scholarly journals The Genomic Resources Collection Policy of the Finnish Museum of Natural History

2021 ◽  
Vol 7 ◽  
Author(s):  
Gunilla Ståhls ◽  
Alexandre Aleixo ◽  
Marko-Tapio Hyvärinen ◽  
Anniina Kuusijärvi ◽  
Leena Myllys ◽  
...  
Keyword(s):  
Natural History ◽  
Biological Diversity ◽  
Animal Tissue ◽  
Collection Management ◽  
Collections Management ◽  
Tissue Samples ◽  
Genomic Resources ◽  
Natural History Collections ◽  
Genome Level ◽  
Research And Education

The Genomic Resources Collection is a separate, independently managed part of the natural history collections of the Finnish Museum of Natural History Luomus specifically intended for consumptive research. The GRC policy deals with the materials that are archived for the very purpose of enabling the study of biological diversity at the genome level, DNA extractions of animal, fungal and plant specimens, and animal tissue samples stored deep-frozen for purposes of future DNA extraction. The GRC policy defines the purpose of the collections, the objectives and content of the procedures and activities related to them, the distribution of responsibilities for collection management and maintenance in Luomus, and the principles of collection accumulation, preservation and accessibility. The aim of the GRC is to store and loan genomic samples for research purposes. In taxonomic coverage the collection overlaps with all the taxonomically delimited specimen collections managed by the Zoology and Botany Units, but is distinguished as being directed to preserve the genomic (DNA) information irrespective of the phenotypic variation that are the focus of specimen collections. The GRC includes both Finnish and foreign samples, all legally and ethically obtained, mostly linked to a specimen voucher in the taxonomic collections. The GRC samples are documented and trackable in Luomus collections management system. In accordance with the Universities Act, the GRC belongs to the national natural science collections of Luomus. For their part, the GRC collection implement the mission of Luomus, which is to be “responsible for the preservation, accumulation and exhibition of the national natural history collections and for research and education relating to them”.

scholarly journals Luomus’ Genomic Resources Collection Available as Open Data Through FinBIF

2019 ◽  
Vol 3 ◽  
Author(s):  
Gunilla Ståhls-Mäkelä ◽  
Anniina Kuusijärvi ◽  
Ville-Matti Riihikoski ◽  
Leif Schulman ◽  
Aino Juslén
Keyword(s):  
Natural History ◽  
Biological Diversity ◽  
Open Data ◽  
Research Groups ◽  
High Quality ◽  
Tissue Samples ◽  
Voucher Specimen ◽  
Nagoya Protocol ◽  
Genomic Resources ◽  
The University

There is an increasing demand for high-quality genetic samples for biodiversity research as the techniques are rapidly developing and the costs are decreasing. The Finnish Museum of Natural History Luomus, an independent research institute within the University of Helsinki holding and developing the national natural history collections, has joined the Global Genome Biodiversity Network (GGBN; http://www.ggbn.org/ggbn_portal/) and established a Genomic Resources Collection (GRC) in 2018. In March 2019, the Luomus GRC comprised 2500 DNA extractions and 4000 vertebrate tissue samples amassed in approximately the last 10 years. The DNA extractions are mainly of lichens, polypores, beetles, flies, molluscs and crustaceans of worldwide origin, reflecting the focal organism groups of research groups in Luomus. The deep-frozen tissue samples are mostly of Finnish birds and mammals, as accessions of vertebrate specimens acquired to Luomus’ collections are sampled. High-quality whole-genome DNA extracts will also be prepared. We expect the GRC to increase rapidly in numbers of samples within the coming years. Furthermore, the collection will also serve the many active research groups in the Faculty of Biological and Environmental Sciences of the University of Helsinki. The GRC collection follows the best practices of the Global Genome Biodiversity Network (GGBN) concerning long-term storage and physical quality of samples, and international agreements (the Convention on Biological Diversity, the Nagoya Protocol, CITES) as regards the legitimacy of the samples. The GRC samples are always cross-linked with the taxonomically identified and georeferenced voucher specimen from which it is separated. Each GRC sample gets a Unique Resource Identifier HTTP-URI, which is a derivative of the unique specimen ID used in Luomus’ Collection Management System (CMS) ‘Kotka’. The sample tubes are cryolabelled with the QR code on the lid of the tube. The voucher specimens are deposited in Luomus’ collections or in another international public repository. The data on the GRC samples form part of the Open Data distributed through the Finnish Biodiversity Information Facility FinBIF species.fi (Data policy: https://laji.fi/en/about/960), and will be made searchable at the web portal in 2019. The specific database functions to meet the needs of Luomus’ GRC are developed by Luomus’ Biodiversity Informatics Unit and implemented in Kotka. We have already implemented part of the database tools to manage the compliance with the Nagoya protocol. The tool for registering material transactions (donations / loans) makes use of the Application Programming Interface (API) provided by the Access and Benefit Sharing Clearing House (ABS-CH) and includes links to the ABS-CH webpage (https://absch.cbd.int/). The ABS-CH shows the contact person or organization details of the provider country, and the country-specific requirements for access to genetic resources, when present. The necessary information and documentation (letter of Prior Informed Consent, Mutually Agreed Terms, Material Transaction Agreement, and other permits) are linked from the material transactions to the relevant specimens.

scholarly journals Leveraging the Benefits of Open Data Services for Natural History Collection Management

2018 ◽  
Vol 2 ◽  
pp. e25882
Author(s):  
Maarten Schermer ◽  
Daphne Duin
Keyword(s):  
Natural History ◽  
The Netherlands ◽  
Large Scale ◽  
Open Data ◽  
Collection Management ◽  
Collections Management ◽  
Biodiversity Data ◽  
Data Services ◽  
Natural History Collections ◽  
Digital Collection

The value of data present in natural history collections for research and collection management cannot be overstated. Naturalis Biodiversity Center, home to one of the largest natural history collections in the world, completed a large-scale digitisation project resulting in the registration of more than 38 million objects, many of them annotated with descriptive metadata, such as geographic coordinates and multimedia content. While digitisation is ongoing, we are now also looking for ways to leverage our digital collection, both for the benefit of collection management and that of networking with other natural history collections. To this end, we developed the Netherlands Biodiversity Data Services, providing centralized access to our collection data via state of the art, open access interfaces. Full, centralized access to the digital collection allows us to combine the data with other sources, such as collection scans focusing on the physical condition and accessibility of the collection. But also with data from external sources, such as the collection information of sister institutions, allowing for combining and comparing data, and exploring areas where collections can reinforce each other. Focusing on availability and accessibility, the services were deliberately designed as a versatile, low-level API to allow the use of our data with a broad variety of applications and services. These applications range from scientific research and remote mobile access to collection information, to “mash ups” with other data sources, apps and application in our own museum. We will demonstrate this range of applications through several examples, including the embedding of data in websites (example, Dutch Caribbean Species Register: http://www.dutchcaribbeanspecies.org/linnaeus_ng/app/views/species/nsr_taxon.php?id=177968&cat=165), use in the development of deep learning models, thematic portals (example, Naturalis meteorite collection: http://bioportal.naturalis.nl/result?theme=meteorites&language=en) and the development of Java- and R-clients. This presentation ties in with Max Caspers' presentation “Advancing collections management with the Netherlands Biodiversity Data Services“, in which he will demonstratie the potential of the services described in this presentation for the area of collections management, specifically.

scholarly journals Looking Back for the Future: Utilizing Sawfish Saws from Natural History Collections to Conserve the Critically Endangered Largetooth Sawfish (Pristis pristis)

2018 ◽  
Vol 2 ◽  
pp. e25806
Author(s):  
Annmarie Fearing ◽  
Kelcee Smith ◽  
Tonya Wiley ◽  
Jeff Whitty ◽  
Kevin Feldheim ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Natural History ◽  
Mitochondrial Control Region ◽  
Genetic Bottleneck ◽  
Critically Endangered ◽  
Past Century ◽  
Term Survival ◽  
Tissue Samples ◽  
The Past ◽  
Natural History Collections

The Critically Endangered (International Union for Conservation of Nature) largetooth sawfish, Pristispristis, was historically distributed in the tropical Pacific, Atlantic and Indian Oceans. Today, ‘viable’ populations are largely limited to northern Australia. Populations that have suffered from drastic declines in abundance, such as those experienced by P.pristis, are typically at risk of having reduced, or low, levels of genetic diversity. Previous research found that P.pristis in Australia have experienced a genetic bottleneck, but it is unclear whether this bottleneck is the result of contemporary declines over the last century, or if it is the result of historic processes. A direct way to assess whether this genetic bottleneck occurred relatively recently is to compare levels of genetic diversity in contemporary and historic populations. Sawfish saws that were taken as trophies over the past century can now be found in natural history collections around the world and can provide DNA from past sawfish populations. We collected tissue samples from 150 dried P.pristis saws found in both private and public natural history collections. Because DNA from natural history specimens tends to be highly degraded, we targeted ten small DNA fragments, ~150 base pairs each, to amplify and sequence the entire mitochondrial control region. These data will provide important baseline information about P.pristis that can be used to quantify any loss of genetic diversity over the past ~100 years and assess their long-term survival potential. If the levels of genetic diversity in contemporary populations are severely reduced from those of past populations, protecting remaining genetic diversity within and between viable populations should be a priority in conservation plans.

scholarly journals Database Tools to Meet the Nagoya Protocol Requirements in a Collection Management System

2019 ◽  
Vol 3 ◽  
Author(s):  
Anniina Kuusijärvi ◽  
Ville-Matti Riihikoski ◽  
Samuli Lehtonen ◽  
Gunilla Ståhls ◽  
Marko Hyvärinen ◽  
...  
Keyword(s):  
Natural History ◽  
Genetic Resources ◽  
Management System ◽  
Biological Diversity ◽  
Genetic Resource ◽  
Third Parties ◽  
Ex Situ ◽  
Collection Management ◽  
Nagoya Protocol ◽  
Collection Management System

The Nagoya Protocol (NP) of the Convention on Biological Diversity requires that genetic resource holders and users obtain, preserve and keep relevant documentation. Users and third parties need to be informed on terms of access, which utilisation is allowed, and which benefits need to be shared when respective genetic resources or associated traditional knowledge is utilised in the meaning of the NP. Following the recommendations in the Code of Conduct & Best Practices of the Consortium of European Taxonomic Facilities (CETAF) CETAF Legislations and Regulations Liaison Group 2019, institutions should implement appropriate data management systems to support compliance with the protocol and keep records on acquisition of biological material, utilization of genetic resources, transfers to third parties, benefits derived and shared, and deaccessioning of specimens or disposal of consumed samples. Here we describe how we have implemented the first set of tools to meet the NP requirements in the Kotka Collection Management System (CMS), which is used by eleven Natural History Museums in Finland. The Kotka CMS is used for storing and managing specimen data and for handling material transactions (loans, exchanges, donations and consumptive loans). Users can enter and store all necessary documentation for both incoming and outgoing material as material transactions, which hold information on e.g., the transaction type, description of the material, important dates, correspondent organization and contact person. Specimens are linked to transactions by their unique identifiers and each transaction also has a unique stable identifier. The first version of the tools for meeting the requirements of the Nagoya protocol on both in situ and ex situ accession of genetic resources have been integrated into the transaction section of the system. For genetic resource users to be able to enter, save and provide all the required information about an incoming genetic resource, we have implemented a set of fields to be completed in the transactions in Kotka CMS (Fig. 1). Users can record, for example, a possible IRCC number (Internationally Recognized Certificate of Compliance), acquisition date and providing country, description of the material, information on Prior Informed Consent, Mutually Agreed Terms, Material Transfer Agreement and other possible permits. The Finnish genomic resource legislation requires a notification within one month of acquisition to the Competent National Authority (CNA; The Finnish Environment Institute and Natural Resources Institute Finland) for any imported genetic resources. The required data for the notification is compiled in Kotka CMS and then sent to the CNA. All the documentation and conditions regulating the utilisation of each specimen and derived samples must follow with the specimen data at all times. To accomplish this all the necessary information and documents are linked from the material transactions to the relevant specimens by unique specimen or sample identifiers. In the specimen view page, links to the full transaction details and history are given, as a single specimen or a derived sample can be part of several different types of transactions. Users also see a summary of the transaction information directly in the specimen view, most importantly whether the specimen is available for genetic research or has any restrictions for use. The Kotka CMS transaction section makes use of the Application Programming Interface (API) provided by the Access and Benefit Sharing Clearing House (ABS-CH). Using the API, Kotka CMS validates the IRCC number if given and provides links to the ABS-CH, for example to the relevant country profile page, the contact details of the CNA, and specific requirements for access to genetic resources when applicable. This way, we provide Kotka CMS users up-to-date information from the original source to support their genetic resource management. We will further improve and develop the tools during the years 2019-2020. Now that the first version is in use, we will make adjustments according to user feedback. We also have a few changes planned, for example, the tools for transferring the necessary information on permits and other details with outgoing specimens to a user in another institution abroad will be updated. All users in Finnish natural history institutions have access to all the information directly in Kotka CMS, as it is a national system. Additionally, both specimen and transaction information searchability will be refined.

scholarly journals DINA—Development of open source and open services for natural history collections & research

2020 ◽  
Vol 4 ◽  
Author(s):  
Falko Glöckler ◽  
James Macklin ◽  
David Shorthouse ◽  
Christian Bölling ◽  
Satpal Bilkhu ◽  
...  
Keyword(s):  
Natural History ◽  
Open Source ◽  
Open Source Software ◽  
Web Application ◽  
Tracking System ◽  
Molecular Data ◽  
Collection Management ◽  
Agile Development ◽  
Natural History Collections ◽  
Code Base

The DINA Consortium (DINA = “DIgital information system for NAtural history data”, https://dina-project.net) is a framework for like-minded practitioners of natural history collections to collaborate on the development of distributed, open source software that empowers and sustains collections management. Target collections include zoology, botany, mycology, geology, paleontology, and living collections. The DINA software will also permit the compilation of biodiversity inventories and will robustly support both observation and molecular data. The DINA Consortium focuses on an open source software philosophy and on community-driven open development. Contributors share their development resources and expertise for the benefit of all participants. The DINA System is explicitly designed as a loosely coupled set of web-enabled modules. At its core, this modular ecosystem includes strict guidelines for the structure of Web application programming interfaces (APIs), which guarantees the interoperability of all components (https://github.com/DINA-Web). Important to the DINA philosophy is that users (e.g., collection managers, curators) be actively engaged in an agile development process. This ensures that the product is pleasing for everyday use, includes efficient yet flexible workflows, and implements best practices in specimen data capture and management. There are three options for developing a DINA module: create a new module compliant with the specifications (Fig. 1), modify an existing code-base to attain compliance (Fig. 2), or wrap a compliant API around existing code that cannot be or may not be modified (e.g., infeasible, dependencies on other systems, closed code) (Fig. 3). create a new module compliant with the specifications (Fig. 1), modify an existing code-base to attain compliance (Fig. 2), or wrap a compliant API around existing code that cannot be or may not be modified (e.g., infeasible, dependencies on other systems, closed code) (Fig. 3). All three of these scenarios have been applied in the modules recently developed: a module for molecular data (SeqDB), modules for multimedia, documents and agents data and a service module for printing labels and reports: The SeqDB collection management and molecular tracking system (Bilkhu et al. 2017) has evolved through two of these scenarios. Originally, the required architectural changes were going to be added into the codebase, but after some time, the development team recognised that the technical debt inherent in the project wasn’t worth the effort of modification and refactoring. Instead a new codebase was created bringing forward the best parts of the system oriented around the molecular data model for Sanger Sequencing and Next Generation Sequencing (NGS) workflows. In the case of the Multimedia and Document Store module and the Agents module, a brand new codebase was established whose technology choices were aligned with the DINA vision. These two modules have been created from fundamental use cases for collection management and digitization workflows and will continue to evolve as more modules come online and broaden their scope. The DINA Labels & Reporting module is a generic service for transforming data in arbitrary printable layouts based on customizable templates. In order to use the module in combination with data managed in collection management software Specify (http://specifysoftware.org) for printing labels of collection objects, we wrapped the Specify 7 API with a DINA-compliant API layer called the “DINA Specify Broker”. This allows for using the easy-to-use web-based template engine within the DINA Labels & Reports module without changing Specify’s codebase. In our presentation we will explain the DINA development philosophy and will outline benefits for different stakeholders who directly or indirectly use collections data and related research data in their daily workflows. We will also highlight opportunities for joining the DINA Consortium and how to best engage with members of DINA who share their expertise in natural science, biodiversity informatics and geoinformatics.

Guidelines for the Documentation and Care of Invertebrate Fossil Collections

2000 ◽  
Vol 10 ◽  
pp. 51-64
Author(s):  
Russell D. White
Keyword(s):  
Natural History ◽  
North American ◽  
Collection Management ◽  
University Faculty ◽  
Natural History Collections ◽  
Invertebrate Paleontology ◽  
Invertebrate Fossils

COLLECTIONS OF invertebrate fossils are commonly maintained in museums, at universities, and by individual researchers and interested private collectors. Twenty years ago, the Committee on North American Resources in Invertebrate Paleontology (CONARIP) estimated that there more than 550 institutions housed invertebrate paleontological macro- and micro- fossil collections (Glenister, 1977). Historically, collections have been developed, managed and maintained by paleontologists as a resource for their research (e.g., museum curator or university faculty) (Hebda, 1985). Since the early 1970s, the field of collection management has evolved and the increased professionalization of collection manager positions has been instrumental in improving the management and preservation of invertebrate fossils as well as other natural history collections (Cato, 1991; Simmons, 1993; Simmons, 1995).

scholarly journals Herbarium collections policy of the Finnish Museum of Natural History

2020 ◽  
Vol 6 ◽  
Author(s):  
Henry Väre ◽  
Leena Myllys ◽  
Risto Väinölä ◽  
Pasi Sihvonen ◽  
Anniina Kuusijärvi ◽  
...  
Keyword(s):  
Natural History ◽  
Digital Collections ◽  
Tissue Samples ◽  
Natural History Collections ◽  
University Level ◽  
Herbarium Collections

The herbarium collections are sub-collections of the Finnish Museum of Natural History Luomus that manages national natural history collections, as referred to in the Universities Act. The general collections policy defines the overall principles and guidelines concerning the collections practices. The sub-collections policies specify its guidelines and instructions, considering the special nature of the sub-collections. The policy for the botanical and mycological herbarium collections guides the activities related to all botanical, mycological and phycological collections in herbaria, hence excluding digital collections, DNA and tissue samples as well as living collections, which have separate policies. The herbarium collections policy defines and outlines the purpose of the collections as is to accrue and preserve natural specimens representing biodiversity for research and university-level teaching. The policy defines the objectives and content of related activities, the division of responsibilities for the administration and care of the collections within the organisation, and the general principles and practices for the acquisition, preservation, availability and use of the collections.

scholarly journals Living plant collections policy of the Finnish Museum of Natural History

2020 ◽  
Vol 6 ◽  
Author(s):  
Marko-Tapio Hyvärinen ◽  
Mikael Lindholm ◽  
Heli Fitzgerald ◽  
Mari Miranto ◽  
Aino Anttila ◽  
...  
Keyword(s):  
Natural History ◽  
Seed Bank ◽  
Botanic Gardens ◽  
Tissue Samples ◽  
Living Plant ◽  
Genomic Resources ◽  
Plant Collections

The collections policy of the Finnish Museum of Natural History Luomus is hierarchically structured. The general collections policy defines the overall principles and guidelines. The sub-collections policies, such as the Living collections policy, comply with and apply the general collections policy and specify its guidelines and instructions, taking the special nature of the sub-collections into account. The living plant collections policy guides the care of the collections in the botanic gardens and the seed bank, excluding DNA and tissue samples which are covered by a separate genomic resources policy. The purpose of the collections policy is to help guide the care of the garden collections and the processing of information relating to the collections, thereby providing the basis for developing the botanic gardens.

scholarly journals Invertebrate collections policy of the Finnish Museum of Natural History

2020 ◽  
Vol 6 ◽  
Author(s):  
Risto Väinölä ◽  
Lauri Kaila ◽  
Jaakko Mattila ◽  
Pasi Sihvonen ◽  
Marko-Tapio Hyvärinen ◽  
...  
Keyword(s):  
Natural History ◽  
Hierarchical Structure ◽  
Assessment Procedure ◽  
Collections Management ◽  
Self Assessment ◽  
Tissue Samples ◽  
The Individual

The collection policy of the Finnish Museum of Natural History Luomus is hierarchically structured. General principles and guidelines are defined in the General Collections Policy. Subordinate to it, the collection policies for the individual sub-collections implement and specify these guidelines and instructions, considering the special nature of each sub-collection. The invertebrate collections policy in 2017 was the first sub-collection policy to observe this hierarchical structure, and was guided by the standards set by the European SYNTHESYS collections management self-assessment procedure. The invertebrate collections policy directs all activities related to the Luomus invertebrate collections (apart from DNA and tissue samples), which comprise the separately managed entomological collections (ca. 9 million specimens) and collections of other invertebrates (0.4 million). The policy defines the purpose of the collections, outlines the objectives and content of procedures and activities related to them, the division of responsibilities for the administration and care of the collections within the organisation, and the principles and practices for the acquisition, preservation, accessibility and use of the collections.

Immunoelectron microscopic localization of elastic tissue in archival material using an improved method

1990 ◽  
Vol 48 (3) ◽  
pp. 794-795
Author(s):  
J. C. Fanning ◽  
J. F. White ◽  
R. Polewski ◽  
E. G. Cleary
Keyword(s):  
Normal Animal ◽  
Animal Tissue ◽  
Elastic Tissue ◽  
Human Tissues ◽  
Improved Method ◽  
Tissue Samples ◽  
Archival Material ◽  
Immuno Electron Microscopy ◽  
Arteries And Veins ◽  
Biochemical Examination

Elastic tissue is an important component of the walls of arteries and veins, of skin, of the lungs and in lesser amounts, of many other tissues. It is responsible for the rubber-like properties of the arteries and for the normal texture of young skin. It undergoes changes in a number of important diseases such as atherosclerosis and emphysema and on exposure of skin to sunlight.We have recently described methods for the localizationof elastic tissue components in normal animal and human tissues. In the study of developing and diseased tissues it is often not possible to obtain samples which have been optimally prepared for immuno-electron microscopy. Sometimes there is also a need to examine retrospectively samples collected some years previously. We have therefore developed modifications to our published methods to allow examination of human and animal tissue samples obtained at surgery or during post mortem which have subsequently been: 1. stored frozen at -35° or -70°C for biochemical examination; 2.

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