Towards a biodiversity knowledge graph

One way to think about "core" biodiversity data is as a network of connected entities, such as taxa, taxonomic names, publications, people, species, sequences, images, and collections that form the "biodiversity knowledge graph". Many questions in biodiversity informatics can be framed as paths in this graph. This article explores this futher, and sketches a set of services and tools we would need in order to construct the graph

Liberating links between datasets using lightweight data publishing: an example using plant names and the taxonomic literature

Constructing a biodiversity knowledge graph will require making millions of cross links between diversity entities in different datasets. Researchers trying to bootstrap the growth of the biodiversity knowledge graph by constructing databases of links between these entities lack obvious ways to publish these sets of links. One appealing and lightweight approach is to create a "datasette", a database that is wrapped together with a simple web server that enables users to query the data. Datasettes can be packaged into Docker containers and hosted online with minimal effort. This approach is illustrated using a dataset of links between globally unique identifiers for plant taxonomic namesand identifiers for the taxonomic articles that published those names

Valuing Caribbean Biodiversity Knowledge

Valuing Caribbean biodiversity for health and wealth requires knowledge of the bioresource so as to better appreciate the myriad of uses and services it provides. Increasing the knowledge base provides increasingly accurate valuation, which hopefully will lead to better management and sustainable use of this biodiversity. The Caribbean region comprises 229,540 km2 of land (only 10% of which is still in original forest cover) and 2,754,000 km2 of ocean. In the region there are about 13,000 identified plant species of which 205 genera and 6500 species are endemic. The marine area, with a maximum depth of 7686 m, includes the world’s second largest barrier reef. It is estimated that the region has 25.6% marine endemic species. Multiple uses have been found for both terrestrial and marine organisms of the Caribbean. Mass extinctions have occurred for Peoples, associated traditional knowledge, terrestrial and marine biodiversity. Sea level rise and increasing temperature are global problems that threaten this area. All this information cannot be covered in one chapter so this review, based on a wide range of publications including our own research, is to raise awareness of these issues and the need to know more while suggesting solutions for discussion

Agricultural biodiversity, knowledge systems and policy decisions

International audienceSince the Earth Summit (1992), there has been an epistemological shift in research on the diversity of living organisms: there has been a switch from the sphere of biology to the sphere of society and the political and human sciences. Managing agricultural diversity, which mainly concerns varietal creation methods, intellectual property rights over genetic resources and access to seeds, does not raise any new challenges but these latter aspects are highlighted due to ecological urgency. We shall show this through the history of maize hybrids. Indeed, there are two major options. In the first option, so-called productivist agriculture, the aim will be to try and modify the environment, to make it more uniform while, at the same time, introducing and marketing a new genotype with broad adaptability or specific adaptation, though in both cases the environment will be artificialized. The second alternative, defended by the champions of smallholder agriculture, consists in growing a range of varieties or varieties populations, which themselves have the ability to adapt, hence a potential for evolution and, thereby, adaptation. The second option is usually greatly preferred by human populations in phase with their environment, as is often the case in the agricultures of the South. In addition, the pluralist principle of the democratic system enables the emergence of all kinds of controversies and those concerning environmental issues are very present as our common way of life is implicated. Within the biology field, quarrels over genetic risk, symbolized by MGOs, are emblematic. It can be seen that these ecological debates are all mediated by science, which holds expert, codified, scientific and easily accessible knowledge. However, since article 8j (CDB, 1992) stating that property rights are applicable to the genetic resources and local knowledge possessed by human communities, there has been renewed interest in the tacit knowledge incorporated in our practices, know-how and collective memories, which are much more difficult to decipher. No player, whether individual or collective, scientific or not, has enough knowledge and legitimacy to solve an environmental problem, which is necessarily of a collective nature, whereas our collective process of policy decisions appears to be increasingly “technocratic”, i.e. resulting from the aggregation of expert opinions. In such a context, some hybrid forums are emerging; they enable minorities to express their views, preferences and values and bring with them a new democratic form. These systems invent procedures for bringing knowledge out of isolation and they trigger collective learning processes. We shall attempt to understand the relation existing between the knowledge and policy decision systems, notably by structuring the functioning of delegation systems, which may generate more or less reasonable positions, depending on their configuration. Based on the results of an interdisciplinary workshop to be held in October 2013 under the NSS-Dialogues association, we shall focus ourselves, as scientists, on the issue of scientific mediation and its status in policy decisions

Enriched biodiversity data as a resource and service

Background: Recent years have seen a surge in projects that produce large volumes of structured, machine-readable biodiversity data. To make these data amenable to processing by generic, open source “data enrichment” workflows, they are increasingly being represented in a variety of standards-compliant interchange formats. Here, we report on an initiative in which software developers and taxonomists came together to address the challenges and highlight the opportunities in the enrichment of such biodiversity data by engaging in intensive, collaborative software development: The Biodiversity Data Enrichment Hackathon. Results: The hackathon brought together 37 participants (including developers and taxonomists, i.e. scientific professionals that gather, identify, name and classify species) from 10 countries: Belgium, Bulgaria, Canada, Finland, Germany, Italy, the Netherlands, New Zealand, the UK, and the US. The participants brought expertise in processing structured data, text mining, development of ontologies, digital identification keys, geographic information systems, niche modeling, natural language processing, provenance annotation, semantic integration, taxonomic name resolution, web service interfaces, workflow tools and visualisation. Most use cases and exemplar data were provided by taxonomists. One goal of the meeting was to facilitate re-use and enhancement of biodiversity knowledge by a broad range of stakeholders, such as taxonomists, systematists, ecologists, niche modelers, informaticians and ontologists. The suggested use cases resulted in nine breakout groups addressing three main themes: i) mobilising heritage biodiversity knowledge; ii) formalising and linking concepts; and iii) addressing interoperability between service platforms. Another goal was to further foster a community of experts in biodiversity informatics and to build human links between research projects and institutions, in response to recent calls to further such integration in this research domain. Conclusions: Beyond deriving prototype solutions for each use case, areas of inadequacy were discussed and are being pursued further. It was striking how many possible applications for biodiversity data there were and how quickly solutions could be put together when the normal constraints to collaboration were broken down for a week. Conversely, mobilising biodiversity knowledge from their silos in heritage literature and natural history collections will continue to require formalisation of the concepts (and the links between them) that define the research domain, as well as increased interoperability between the software platforms that operate on these concepts

Training and hackathon on building biodiversity knowledge graphs

Knowledge graphs have the potential to unite disconnected digitized biodiversity data, and there are a number of efforts underway to build biodiversity knowledge graphs. More generally, the recent popularity of knowledge graphs, driven in part by the advent and success of the Google Knowledge Graph, has breathed life into the ongoing development of semantic web infrastructure and prototypes in the biodiversity informatics community. We describe a one week training event and hackathon that focused on applying three specific knowledge graph technologies – the Neptune graph database; Metaphactory; and Wikidata - to a diverse set of biodiversity use cases. We give an overview of the training, the projects that were advanced throughout the week, and the critical discussions that emerged. We believe that the main barriers towards adoption of biodiversity knowledge graphs are the lack of understanding of knowledge graphs and the lack of adoption of shared unique identifiers. Furthermore, we believe an important advancement in the outlook of knowledge graph development is the emergence of Wikidata as an identifier broker and as a scoping tool. To remedy the current barriers towards biodiversity knowledge graph development, we recommend continued discussions at workshops and at conferences, which we expect to increase awareness and adoption of knowledge graph technologies

Contrasting effects of visiting urban green-space and the countryside on biodiversity knowledge and conservation support

Conservation policy frequently assumes that increasing people’s exposure to green-space enhances their knowledge of the natural world and desire to protect it. Urban development is, however, considered to be driving declining connectedness to nature. Despite this the evidence base supporting the assumption that visiting green-spaces promotes biodiversity knowledge and conservation support, and the impacts of urbanization on these relationships, is surprisingly limited. Using data from door-to-door surveys of nearly 300 residents in three pairs of small and large urban areas in England we demonstrate that people who visit green-space more regularly have higher biodiversity knowledge and support for conservation (measured using scales of pro-environmental behavior). Crucially these relationships only arise when considering visits to the countryside and not the frequency of visits to urban green-space. These patterns are robust to a suite of confounding variables including nature orientated motivations for visiting green-space, socio-economic and demographic factors, garden-use and engagement with natural history programs. Despite this the correlations that we uncover cannot unambiguously demonstrate that visiting the countryside improves biodiversity knowledge and conservation support. We consider it likely, however, that two mechanisms operate through a positive feedback loop i.e. increased visits to green-space promote an interest in and knowledge of biodiversity and support for conservation, which in turn further increase the desire to visit green-space and experience nature. The intensity of urbanization around peoples’ homes, but not city size, is negatively associated with their frequency of countryside visits and biodiversity knowledge. Designing less intensely urbanized cities with good access to the countryside, combined with conservation policies that promote access to the countryside thus seems likely to maximize urban residents’ biodiversity knowledge and support for conservation

Publication trends in global biodiversity research on protected areas

One of the main strategies to reduce the global loss of biodiversity has been the establishment of protected areas (PAs). High quality biodiversity knowledge is essential to successfully design PAs and PA networks, and to assess their conservation effectiveness. However, biodiversity knowledge is taxonomically and geographically biased. Even though PAs are typically more intensively surveyed than surrounding landscapes, they cannot avoid biodiversity knowledge shortfalls and biases. To investigate this, we performed a systematic literature review to assess publication trends in global biodiversity research taking place in PAs. Our data indicate that animals are more studied than plants, with vertebrates overrepresented in relation to invertebrates. Biodiversity in PAs has been mainly measured taxonomically (species richness or species diversity), while functional and phylogenetic diversity have rarely been considered. Finally, as predicted, there was a geographic bias towards European and USA terrestrial protected areas. These observed trends mirror more general studies of biodiversity knowledge shortfalls and could have direct negative consequences for conservation policy and practice. Reducing these biases and shortfalls is essential for more effective use of limited conservation resourcesSLC was supported by a FPI predoctoral grant financed by the Autonoma ´ University of Madrid. RJL was supported via the European Union’s Horizon 2020 research and innovation programme under grant agreement No 854248. AMCS was supported by the Ramon ´ y Cajal program (RYC2020-029407-I), financed by the Spanish Ministerio de Ciencia e Innovacio

A Census of Marine Biodiversity Knowledge, Resources, and Future Challenges

15 pages, 7 figures, 6 tablesThe Census of Marine Life (2000–2010) was the largest global research programme on marine biodiversity. This paper integrated the findings of reviews of major world regions by the Census and provides a global perspective on what is known and what are the major scientific gaps. Study metrics were regional species richness, numbers of endemic and alien species, numbers of species identification guides and taxonomic experts, and a state-of-knowledge index. The threats to biodiversity were classified across the regions. A poor to moderate correlation between species richness and seabed area, and sea volume, and no correlations with topographic variation, were attributed to sparse, uneven and unrepresentative sampling in much of the global marine environment. Many habitats have been poorly sampled, particularly in deeper seas, and several species-rich taxonomic groups, especially of smaller organisms, remain poorly studied. Crustacea, Mollusca, and Pisces comprised approximately half of all known species across the regions. The proportion that these and other taxa comprised of all taxa varied sufficiently to question whether the relative number of species within phyla and classes are constant throughout the world. Overfishing and pollution were identified as the main threats to biodiversity across all regions, followed by alien species, altered temperature, acidification, and hypoxia, although their relative importance varied among regions. The findings were replicated worldwide, in both developed and developing countries: i.e. major gaps exist in sampling effort and taxonomic expertise that impair society's ability to discover new species and identify and understand species of economic and ecological importance. There was a positive relationship between the availability of species identification guides and knowledge of biodiversity, including the number of species and alien species. Available taxonomic guides and experts correlated negatively with endemic species, suggesting that the more we study the ocean the fewer endemic species are evident. There is a need to accelerate the discovery of marine biodiversity, since much of it may be lost without even being known. We discuss how international collaboration between developed and developing countries is essential for improving productivity in the discovery and management of marine biodiversity, and how various sectors may contribute to thisThe contribution of HO was financed by research grant from the Estonian Ministry of Education and Research (no. SF0180005s10). MC was supported financially by the European Commission Marie Curie Post-doctoral Fellowship through the International Outgoing Fellowships (Call FP7-PEOPLE-2007-4-1-IOF) for the ECOFUN project and by Dalhousie University, Canada. RD was supported by the projects HERMIONE (EU-FPVII), VECTOR and OBAMA (MIUR, Italy). PM was supported by the Decanato de Investigación y Desarrollo, Universidad Simón BolívarPeer reviewe

A Census of Marine Biodiversity Knowledge, Resources, and Future Challenges.

ABSTRACT. The Census of Marine Life (2000–2010) was the largest global research programme on marine biodiversity. This paper integrated the findings of reviews of major world regions by the Census and provides a global perspective on what is known and what are the major scientific gaps. Study metrics were regional species richness, numbers of endemic and alien species, numbers of species identification guides and taxonomic experts, and a state-of-knowledge index. The threats to biodiversity were classified across the regions. A poor to moderate correlation between species richness and seabed area, and sea volume, and no correlations with topographic variation, were attributed to sparse, uneven and unrepresentative sampling in much of the global marine environment. Many habitats have been poorly sampled, particularly in deeper seas, and several species-rich taxonomic groups, especially of smaller organisms, remain poorly studied. Crustacea, Mollusca, and Pisces comprised approximately half of all known species across the regions. The proportion that these and other taxa comprised of all taxa varied sufficiently to question whether the relative number of species within phyla and classes are constant throughout the world. Overfishing and pollution were identified as the main threats to biodiversity across all regions, followed by alien species, altered temperature, acidification, and hypoxia, although their relative importance varied among regions. The findings were replicated worldwide, in both developed and developing countries: i.e. major gaps exist in sampling effort and taxonomic expertise that impair society's ability to discover new species and identify and understand species of economic and ecological importance. There was a positive relationship between the availability of species identification guides and knowledge of biodiversity, including the number of species and alien species. Available taxonomic guides and experts correlated negatively with endemic species, suggesting that the more we study the ocean the fewer endemic species are evident. There is a need to accelerate the discovery of marine biodiversity, since much of it may be lost without even being known. We discuss how international collaboration between developed and developing countries is essential for improving productivity in the discovery and management of marine biodiversity, and how various sectors may contribute to this