scholarly journals Multi-domain Collection Management Simplified — the Finnish National Collection Management System Kotka

2020 ◽  
Vol 4 ◽  
Author(s):  
Mikko Heikkinen ◽  
Anniina Kuusijärvi ◽  
Ville-Matti Riihikoski ◽  
Leif Schulman
Keyword(s):  
Natural History ◽  
Coordinate System ◽  
Collection Management ◽  
Free Text ◽  
Natural History Museums ◽  
History Museums ◽  
Darwin Core ◽  
Corvus Corone ◽  
Corvus Cornix ◽  
Biodiversity Information

Many natural history museums share a common problem: a multitude of legacy collection management systems (CMS) and the difficulty of finding a new system to replace them. Kotka is a CMS developed starting in 2011 at the Finnish Museum of Natural History (Luomus) and Finnish Biodiversity Information Facility (FinBIF) (Heikkinen et al. 2019, Schulman et al. 2019) to solve this problem. It has grown into a national system used by all natural history museums in Finland, and currently contains over two million specimens from several domains (zoological, botanical, paleontological, microbial, tissue sample and botanic garden collections). Kotka is a web application where data can be entered, edited, searched and exported through a browser-based user interface. It supports designing and printing specimen labels, handling collection metadata and specimen transactions, and helps support Nagoya protocol compliance. Creating a shared system for multiple institutions and collection types is difficult due to differences in their current processes, data formats, future needs and opinions. The more independent actors there are involved, the more complicated the development becomes. Successful development requires some trade-offs. Kotka has chosen features and development principles that emphasize fast development into a multitude of different purposes. Kotka was developed using agile methods with a single person (a product owner) making development decisions, based on e.g., strategic objectives, customer value and user feedback. Technical design emphasizes efficient development and usage over completeness and formal structure of the data. It applies simple and pragmatic approaches and improves collection management by providing practical tools for the users. In these regards, Kotka differs in many ways from a traditional CMS. Kotka stores data in a mostly denormalized free text format and uses a simple hierarchical data model. This allows greater flexibility and makes it easy to add new data fields and structures based on user feedback. Data harmonization and quality assurance is a continuous process, instead of doing it before entering data into the system. For example, specimen data with a taxon name can be entered into Kotka before the taxon name has been entered into the accompanying FinBIF taxonomy database. Example: simplified data about two specimens in Kotka, which have not been fully harmonized yet. Taxon: Corvus corone cornix Country: FI Collector: Doe, John Coordinates: 668, 338 Coordinate system: Finnish uniform coordinate system Taxon: Corvus corone cornix Country: FI Collector: Doe, John Coordinates: 668, 338 Coordinate system: Finnish uniform coordinate system Taxon: Corvus cornix Country: Finland Collector: Doe, J. Coordinates: 60.2442, 25,7201 Coordinate system: WGS84 Taxon: Corvus cornix Country: Finland Collector: Doe, J. Coordinates: 60.2442, 25,7201 Coordinate system: WGS84 Kotka’s data model does not follow standards, but has grown organically to reflect practical needs from the users. This is true particularly of data collected in research projects, which are often unique and complicated (e.g. complex relationships between species), requiring new data fields and/or storing data as free text. The majority of the data can be converted into simplified standard formats (e.g. Darwin Core) for sharing. The main challenge with this has been vague definitions of many data sharing formats (e.g. Darwin Core, CETAF Specimen Preview Profile (CETAF 2020), allowing different interpretations. Kotka trusts its users: it places very few limitations on what users can do, and has very simple user role management. Kotka stores the full history of all data, which allows fixing any possible errors and prevents data loss. Kotka is open source software, but is tightly coupled with the infrastructure of the Finnish Biodiversity Information Facility (FinBIF). Currently, it is only offered as an online service (Software as a Service) hosted by FinBIF. However, it could be developed into a more modular system that could, for example, utilize multiple different database backends and taxonomy data sources.

scholarly journals The Semantic Field Book Annotator

2019 ◽  
Vol 3 ◽  
Author(s):  
Lise Stork ◽  
Andreas Weber ◽  
Katherine Wolstencroft
Keyword(s):  
Natural History ◽  
Open Data ◽  
Semantic Field ◽  
Natural History Museums ◽  
History Museums ◽  
Authority File ◽  
Darwin Core ◽  
International Authority ◽  
Field Notes ◽  
Semantic Resources

Biodiversity research expeditions to the globe’s most biodiverse areas have been conducted for several hundred years. Natural history museums contain a wealth of historical materials from such expeditions, but they are stored in a fragmented way. As a consequence links between the various resources, e.g., specimens, illustrations and field notes, are often lost and are not easily re-established. Natural history museums have started to use persistent identifiers for physical collection objects, such as specimens, as well as associated information resources, such as web pages and multimedia. As a result, these resources can more easily be linked, using Linked Open Data (LOD), to information sources on the web. Specimens can be linked to taxonomic backbones of data providers, e.g., the Encyclopedia Of Life (EOL), the Global Biodiversity Information Facility (GBIF), or publications with Digital Object Identifiers (DOI). For the content of biodiversity expedition archives, (e.g. field notes), no such formalisations exist. However, linking the specimens to specific handwritten notes taken in the field can increase their scientific value. Specimens are generally accompanied by a label containing the location of the site where the specimen was collected, the collector’s name and the classification. Field notes often augment the basic metadata found with specimens with important details concerning, for instance, an organism’s habitat and morphology. Therefore, inter-collection interoperability of multimodal resources is just as important as intra-collection interoperability of unimodal resources. The linking of field notes and illustrations to specimens entails a number of challenges: historical handwritten content is generally difficult to read and interpret, especially due to changing taxonomic systems, nomenclature and collection practices. It is vital that: the content is structured in a similar way as the specimens, so that links can more easily be re-established either manually or in an automated way; for consolidation, the content is enriched with outgoing links to semantic resources, such as Geonames or Virtual International Authority File (VIAF); and this process is a transparent one: how links are established, why and by whom, should be stored to encourage scholarly discussions and to promote the attribution of efforts. the content is structured in a similar way as the specimens, so that links can more easily be re-established either manually or in an automated way; for consolidation, the content is enriched with outgoing links to semantic resources, such as Geonames or Virtual International Authority File (VIAF); and this process is a transparent one: how links are established, why and by whom, should be stored to encourage scholarly discussions and to promote the attribution of efforts. In order to address some of these issues, we have built a tool, the Semantic Field Book Annotator (SFB-A), that allows for the direct annotation of digitised (scanned) pages of field books and illustrations with Linked Open Data (LOD). The tool guides the user through the annotation process, so that semantic links are automatically generated in a formalised way. These annotations and links are subsequently stored in an RDF triplestore. As the use of the Darwin Core standard is considered best practice among collection managers for the digitisation of their specimens, our tool is equipped with an ontology based on Darwin Core terms, the NHC-Ontology, which extends the Darwin Semantic Web (DSW) ontology. The tool can annotate any image, be it an image of a specimen with a textual label, an illustration with a textual label or a handwritten species description. Interoperability of annotations between the various resources within a collection is therefore ensured. Terms in the ontology are structured using OWL web ontology language. This allows for more complex tasks such as OWL reasoning and semantic queries, and facilitates the creation of a richer knowledge base that is more amenable to research.

scholarly journals Butterflies in bags: permanent storage of Lepidoptera in glassine envelopes

2019 ◽  
Vol 42 (1) ◽  
pp. 1-16
Author(s):  
Max Caspers ◽  
Luc Willemse ◽  
Eulàlia Gassó Miracle ◽  
Erik J. van Nieukerken
Keyword(s):  
Natural History ◽  
Management Practices ◽  
Collection Management ◽  
The Internet ◽  
Natural History Museums ◽  
Data Registration ◽  
History Museums ◽  
Use Of Resources ◽  
Alternative Method ◽  
Permanent Storage

In terms of amateurs and professionals studying and collecting insects, Lepidoptera represent one of the most popular groups. It is this popularity, in combination with wings being routinely spread during mounting, which results in Lepidoptera often taking up the largest number of drawers and space in entomological collections. As resources grow increasingly scarce in natural history museums, any process that results in more efficient use of resources is a welcome addition to collection management practices. Therefore, we propose an alternative method to process papered Lepidoptera: a workflow to digitize (imaging and data registration) papered specimens and to store them (semi)permanently, still unmounted, in glassine envelopes. The mounting of specimens will be limited to those for which it is considered essential. The entire workflow of digitization and repacking can be carried out by non-expert volunteers. By releasing data and images on the internet, taxonomic experts worldwide can assist with identifications. This method was tested for Papilionidae. Results suggest that the workflow and permanent storage in glassine envelopes described here can be applied to most groups of Lepidoptera.

Fund natural-history museums, not de-extinction

Nature ◽  
2021 ◽  
Vol 598 (7879) ◽  
pp. 32-32
Author(s):  
Corrie S. Moreau ◽  
Jessica L. Ware
Keyword(s):  
Natural History ◽  
Natural History Museums ◽  
History Museums

scholarly journals The Global Museum: natural history collections and the future of evolutionary science and public education

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8225 ◽  
Author(s):  
Freek T. Bakker ◽  
Alexandre Antonelli ◽  
Julia A. Clarke ◽  
Joseph A. Cook ◽  
Scott V. Edwards ◽  
...  
Keyword(s):  
Natural History ◽  
Educational Innovation ◽  
Global Scale ◽  
Academic Community ◽  
Full Potential ◽  
Natural History Museums ◽  
Long Term Storage ◽  
History Museums ◽  
Natural History Collections ◽  
Museum Data

Natural history museums are unique spaces for interdisciplinary research and educational innovation. Through extensive exhibits and public programming and by hosting rich communities of amateurs, students, and researchers at all stages of their careers, they can provide a place-based window to focus on integration of science and discovery, as well as a locus for community engagement. At the same time, like a synthesis radio telescope, when joined together through emerging digital resources, the global community of museums (the ‘Global Museum’) is more than the sum of its parts, allowing insights and answers to diverse biological, environmental, and societal questions at the global scale, across eons of time, and spanning vast diversity across the Tree of Life. We argue that, whereas natural history collections and museums began with a focus on describing the diversity and peculiarities of species on Earth, they are now increasingly leveraged in new ways that significantly expand their impact and relevance. These new directions include the possibility to ask new, often interdisciplinary questions in basic and applied science, such as in biomimetic design, and by contributing to solutions to climate change, global health and food security challenges. As institutions, they have long been incubators for cutting-edge research in biology while simultaneously providing core infrastructure for research on present and future societal needs. Here we explore how the intersection between pressing issues in environmental and human health and rapid technological innovation have reinforced the relevance of museum collections. We do this by providing examples as food for thought for both the broader academic community and museum scientists on the evolving role of museums. We also identify challenges to the realization of the full potential of natural history collections and the Global Museum to science and society and discuss the critical need to grow these collections. We then focus on mapping and modelling of museum data (including place-based approaches and discovery), and explore the main projects, platforms and databases enabling this growth. Finally, we aim to improve relevant protocols for the long-term storage of specimens and tissues, ensuring proper connection with tomorrow’s technologies and hence further increasing the relevance of natural history museums.

scholarly journals NATURAL HISTORY MUSEUMS

2021 ◽  
pp. 24-28
Author(s):  
Dimítri De Araújo Costa ◽  
Nuno Gomes ◽  
Harold Cantallo ◽  
Carlos Antunes
Keyword(s):  
Natural History ◽  
Public Awareness ◽  
Natural World ◽  
Scientific Culture ◽  
Natural History Museums ◽  
Type Specimens ◽  
Local Fauna ◽  
History Museums ◽  
The World ◽  
Object Of Study

Society in general is distant from scientific culture, it is required to bring scientific knowledge closer to the population. In this context, an effective and attractive way for scientific dissemination is the establishment of natural history museums, which are institutions of knowledge, displaying the past. Natural history museums have the natural world as their object of study; and their collections may contain the most diverse types of materials (local and/or from various parts of the world), such as zoological, botanical, geological, archaeological, among others. Scientific collections are the largest and most important source of authoritative biodiversity data, contributing to studies of biodiversity composition, evolutionary (morphological and genetic), biogeographical, phenological, as well as geological. The materials present in these collections may serve for temporal comparison, being useful to produce predictive models. Likewise, they have a fundamental role in safeguarding type specimens, i.e. the first organisms identified to describe and name a new species. In addition, there is the component available to visitors in general, in order to raise public awareness on the preservation of the local fauna and flora and of other places in the world. In this way, the museums serve both the academic-scientific public and visitors who come to these sites for recreational purposes. It is intended to promote, in Vila Nova de Cerveira, the Natural History Museum of the Iberian Peninsula - NatMIP (“Museu de História Natural da Península Ibérica”), which intends to collect materials for scientific purposes, mainly Iberian.

scholarly journals Gender, Museums and Science: Wanda Hanke’s Ethnological Collections (1933–1958)

2016 ◽  
Vol 10 (1) ◽  
pp. 33-69 ◽  
Author(s):  
Mariana M. O. Sombrio
Keyword(s):  
Natural History ◽  
South America ◽  
Natural History Museums ◽  
Extensive Data ◽  
History Museums ◽  
Indigenous Groups ◽  
Medicine And Philosophy ◽  
The Status ◽  
History Of ◽  
Female Scientists

Abstract This paper will explore the significance of the expeditions under- taken by Wanda Hanke (1893-1958) in South America, of the networks she established in the region, as well as of her contributions to ethnological studies, in particular her compilation of extensive data and collections. Through Hanke's experience, it is possible to elucidate aspects of the history of ethnology and that of the history of museums in Brazil, as well as to emphasize the status of female participation in these areas. Wanda Hanke spent 25 years of her life studying the indigenous groups of Argentina, Bolivia, Brazil and Paraguay and collecting ethnological objects for natural history museums. Trained in medicine and philosophy, she began to dedicate herself to ethnological studies in her forties, and she travelled alone, an uncommon characteristic among female scientists in the 1940s, in Brazil.

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