The Darwin Core extension for genebanks opens up new opportunities for sharing genebank datasets

Darwin Core (DwC) defines a standard set of terms to describe the primary biodiversity data. Primary biodiversity data are data records derived from direct observation of species occurrences in nature or describing specimens in biological collections. The Darwin Core terms can be seen as an extension to the standard Dublin Core metadata terms. The new Darwin Core extension for genebanks declares the additional terms required for describing genebank datasets, and is based on established standards from the plant genetic resources community. The Global Biodiversity Information Facility (GBIF) provides an information infrastructure for biodiversity data including a suite of software tools for data publishing, distributed data access, and the capture of biodiversity data. The Darwin Core extension for genebanks is a key component that provides access for the genebanks and the plant genetic resources community to the GBIF informatics infrastructure including the new toolkits for data exchange. This paper provides one of the first examples and guidelines for how to create extensions to the Darwin Core standard

A regional approach to Nordic crop wild relative in situ conservation planning

Crop wild relatives (CWR) can provide one solution to future challenges on food security, sustainable agriculture and adaptation to climate change. Diversity found in CWR can be essential for adapting crops to these new demands. Since the need to improve in situ conservation of CWR has been recognized by the Convention on Biological Diversity (CBD) (2010) and the Global Strategy for Plant Conservation (2011-2020), it is important to develop ways to safeguard these important genetic resources. The Nordic flora includes many species related to food, forage and other crop groups, but little has been done to systematically secure these important wild resources. A Nordic regional approach to CWR conservation planning provided opportunities to network, find synergies, share knowledge, plan the conservation and give policy inputs on a regional level. A comprehensive CWR checklist for the Nordic region was generated and then prioritized by socio-economic value and utilization potential. Nordic CWR checklist was formed of 2553 taxa related to crop plants. Out of these, 114 taxa including 83 species were prioritized representing vegetable, cereal, fruit, berry, nut and forage crop groups. The in situ conservation planning of the priority CWR included ecogeographic and complementarity analyses to identify a potential network of genetic reserve sites in the region. Altogether 971,633 occurrence records of the priority species were analysed. A minimum number of sites within and outside existing conservation areas were identified that had the potential to support a maximum number of target species of maximum intraspecific diversity.Peer reviewe

Nordic Crop Wild Relative conservation : A report from two cooperation projects 2015-2019

The report summarizes results from a cooperation among all the Nordic countries during the period 2015 – 2019 (two projects). The work has focused on the conservation of Crop Wild Relatives (CWR), i.e. wild plant species closely related to crops. They are of special importance to humanity since traits of potential value for food security and climate change adaptation can be transferred from CWR into crops. The projects represent the first joint action on the Nordic level regarding in situ conservation of CWR. Substantial progress has been made regarding CWR conservation planning, including development of a Nordic CWR checklist and identification of suitable sites for CWR conservation. A set of recommended future actions was developed, with the most important one being initiation of active in situ conservation of CWR in all Nordic countries

Meeting report : GBIF hackathon-workshop on Darwin Core and sample data (22-24 May 2013)

© The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Standards in Genomic Sciences 9 (2014): 585-598, doi:10.4056/sigs.4898640.The workshop-hackathon was convened by the Global Biodiversity Information Facility (GBIF) at its secretariat in Copenhagen over 22-24 May 2013 with additional support from several projects (RCN4GSC, EAGER, VertNet, BiSciCol, GGBN, and Micro B3). It assembled a team of experts to address the challenge of adapting the Darwin Core standard for a wide variety of sample data. Topics addressed in the workshop included 1) a review of outstanding issues in the Darwin Core standard, 2) issues relating to publishing of biodiversity data through Darwin Core Archives, 3) use of Darwin Core Archives for publishing sample and monitoring data, 4) the case for modifying the Darwin Core Text Guide specification to support many-to-many relations, and 5) the generalization of the Darwin Core Archive to a “Biodiversity Data Archive”. A wide variety of use cases were assembled and discussed in order to inform further developments.We gratefully acknowledge support from the Global Biodiversity Information Facility (GBIF), from the Global Genome Biodiversity Network (GGBN), from the EU 7FP Biodiversity, Bioinformatics, Biotechnology project (Micro B3), and from the US National Science Foundation (NSF) through the following grants: DBI-0840989 [Research Coordination Network for the Ge-nomic Standards Consortium (RCN4GSC)], IIS-1255035 [EAGER: An Interoperable Information Infrastructure for Biodiversity Research (I3BR)], ABI Development: Collaborative Research: VertNet, a New Model for Bio-diversity Networks (DBI-1062193), and Collaborative Research: BiSciCol Tracker: Towards a tagging and tracking infrastructure for biodiversity science collec-tions (DBI-0956426)

COMPARTIR DATOS DE BIODIVERSIDAD A TRAVÉS DE GBIF COLOMBIA: Una invitación al sector empresarial

La infraestructura Global de Información en Biodiversidad (GBIF) es la red de datos sobre biodiversidad más grande del mundo. Como infraestructura internacional de datos abiertos, permite que cualquier persona pueda acceder, compartir y utilizar información sobre las especies de nuestro planetaBogoáSiB Colombi

Nordic LifeWatch cooperation, final report: A joint initiative from Denmark, Iceland, Finland, Norway and Sweden

The main goal of the present report is to outline the possibilities for an enhanced cooperation between the Nordic countries within eScience and biodiversity. LifeWatch is one of several ESFRI projects which aim to establish eInfrastructures and databases in the field of biodiversity and ecosystem research. Similarities between Nordic countries are extensive in relation to a number of biodiversity related issues. Most species in Nordic countries are common, and frequently the same challenges concerning biodiversity and ecosystem services are addressed in the different countries. The present report has been developed by establishing a Nordic LifeWatch network with delegates from each of the Nordic countries. The report has been written jointly by the delegates, and the work was organized by establishing working groups with the following themes: strategic issues, technical development, legal framework and communication. Written during two workshops, Skype meetings and emailing, the following main issues are discussed in the present report: * Scientific needs for improved access to biodiversity data and advanced eScience research infrastructure in the Nordic countries. * Future challenges and priorities facing the international biodiversity research community. * Scientific potential of openly accessible biodiversity and environmental data for individual researchers and institutions. * Spin-off effects of open access for the general public. * Internationally standardized Nordic metadata inventory. * Legal framework and challenges associated with environmental-, climate-, and biodiversity data sharing, communication, training and scientific needs. * Finally, some strategic steps towards realizing a Nordic LifeWatch construction and operational phase are discussed. Easy access to open data on biodiversity and the environment is crucial for many researchers and research institutions, as well as environmental administration. Easy access to data from different fields of science creates an environment for new scientific ideas to emerge. This potential of generating new, interdisciplinary approaches to pre-existing problems is one of the key features of open-access data platforms that unify diverse data sources. Interdisciplinary elements, access to data over larger gradients, compatible eSystems and eTools to handle large amounts of data are extremely important and, if further developed, represent significant steps towards analysis of biological effects of climate change, human impact and development of operational ecosystem service assessment techniques. It is concluded that significant benefits regarding both scientific potential, technical developments and financial investments can be obtained by constructing a common Nordic LifeWatch eInfrastructure. Several steps concerning organizing and funding of a future Nordic LifeWatch are discussed, and an action plan towards 2020 is suggested. To analyze the potential for future Nordic LifeWatch in detail, our main conclusion is to arrange a Nordic LifeWatch conference as soon as possible. This conference should involve Nordic research councils, scientists and relevant stakeholders. The national delegates from the participating countries in the Nordic LifeWatch project are prepared to present details from the report and developments so far as a basis for further development of Nordic LifeWatch. The present work is financed by NordForsk and in-kind contributions from participating institutions

Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers

BioDATA - Biodiversity Data for Internationalisation in Higher Education

BioDATA is an international project on developing skills in biodiversity data management and data publishing. Between 2018 and 2021, undergraduate and postgraduate students from Armenia, Belarus, Tajikistan, and Ukraine, have an opportunity to take part in the intensive courses to become certified professionals in biodiversity data management. They will gain practical skills and obtain appropriate knowledge on: international data standards (Darwin Core); data cleaning software, data publishing software such as the Integrated Publishing Toolkit (IPT), and preparation of data papers. Working with databases, creating datasets, managing data for statistical analyses and publishing research papers are essential for the everyday tasks of a modern biologist. At the same time, these skills are rarely taught in higher education. Most of the contemporary professionals in biodiversity have to gain these skills independently, through colleagues, or through supervision. In addition, all the participants familiarize themselves with one of the important international research data infrastructures such as the Global Biodiversity Information Facility (GBIF). The project is coordinated by the University of Oslo (Norway) and supported by the Global Biodiversity Information Facility (GBIF). The project is funded by the Norwegian Agency for International Cooperation and Quality Enhancement in Higher Education (DIKU)