Peter Desmet

The GBIF integrated publishing toolkit: facilitating the efficient publishing of biodiversity data on the internet.

The planet is experiencing an ongoing global biodiversity crisis. Measuring the magnitude and rate of change more effectively requires access to organized, easily discoverable, and digitally-formatted biodiversity data, both legacy and new, from across the globe. Assembling this coherent digital representation of biodiversity requires the integration of data that have historically been analog, dispersed, and heterogeneous. The Integrated Publishing Toolkit (IPT) is a software package developed to support biodiversity dataset publication in a common format. The IPT’s two primary functions are to 1) encode existing species occurrence datasets and checklists, such as records from natural history collections or observations, in the Darwin Core standard to enhance interoperability of data, and 2) publish and archive data and metadata for broad use in a Darwin Core Archive, a set of files following a standard format. Here we discuss the key need for the IPT, how it has developed in response to community input, and how it continues to evolve to streamline and enhance the interoperability, discoverability, and mobilization of new data types beyond basic Darwin Core records. We close with a discussion how IPT has impacted the biodiversity research community, how it enhances data publishing in more traditional journal venues, along with new features implemented in the latest version of the IPT, and future plans for more enhancements.

Database of Vascular Plants of Canada (VASCAN): a community contributed taxonomic checklist of all vascular plants of Canada, Saint Pierre and Miquelon, and Greenland

Abstract The Database of Vascular Plants of Canada or VASCAN (http://data.canadensys.net/vascan) is a comprehensive and curated checklist of all vascular plants reported in Canada, Greenland (Denmark), and Saint Pierre and Miquelon (France). VASCAN was developed at the Université de Montréal Biodiversity Centre and is maintained by a group of editors and contributors. For every core taxon in the checklist (species, subspecies, or variety), VASCAN provides the accepted scientific name, the accepted French and English vernacular names, and their synonyms/alternatives in Canada, as well as the distribution status (native, introduced, ephemeral, excluded, extirpated, doubtful or absent) of the plant for each province or territory, and the habit (tree, shrub, herb and/or vine) of the plant in Canada. For reported hybrids (nothotaxa or hybrid formulas) VASCAN also provides the hybrid parents, except if the parents of the hybrid do not occur in Canada. All taxa are linked to a classification. VASCAN refers to a source for all name, classification and distribution information. All data have been released to the public domain under a CC0 waiver and are available through Canadensys and the Global Biodiversity Information Facility (GBIF). VASCAN is a service to the scientific community and the general public, including administrations, companies, and non-governmental organizations.

GPS tracking data of Lesser Black-backed Gulls and Herring Gulls breeding at the southern North Sea coast.

Abstract In this data paper, Bird tracking - GPS tracking of Lesser Black-backed Gulls and Herring Gulls breeding at the southern North Sea coast is described, a species occurrence dataset published by the Research Institute for Nature and Forest (INBO). The dataset (version 5.5) contains close to 2.5 million occurrences, recorded by 101 GPS trackers mounted on 75 Lesser Black-backed Gulls and 26 Herring Gulls breeding at the Belgian and Dutch coast. The trackers were developed by the University of Amsterdam Bird Tracking System (UvA-BiTS, http://www.uva-bits.nl). These automatically record and transmit bird movements, which allows us and others to study their habitat use and migration behaviour in great detail. Our bird tracking network is operational since 2013. It is funded for LifeWatch by the Hercules Foundation and maintained in collaboration with UvA-BiTS and the Flanders Marine Institute (VLIZ). The recorded data are periodically released in bulk as open data (http://dataset.inbo.be/bird-tracking-gull-occurrences), and are also accessible through CartoDB and the Global Biodiversity Information Facility (GBIF).

Innovative Visualizations Shed Light on Avian Nocturnal Migration.

Globally, billions of flying animals undergo seasonal migrations, many of which occur at night. The temporal and spatial scales at which migrations occur and our inability to directly observe these nocturnal movements makes monitoring and characterizing this critical period in migratory animals’ life cycles difficult. Remote sensing, therefore, has played an important role in our understanding of large-scale nocturnal bird migrations. Weather surveillance radar networks in Europe and North America have great potential for long-term low-cost monitoring of bird migration at scales that have previously been impossible to achieve. Such long-term monitoring, however, poses a number of challenges for the ornithological and ecological communities: how does one take advantage of this vast data resource, integrate information across multiple sensors and large spatial and temporal scales, and visually represent the data for interpretation and dissemination, considering the dynamic nature of migration? We assembled an interdisciplinary team of ecologists, meteorologists, computer scientists, and graphic designers to develop two different flow visualizations, which are interactive and open source, in order to create novel representations of broad-front nocturnal bird migration to address a primary impediment to long-term, large-scale nocturnal migration monitoring. We have applied these visualization techniques to mass bird migration events recorded by two different weather surveillance radar networks covering regions in Europe and North America. These applications show the flexibility and portability of such an approach. The visualizations provide an intuitive representation of the scale and dynamics of these complex systems, are easily accessible for a broad interest group, and are biologically insightful. Additionally, they facilitate fundamental ecological research, conservation, mitigation of human–wildlife conflicts, improvement of meteorological products, and public outreach, education, and engagement.

Seven recommendations to make your invasive alien species data more useful

Science-based strategies to tackle biological invasions depend on recent, accurate, well-documented, standardised and openly accessible information on alien species. Currently and historically, biodiversity data are scattered in numerous disconnected data silos that lack interoperability. The situation is no different for alien species data, and this obstructs efficient retrieval, combination, and use of these kinds of information for research and policy-making. Standardization and interoperability are particularly important as many alien species related research and policy activities require pooling data. We describe seven ways that data on alien species can be made more accessible and useful: 1) Create data management plans; 2) Increase interoperability of information sources; 3) Document data through metadata; 4) Format data using existing standards; 5) Adopt controlled vocabularies; 6) Increase data availability; and 7) Ensure long-term data preservation. We identify four properties specific and integral to alien species data (species status, introduction pathway, degree of establishment, and impact mechanism) that are either missing from existing data standards or lack a recommended controlled vocabulary. Improved access to accurate, real-time and historical data will repay the long-term investment in data management infrastructure, by providing more accurate, timely and realistic analyses. If we improve core biodiversity data standards by developing their relevance to alien species, it will allow the automation of common activities regarding data processing in support of environmental policy. Furthermore, we call for considerable effort to maintain, update, standardise, archive, and aggregate datasets, to ensure proper valorisation of alien species data and information before they become obsolete or lost.

A database on the distribution of butterflies (Lepidoptera) in northern Belgium (Flanders and the Brussels Capital Region)

Abstract In this data paper, we describe two datasets derived from two sources, which collectively represent the most complete overview of butterflies in Flanders and the Brussels Capital Region (northern Belgium). The first dataset (further referred to as the INBO dataset – http://doi.org/10.15468/njgbmh) contains 761,660 records of 70 species and is compiled by the Research Institute for Nature and Forest (INBO) in cooperation with the Butterfly working group of Natuurpunt (Vlinderwerkgroep). It is derived from the database Vlinderdatabank at the INBO, which consists of (historical) collection and literature data (1830-2001), for which all butterfly specimens in institutional and available personal collections were digitized and all entomological and other relevant publications were checked for butterfly distribution data. It also contains observations and monitoring data for the period 1991-2014. The latter type were collected by a (small) butterfly monitoring network where butterflies were recorded using a standardized protocol. The second dataset (further referred to as the Natuurpunt dataset – http://doi.org/10.15468/ezfbee) contains 612,934 records of 63 species and is derived from the database http://waarnemingen.be, hosted at the nature conservation NGO Natuurpunt in collaboration with Stichting Natuurinformatie. This dataset contains butterfly observations by volunteers (citizen scientists), mainly since 2008. Together, these datasets currently contain a total of 1,374,594 records, which are georeferenced using the centroid of their respective 5 × 5 km² Universal Transverse Mercator (UTM) grid cell. Both datasets are published as open data and are available through the Global Biodiversity Information Facility (GBIF).

VIS – A database on the distribution of fishes in inland and estuarine waters in Flanders, Belgium

Abstract The Research Institute for Nature and Forest (INBO) has been performing standardized fish stock assessments in Flanders, Belgium. This Flemish Fish Monitoring Network aims to assess fish populations in public waters at regular time intervals in both inland waters and estuaries. This monitoring was set up in support of the Water Framework Directive, the Habitat Directive, the Eel Regulation, the Red List of fishes, fish stock management, biodiversity research, and to assess the colonization and spreading of non-native fish species. The collected data are consolidated in the Fish Information System or VIS. From VIS, the occurrence data are now published at the INBO IPT as two datasets: ‘VIS - Fishes in inland waters in Flanders, Belgium’ and ‘VIS - Fishes in estuarine waters in Flanders, Belgium’. Together these datasets represent a complete overview of the distribution and abundance of fish species pertaining in Flanders from late 1992 to the end of 2012. This data paper discusses both datasets together, as both have a similar methodology and structure. The inland waters dataset contains over 350,000 fish observations, sampled between 1992 and 2012 from over 2,000 locations in inland rivers, streams, canals, and enclosed waters in Flanders. The dataset includes 64 fish species, as well as a number of non-target species (mainly crustaceans). The estuarine waters dataset contains over 44,000 fish observations, sampled between 1995 and 2012 from almost 50 locations in the estuaries of the rivers Yser and Scheldt (“Zeeschelde”), including two sampling sites in the Netherlands. The dataset includes 69 fish species and a number of non-target crustacean species. To foster broad and collaborative use, the data are dedicated to the public domain under a Creative Commons Zero waiver and reference the INBO norms for data use.

Waarnemingen.be – Plant occurrences in Flanders and the Brussels Capital Region, Belgium

Abstract Waarnemingen.be - Plant occurrences in Flanders and the Brussels Capital Region, Belgium is a species occurrence dataset published by Natuurpunt. The dataset contains almost 1.2 million plant occurrences of 1,222 native vascular plant species, mostly recorded by volunteers (citizen scientists), mainly since 2008. The occurrences are derived from the database http://www.waarnemingen.be, hosted by Stichting Natuurinformatie and managed by the nature conservation NGO Natuurpunt. Together with the datasets Florabank1 (Van Landuyt and Brosens 2017) and the Belgian IFBL (Instituut voor Floristiek van België en Luxemburg) Flora Checklists (Van Landuyt and Noé 2015), the dataset represents the most complete overview of indigenous plants in Flanders and the Brussels Capital Region.