access, interoperate and reuse the data (FAIR). Based on hands-on examples some of the most important and already agreed standards on objects, persons, collections and institutions are introduced and explained.

Speaker: Peter Schuchert, Research Officer & Alexis Beck, ICT Engineer, Natural History Museum Geneva

Summary:

In 2020, the Geneva museum started to migrate its collection data from a Filemaker solution to the SPECIFY 6 application and we hope to complete this process within the next few months, having transferred more than 500 000 records. SPECIFY 6 is a widely used open source client application that uses a MySQL type database engine. The underlying data model of SPECIFY is exemplary for managing natural history specimens of biological origin and is presented here in a simplified way. However, the provided default user interface was too simple for our needs and we had to modify it quite extensively, in particular for the geological objects. As an example, the user interface for one of our collections – the non-arthropod invertebrates - will be presented and its function explained. Problems of the data migration process and the SPECIFY application will be outlined.

Speaker: Jurriaan deVos, Senior Scientist & Curator of the Herbaria, University Basel

Summary:

Best-practices recommendations for digitizing standard biological specimens are now readily available. However, non-standard specimens, as common for historic herbaria, remain challenging to adequately represent digitally. In this presentation I will use examples from 16th and 18th century herbaria from Basel to explain how we upgrade metadata from old Excel-list inventories to conform to DwC standards. Moreover, I explain how particularly challenging specimens are newly interpreted in this context, specifically dealing with unmounted specimens with multiple labels. For these purposes, the relevant, most important DwC fields will also be clarified.

Speaker: Jean-Luc Gattolliat, Curator at Museum of zoology, Lausanne

Summary:

Mayflies (Ephemeroptera) and Stoneflies (Plecoptera) are two small orders (less than 4000 species each) of aquatic insects. Around 100 000 occurrences are stored in Swiss museums, 75% stored in Lausanne, 20% in Basel, Geneva and Zurich. Specimens are stored in fluid, pinned or on microscopic slides. We started the project with small collections or partially digitalised collections. For larger collections, we want to implement new pipelines to automatically take multiple images from different angles of the specimens or vials. The images of the specimens and labels are assembled into a single recombined image; the data is automatically extracted using OCR (optical character recognition).

Speaker: Celia Bueno, Curator of Vertebrates and Mollusks, Natural History Museum Neuchatel

Summary:

In order to build a coherent inventory of the mollusk collection, a first phase was to set up working structures to train and supervise the temporary staff. The second step will consist of a homogenization of the data at the level of provenance (collector and georeferencing) and systematic to ensure a robust structure of the data.

Speaker: Mathieu Perret, Curator & Senior lecturer, Conservatory and Botanical Garden Geneva

Summary:

Amount of genetic and genomic information linked to or directly generated from museum or herbarium specimens is increasing at an exponential rate. Although this information is now largely used to describe and monitor biodiversity, DNA samples and sequences are still poorly related to broader biodiversity information available in GBIF and in the national data centers. Here we propose to use the available DwC standards and newly defined attributes to record DNA-derived data in the GBIF, in order to secure the link between the specimens and all the genetic data and samples deriving from them. We will illustrate this approach with examples from our SwissCollNet project aiming at developing an extended DNA-bank for plants.

Speaker: Loïc Costeur, Head of Earth Sciences & Curator Vertebrate Palaeontology, Natural History Museum Basel

Summary:

Imaging natural history collections is a way of producing metadata that will be made available for different aspects of collection management. It may help managing your collection on an everyday basis when considering imaging collection units at tray level, it may provide large-scale data that can be used in citizen science projects, but it is also a way of preserving and sharing morphological data of rare or endangered specimens using 3D digitization techniques. Mass production of images is not an easy task since it is both time consuming when considering complex objects and requires large space to save the data. I will briefly review the pros and cons of imaging collections, show the best practices for producing the data and saving them, as well as show what standards are defined to date. Finally, I will provide a first feedback based on our running SwissCollNet project aimed at imaging fossil types and reference specimens.

Speaker: Alice Cibois, Natural History Museum Geneva & Michelle Price, Conservatory and Botanical Garden
Geneva, President and member of SwissCollNet Board of Experts