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 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 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 Global Genome Biodiversity Network – Infrastructure for genomic research

2018 ◽  
Vol 2 ◽  
pp. e25289
Author(s):  
Katharine Barker
Keyword(s):  
Natural History ◽  
Best Practices ◽  
Code Of Conduct ◽  
Quality Standards ◽  
Genomic Research ◽  
Natural History Museums ◽  
High Quality ◽  
Nagoya Protocol ◽  
History Museums ◽  
Central Registry

Genomic research depends upon access to DNA or tissue collected and preserved according to high-quality standards. At present, the collections in most natural history museums do not sufficiently address these standards. In response to these challenges, natural history museums, culture collections, herbaria, botanical gardens and others have started to build high-quality biodiversity biobanks. Unfortunately, information about these collections remains fragmented, scattered and largely inaccessible. Without a central registry of relevant institutions, it is difficult and time-consuming to locate the needed samples. The Global Genome Biodiversity Network (GGBN) was created to fill this gap by establishing a central access point for locating samples meeting quality standards for genome-scale applications, while complying with national and international legislations and conventions (e.g. the Nagoya Protocol). The GGBN is rapidly growing and currently has 70 members and works closely together with GBIF, SPNHC, CETAF, INSDC, BOLD, ESBB, ISBER, GSC and others to reach its goals. Knowledge of biodiversity biobank content is urgently needed to enable concerted efforts and strategies in collecting and sampling new material and making ABS a reality. GGBN provides an infrastructure for making genomic samples discoverable and accessible. While respecting national law, GGBN requires that its members comply with the provisions of the Nagoya-protocol. Thus researchers, collection-holding institutions, and networks should adopt a common Best Practice approach to manage ABS, as has been developed by GGBN. A Code of Conduct; recommendations for implementing the Code of Conduct (the Best Practices), and implementation tools, such as standard Material Transfer Agreements (MTA) and mandatory and recommended data fields in collection databases, are tools which will aid compliance. This talk provides an overview of GGBN and comprises updates on GGBN’s best practices on ABS and the Nagoya Protocol, with examples of their use and applicability.

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.

Fundamental Research into Thin Films in a Developing Country

1972 ◽  
Vol 30 ◽  
pp. 500-501
Author(s):  
J.A. Eades ◽  
E. Grünbaum
Keyword(s):  
Thin Films ◽  
Growth Process ◽  
Empirical Process ◽  
Nucleation And Growth ◽  
Research Groups ◽  
Film Research ◽  
Fundamental Research ◽  
Controlled Deposition ◽  
The One ◽  
The University

In the last decade and a half, thin film research, particularly research into problems associated with epitaxy, has developed from a simple empirical process of determining the conditions for epitaxy into a complex analytical and experimental study of the nucleation and growth process on the one hand and a technology of very great importance on the other. During this period the thin films group of the University of Chile has studied the epitaxy of metals on metal and insulating substrates. The development of the group, one of the first research groups in physics to be established in the country, has parallelled the increasing complexity of the field.The elaborate techniques and equipment now needed for research into thin films may be illustrated by considering the plant and facilities of this group as characteristic of a good system for the controlled deposition and study of thin films.

John Robertson Henderson (1863–1925): Scotland, India and anomuran taxonomy

2020 ◽  
Vol 47 (1) ◽  
pp. 63-75
Author(s):  
P. G. Moore
Keyword(s):  
Natural History ◽  
Scientific Research ◽  
Christian College ◽  
Apparent Absence ◽  
University Of Edinburgh ◽  
Marine Station ◽  
The University ◽  
Crustacean Taxonomy

John Robertson Henderson was born in Scotland and educated at the University of Edinburgh, where he qualified as a doctor. His interest in marine natural history was fostered at the Scottish Marine Station for Scientific Research at Granton (near Edinburgh) where his focus on anomuran crustaceans emerged, to the extent that he was eventually invited to compile the anomuran volume of the Challenger expedition reports. He left Scotland for India in autumn 1885 to take up the Chair of Zoology at Madras Christian College, shortly after its establishment. He continued working on crustacean taxonomy, producing substantial contributions to the field; returning to Scotland in retirement in 1919. The apparent absence of communication with Alfred William Alcock, a surgeon-naturalist with overlapping interests in India, is highlighted but not resolved.

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