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

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

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

Analogue Invention: S. and House of Leaves as Integrated Texts

Since the turn of the millennium there has been an emergence of novels that incorporate unorthodox page design as part of their narrative toolbox, some of which have acquired a cult following that still comb through their atypically designed pages. This thesis provides a qualitative study of modern publications that use digital typesetting to produce an untraditional analogue experience. The contemporary materialist field is often primarily concerned with hypertexts and other forms of digital literature, while this thesis is focused on the potential still present in physical books. Because categorization of this kind of atypically designed book is lacking, I suggest the term “integrated texts” to describe them. The definition of this term as well as a general description is provided in chapter 1. Chapter 2 and 3 will provide case studies of Danielewski’s House of Leaves and Abrams & Dorst’s S. to illustrate how integrated texts work. Both of which remediate their themes through multiple levels of storytelling but through drastically different techniques. House of Leaves’s ludic text making and experimental page design look nothing like S.’ marginalia and use of paratextual inserts, but both are examples of integrated text. This thesis argues for the aesthetic potential in moving beyond the traditional borders of the page

Analogue Invention: S. and House of Leaves as Integrated Texts

Since the turn of the millennium there has been an emergence of novels that incorporate unorthodox page design as part of their narrative toolbox, some of which have acquired a cult following that still comb through their atypically designed pages. This thesis provides a qualitative study of modern publications that use digital typesetting to produce an untraditional analogue experience. The contemporary materialist field is often primarily concerned with hypertexts and other forms of digital literature, while this thesis is focused on the potential still present in physical books. Because categorization of this kind of atypically designed book is lacking, I suggest the term “integrated texts” to describe them. The definition of this term as well as a general description is provided in chapter 1. Chapter 2 and 3 will provide case studies of Danielewski’s House of Leaves and Abrams & Dorst’s S. to illustrate how integrated texts work. Both of which remediate their themes through multiple levels of storytelling but through drastically different techniques. House of Leaves’s ludic text making and experimental page design look nothing like S.’ marginalia and use of paratextual inserts, but both are examples of integrated text. This thesis argues for the aesthetic potential in moving beyond the traditional borders of the page

Chapter 42: Information, knowledge and agricultural biodiversity

Plant genetic resources for food and agriculture include an estimated 7.4 million ex situ accessions conserved in genebank collections. An estimated 40% of these accessions are both electronically documented and freely available from online genebank data platforms such as Genesys (Alercia and Mackay, 2013; www.genesyspgr.org/) and EURISCO (FAO, 2010; Dias et al, 2011; http://eurisco.ipkgatersleben.de/). Approximately 21% of the world’s flora is classified as a crop wild relative and as such a potential gene donor for crops (Maxted and Kell, 2009). The Global Biodiversity Information Facility (GBIF) (Telenius, 2011) integrates and provides extensive occurrence information about collection data, including genebank accessions ex situ and wild plants in situ, including many crop wild relatives. However, neither GBIF nor the genebank data portals focus on providing data on the molecular genetic diversity or conservation status of the collections. Some ex situ genebank accessions do provide associated measurement data from characterization and evaluation trials. However, the lack of easy access to experimental trait information online continues to be reported as a major limitation to the efficient use of plant genetic resources (FAO, 2010). Data on ex situ genebank collections, crop wild relative in situ populations, genetic data, and trait measurements are generally created and made available by different sub-groups of practitioners, and each sub-group has showed a tendency to develop its own documentation practices and data standards. This chapter will describe how knowledge organization principles can be used to create a more unified data landscape for agricultural biodiversity. It is concluded that the introduction of persistent and globally unique digital identifiers, resolvable to machine-readable information, and based on a standardized and formally declared data domain model is one of the fundamental first steps for an effective integration of agricultural biodiversity information (FAO, 2014). This is an Accepted Manuscript of a book chapter published by Routledge in Routledge Handbook of Agricultural Biodiversity on 04.10.2017, available online: https://www.routledge.com/Routledge-Handbook-of-Agricultural-Biodiversity/Hunter-Guarino-Spillane-McKeown/p/book/978041574692