Bridging Biodiversity and Health: The Global Biodiversity Information Facility's initiative on open data on vectors of human diseases.

There is an increased awareness of the importance of data publication, data sharing, and open science to support research, monitoring and control of vector-borne disease (VBD). Here we describe the efforts of the Global Biodiversity Information Facility (GBIF) as well as the World Health Special Programme on Research and Training in Diseases of Poverty (TDR) to promote publication of data related to vectors of diseases. In 2020, a GBIF task group of experts was formed to provide advice and support efforts aimed at enhancing the coverage and accessibility of data on vectors of human diseases within GBIF. Various strategies, such as organizing training courses and publishing data papers, were used to increase this content. This editorial introduces the outcome of a second call for data papers partnered by the TDR, GBIF and GigaScience Press in the journal GigaByte. Biodiversity and infectious diseases are linked in complex ways. These links can involve changes from the microorganism level to that of the habitat, and there are many ways in which these factors interact to affect human health. One way to tackle disease control and possibly elimination, is to provide stakeholders with access to a wide range of data shared under the FAIR principles, so it is possible to support early detection, analyses and evaluation, and to promote policy improvements and/or development.

Global indicators of the environmental impacts of invasive alien species and their information adequacy.

Monitoring the extent to which invasive alien species (IAS) negatively impact the environment is crucial for understanding and mitigating biological invasions. Indeed, such information is vital for achieving Target 6 of the Kunming-Montreal Global Biodiversity Framework. However, to-date indicators for tracking the environmental impacts of IAS have been either lacking or insufficient. Capitalizing on advances in data availability and impact assessment protocols, we developed environmental impact indicators to track realized and potential impacts of IAS. We also developed an information status indicator to assess the adequacy of the data underlying the impact indicators. We used data on 75 naturalized amphibians from 82 countries to demonstrate the indicators at a global scale. The information status indicator shows variation in the reliability of the data and highlights areas where absence of impact should be interpreted with caution. Impact indicators show that growth in potential impacts are dominated by predatory species, while potential impacts from both predation and disease transmission are distributed worldwide. Using open access data, the indicators are reproducible and adaptable across scales and taxa and can be used to assess global trends and distributions of IAS, assisting authorities in prioritizing control efforts and identifying areas at risk of future invasions. This article is part of the theme issue 'Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere'.

Envisaging a global infrastructure to exploit the potential of digitised collections.

Tens of millions of images from biological collections have become available online over the last two decades. In parallel, there has been a dramatic increase in the capabilities of image analysis technologies, especially those involving machine learning and computer vision. While image analysis has become mainstream in consumer applications, it is still used only on an artisanal basis in the biological collections community, largely because the image corpora are dispersed. Yet, there is massive untapped potential for novel applications and research if images of collection objects could be made accessible in a single corpus. In this paper, we make the case for infrastructure that could support image analysis of collection objects. We show that such infrastructure is entirely feasible and well worth investing in.

More than a Bit of Fun: The Multiple Outcomes of a Bioblitz.

Bioblitzes are a popular approach to engage people and collect biodiversity data. Despite this, few studies have actually evaluated the multiple outcomes of bioblitz activities. We used a systematic review, an analysis of data from more than 1000 bioblitzes, and a detailed analysis of one specific bioblitz to inform our inquiry. We evaluated five possible bioblitz outcomes, which were creating a species inventory, engaging people in biological recording, enhancing learning about nature, discovering a species new to an area, and promoting an organization. We conclude that bioblitzes are diverse but overall effective at their aims and have advantages over unstructured biodiversity recording. We demonstrate for the first time that bioblitzes increase the recording activity of the participants for several months after the event. In addition, we provide evidence that bioblitzes are effective at bringing people and organizations together to build communities of professionals and amateurs, critical for conserving and protecting biodiversity.

Biodiversity data supports research on human infectious diseases: Global trends, challenges, and opportunities.

The unprecedented generation of large volumes of biodiversity data is consistently contributing to a wide range of disciplines, including disease ecology. Emerging infectious diseases are usually zoonoses caused by multi-host pathogens. Therefore, their understanding may require the access to biodiversity data related to the ecology and the occurrence of the species involved. Nevertheless, despite several data-mobilization initiatives, the usage of biodiversity data for research into disease dynamics has not yet been fully leveraged. To explore current contribution, trends, and to identify limitations, we characterized biodiversity data usage in scientific publications related to human health, contrasting patterns of studies citing the Global Biodiversity Information Facility (GBIF) with those obtaining data from other sources. We found that the studies mainly obtained data from scientific literature and other not aggregated or standardized sources. Most of the studies explored pathogen species and, particularly those with GBIF-mediated data, tended to explore and reuse data of multiple species (>2). Data sources varied according to the taxa and epidemiological roles of the species involved. Biodiversity data repositories were mainly used for species related to hosts, reservoirs, and vectors, and barely used as a source of pathogens data, which was usually obtained from human and animal-health related institutions. While both GBIF- and not GBIF-mediated data studies explored similar diseases and topics, they presented discipline biases and different analytical approaches. Research on emerging infectious diseases may require the access to geographical and ecological data of multiple species. The One Health challenge requires interdisciplinary collaboration and data sharing, which is facilitated by aggregated repositories and platforms. The contribution of biodiversity data to understand infectious disease dynamics should be acknowledged, strengthened, and promoted.

Identifying, reducing, and communicating uncertainty in community science: a focus on alien species.

Community science (also often referred to as citizen science) provides a unique opportunity to address questions beyond the scope of other research methods whilst simultaneously engaging communities in the scientific process. This leads to broad educational benefits, empowers people, and can increase public awareness of societally relevant issues such as the biodiversity crisis. As such, community science has become a favourable framework for researching alien species where data on the presence, absence, abundance, phenology, and impact of species is important in informing management decisions. However, uncertainties arising at different stages can limit the interpretation of data and lead to projects failing to achieve their intended outcomes. Focusing on alien species centered community science projects, we identified key research questions and the relevant uncertainties that arise during the process of developing the study design, for example, when collecting the data and during the statistical analyses. Additionally, we assessed uncertainties from a linguistic perspective, and how the communication stages among project coordinators, participants and other stakeholders can alter the way in which information may be interpreted. We discuss existing methods for reducing uncertainty and suggest further solutions to improve data reliability. Further, we make suggestions to reduce the uncertainties that emerge at each project step and provide guidance and recommendations that can be readily applied in practice. Reducing uncertainties is essential and necessary to strengthen the scientific and community outcomes of community science, which is of particular importance to ensure the success of projects aimed at detecting novel alien species and monitoring their dynamics across space and time. Supplementary Information: The online version contains supplementary material available at 10.1007/s10530-022-02858-8.

Promoting scientific literacy in evolution through citizen science.

Evolutionary understanding is central to biology. It is also an essential prerequisite to understanding and making informed decisions about societal issues such as climate change. Yet, evolution is generally poorly understood by civil society and many misconceptions exist. Citizen science, which has been increasing in popularity as a means to gather new data and promote scientific literacy, is one strategy through which people could learn about evolution. However, despite the potential for citizen science to promote evolution learning opportunities, very few projects implement them. In this paper, we make the case for incorporating evolution education into citizen science, define key learning goals, and suggest opportunities for designing and evaluating projects in order to promote scientific literacy in evolution.

Country Compendium of the Global Register of Introduced and Invasive Species.

The Country Compendium of the Global Register of Introduced and Invasive Species (GRIIS) is a collation of data across 196 individual country checklists of alien species, along with a designation of those species with evidence of impact at a country level. The Compendium provides a baseline for monitoring the distribution and invasion status of all major taxonomic groups, and can be used for the purpose of global analyses of introduced (alien, non-native, exotic) and invasive species (invasive alien species), including regional, single and multi-species taxon assessments and comparisons. It enables exploration of gaps and inferred absences of species across countries, and also provides one means for updating individual GRIIS Checklists. The Country Compendium is, for example, instrumental, along with data on first records of introduction, for assessing and reporting on invasive alien species targets, including for the Convention on Biological Diversity and Sustainable Development Goals. The GRIIS Country Compendium provides a baseline and mechanism for tracking the spread of introduced and invasive alien species across countries globally. Design Type(s) Data integration objective ● Observation design Measurement Type(s) Alien species occurrence ● Evidence of impact invasive alien species assessment objective Technology Type(s) Agent expert ● Data collation Factor Type(s) Geographic location ● Origin / provenance ● Habitat Sample Characteristics - Organism Animalia ● Bacteria ● Chromista ● Fungi ● Plantae ● Protista (Protozoa) ● Viruses Sample Characteristics - Location Global countries.

The disambiguation of people names in biological collections.

Scientific collections have been built by people. For hundreds of years, people have collected, studied, identified, preserved, documented and curated collection specimens. Understanding who those people are is of interest to historians, but much more can be made of these data by other stakeholders once they have been linked to the people's identities and their biographies. Knowing who people are helps us attribute work correctly, validate data and understand the scientific contribution of people and institutions. We can evaluate the work they have done, the interests they have, the places they have worked and what they have created from the specimens they have collected. The problem is that all we know about most of the people associated with collections are their names written on specimens. Disambiguating these people is the challenge that this paper addresses. Disambiguation of people often proves difficult in isolation and can result in staff or researchers independently trying to determine the identity of specific individuals over and over again. By sharing biographical data and building an open, collectively maintained dataset with shared knowledge, expertise and resources, it is possible to collectively deduce the identities of individuals, aggregate biographical information for each person, reduce duplication of effort and share the information locally and globally. The authors of this paper aspire to disambiguate all person names efficiently and fully in all their variations across the entirety of the biological sciences, starting with collections. Towards that vision, this paper has three key aims: to improve the linking, validation, enhancement and valorisation of person-related information within and between collections, databases and publications; to suggest good practice for identifying people involved in biological collections; and to promote coordination amongst all stakeholders, including individuals, natural history collections, institutions, learned societies, government agencies and data aggregators.

A botanical demonstration of the potential of linking data using unique identifiers for people.

Natural history collection data available digitally on the web have so far only made limited use of the potential of semantic links among themselves and with cross-disciplinary resources. In a pilot study, botanical collections of the Consortium of European Taxonomic Facilities (CETAF) have therefore begun to semantically annotate their collection data, starting with data on people, and to link them via a central index system. As a result, it is now possible to query data on collectors across different collections and automatically link them to a variety of external resources. The system is being continuously developed and is already in production use in an international collection portal.

Liberating host-virus knowledge from biological dark data.

Connecting basic data about bats and other potential hosts of SARS-CoV-2 with their ecological context is crucial to the understanding of the emergence and spread of the virus. However, when lockdowns in many countries started in March, 2020, the world's bat experts were locked out of their research laboratories, which in turn impeded access to large volumes of offline ecological and taxonomic data. Pandemic lockdowns have brought to attention the long-standing problem of so-called biological dark data: data that are published, but disconnected from digital knowledge resources and thus unavailable for high-throughput analysis. Knowledge of host-to-virus ecological interactions will be biased until this challenge is addressed. In this Viewpoint, we outline two viable solutions: first, in the short term, to interconnect published data about host organisms, viruses, and other pathogens; and second, to shift the publishing framework beyond unstructured text (the so-called PDF prison) to labelled networks of digital knowledge. As the indexing system for biodiversity data, biological taxonomy is foundational to both solutions. Building digitally connected knowledge graphs of host-pathogen interactions will establish the agility needed to quickly identify reservoir hosts of novel zoonoses, allow for more robust predictions of emergence, and thereby strengthen human and planetary health systems.

Holistic understanding of contemporary ecosystems requires integration of data on domesticated, captive and cultivated organisms.

Domestic and captive animals and cultivated plants should be recognised as integral components in contemporary ecosystems. They interact with wild organisms through such mechanisms as hybridization, predation, herbivory, competition and disease transmission and, in many cases, define ecosystem properties. Nevertheless, it is widespread practice for data on domestic, captive and cultivated organisms to be excluded from biodiversity repositories, such as natural history collections. Furthermore, there is a lack of integration of data collected about biodiversity in disciplines, such as agriculture, veterinary science, epidemiology and invasion science. Discipline-specific data are often intentionally excluded from integrative databases in order to maintain the "purity" of data on natural processes. Rather than being beneficial, we argue that this practise of data exclusivity greatly limits the utility of discipline-specific data for applications ranging from agricultural pest management to invasion biology, infectious disease prevention and community ecology. This problem can be resolved by data providers using standards to indicate whether the observed organism is of wild or domestic origin and by integrating their data with other biodiversity data (e.g. in the Global Biodiversity Information Facility). Doing so will enable efforts to integrate the full panorama of biodiversity knowledge across related disciplines to tackle pressing societal questions.

Hybridization of Oxalis corniculata and O. dillenii in their non-native range.

Many species have been introduced beyond their native ranges and many have become global weeds. Human mediated dispersal has removed the geographic isolation of these species, reversing millions of years of independent evolution. Examples are the Oxalis species in section Corniculatae where several species have become invasive. Here we characterize and formally describe a hybrid between O. dillenii and O. corniculata, which occurs spontaneously in Belgium and Japan. Oxalis corniculata is probably native to Japan, but both species are alien to Belgium and O. dillenii is native to North America. We formally name this hybrid as Oxalis × vanaelstii. Although this hybrid is sterile, it is nevertheless vigorous and perennial. Both parent species grow as weeds in gardens; therefore, it is likely to be more common than currently appreciated in countries where these species co-occur.

A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses.

BACKGROUND: Pandemics, even more than other medical problems, require swift integration of knowledge. When caused by a new virus, understanding the underlying biology may help finding solutions. In a setting where there are a large number of loosely related projects and initiatives, we need common ground, also known as a "commons." Wikidata, a public knowledge graph aligned with Wikipedia, is such a commons and uses unique identifiers to link knowledge in other knowledge bases. However, Wikidata may not always have the right schema for the urgent questions. In this paper, we address this problem by showing how a data schema required for the integration can be modeled with entity schemas represented by Shape Expressions. RESULTS: As a telling example, we describe the process of aligning resources on the genomes and proteomes of the SARS-CoV-2 virus and related viruses as well as how Shape Expressions can be defined for Wikidata to model the knowledge, helping others studying the SARS-CoV-2 pandemic. How this model can be used to make data between various resources interoperable is demonstrated by integrating data from NCBI (National Center for Biotechnology Information) Taxonomy, NCBI Genes, UniProt, and WikiPathways. Based on that model, a set of automated applications or bots were written for regular updates of these sources in Wikidata and added to a platform for automatically running these updates. CONCLUSIONS: Although this workflow is developed and applied in the context of the COVID-19 pandemic, to demonstrate its broader applicability it was also applied to other human coronaviruses (MERS, SARS, human coronavirus NL63, human coronavirus 229E, human coronavirus HKU1, human coronavirus OC4).

A checklist recipe: making species data open and FAIR.

Species checklists are a crucial source of information for research and policy. Unfortunately, many traditional species checklists vary wildly in their content, format, availability and maintenance. The fact that these are not open, findable, accessible, interoperable and reusable (FAIR) severely hampers fast and efficient information flow to policy and decision-making that are required to tackle the current biodiversity crisis. Here, we propose a reproducible, semi-automated workflow to transform traditional checklist data into a FAIR and open species registry. We showcase our workflow by applying it to the publication of the Manual of Alien Plants, a species checklist specifically developed for the Tracking Invasive Alien Species (TrIAS) project. Our approach combines source data management, reproducible data transformation to Darwin Core using R, version control, data documentation and publication to the Global Biodiversity Information Facility (GBIF). This checklist publication workflow is openly available for data holders and applicable to species registries varying in thematic, taxonomic or geographical scope and could serve as an important tool to open up research and strengthen environmental decision-making.

Site selection by geese in a suburban landscape.

BACKGROUND: In European and North American cities geese are among the most common and most visible large herbivores. As such, their presence and behaviour often conflict with the desires of the human residents. Fouling, noise, aggression and health concerns are all cited as reasons that there are "too many". Lethal control is often used for population management; however, this raises questions about whether this is a sustainable strategy to resolve the conflict between humans and geese when, paradoxically, it is humans that are responsible for creating the habitat and often providing the food and protection of geese at other times. We hypothesise that the landscaping of suburban parks can be improved to decrease its attractiveness to geese and to reduce the opportunity for conflict between geese and humans. METHODS: Using observations collected over five years from a botanic garden situated in suburban Belgium and data from the whole of Flanders in Belgium, we examined landscape features that attract geese. These included the presence of islands in lakes, the distance from water, barriers to level flight and the size of exploited areas. The birds studied were the tadornine goose Alopochen aegyptiaca (L. 1766) (Egyptian goose) and the anserine geese, Branta canadensis (L. 1758) (Canada goose), Anser anser (L. 1758) (greylag goose) and Branta leucopsis (Bechstein, 1803) (barnacle goose). Landscape modification is a known method for altering goose behaviour, but there is little information on the power of such methods with which to inform managers and planners. RESULTS: Our results demonstrate that lakes with islands attract more than twice as many anserine geese than lakes without islands, but make little difference to Egyptian geese. Furthermore, flight barriers between grazing areas and lakes are an effective deterrent to geese using an area for feeding. Keeping grazing areas small and surrounded by trees reduces their attractiveness to geese. CONCLUSION: The results suggest that landscape design can be used successfully to reduce the number of geese and their conflict with humans. However, this approach has its limitations and would require humans to compromise on what they expect from their landscaped parks, such as open vistas, lakes, islands and closely cropped lawns.

Designing an Herbarium Digitisation Workflow with Built-In Image Quality Management.

Digitisation of natural history collections has evolved from creating databases for the recording of specimens' catalogue and label data to include digital images of specimens. This has been driven by several important factors, such as a need to increase global accessibility to specimens and to preserve the original specimens by limiting their manual handling. The size of the collections pointed to the need of high throughput digitisation workflows. However, digital imaging of large numbers of fragile specimens is an expensive and time-consuming process that should be performed only once. To achieve this, the digital images produced need to be useful for the largest set of applications possible and have a potentially unlimited shelf life. The constraints on digitisation speed need to be balanced against the applicability and longevity of the images, which, in turn, depend directly on the quality of those images. As a result, the quality criteria that specimen images need to fulfil influence the design, implementation and execution of digitisation workflows. Different standards and guidelines for producing quality research images from specimens have been proposed; however, their actual adaptation to suit the needs of different types of specimens requires further analysis. This paper presents the digitisation workflow implemented by Meise Botanic Garden (MBG). This workflow is relevant because of its modular design, its strong focus on image quality assessment, its flexibility that allows combining in-house and outsourced digitisation, processing, preservation and publishing facilities and its capacity to evolve for integrating alternative components from different sources. The design and operation of the digitisation workflow is provided to showcase how it was derived, with particular attention to the built-in audit trail within the workflow, which ensures the scalable production of high-quality specimen images and how this audit trail ensures that new modules do not affect either the speed of imaging or the quality of the images produced.