Publications by authors named "Peter Desmet"

13 Publications

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A checklist recipe: making species data open and FAIR.

Database (Oxford) 2020 01;2020

Meise Botanic Garden, Nieuwelaan 38, B-1860 Meise, Belgium.

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.
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http://dx.doi.org/10.1093/database/baaa084DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7661093PMC
January 2020

GPS tracking data of Western marsh harriers breeding in Belgium and the Netherlands.

Zookeys 2020 8;947:143-155. Epub 2020 Jul 8.

Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Science Park 904, 1098, XH, Amsterdam, The Netherlands University of Amsterdam Amsterdam Netherlands.

In this data paper three datasets are described containing GPS tracking and acceleration data of Western marsh harriers () breeding in Belgium and the Netherlands. The Western marsh harrier is included as a threatened bird species in Annex I of the European Bird Directive due to the steep decline in population densities. In order to collect data of habitat use and migration behaviour, Western marsh harriers were equipped with light-weight solar powered GPS trackers developed by the Institute for Biodiversity and Ecosystem Dynamics (IBED) at the University of Amsterdam (University of Amsterdam Bird Tracking System, UvA-BiTS). These trackers automatically collect and store data on the bird's activity and 3D position in time and transmit these data to ground stations. The datasets were collected by the Research Institute for Nature and Forest (INBO) and the Dutch Montagu's Harrier Foundation. Tracked Western marsh harriers were breeding in the northeast of the Dutch province of Groningen and on the opposite side of the river Ems in Germany (H_GRONINGEN), in the region of Waterland-Oudeman near the Belgian-Dutch border (MH_WATERLAND), and at the left bank of the Scheldt estuary, close to the Belgian-Dutch border and north of the city of Antwerp (MH_ANTWERPEN). Most individuals remained within 10 km from their nesting sites during the breeding season and wintered in West Africa. H_GRONINGEN contains 987,493 GPS fixes and 3,853,859 acceleration records of four individuals since 2012. MH_WATERLAND contains 377,910 GPS fixes of seven individuals. Sampling in this region began in 2013. Three more Western marsh harriers were tagged in the Scheldt estuary near Antwerp more recently in 2018 (one individual) and 2019 (two individuals) for the MH_ANTWERPEN study, which contains 47,917 GPS fixes and 227,746 acceleration records. The three Western marsh harrier datasets were published as separate studies in Movebank (https://www.movebank.org) and archived as data packages in Zenodo (https://www.zenodo.org) to ensure long-term preservation and versioning of the data.
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http://dx.doi.org/10.3897/zookeys.947.52570DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7363740PMC
July 2020

Rapidly progressive dementia in a nonagenarian with acute disseminated encephalomyelitis.

Authors:
Peter Desmet

Acta Clin Belg 2022 Feb 30;77(1):130-136. Epub 2020 Jun 30.

Department of Geriatric Medicine, AZ Nikolaas, Sint-Niklaas, Belgium.

We describe a case of rapidly progressive dementia (RPD) in a nonagenarian. Dementia was caused by an acute disseminated encephalomyelitis (ADEM). Although not frequently diagnosed in the very elderly acute disseminated encephalomyelitis should not be overlooked for it is a treatable condition. A recent infection followed by rapid cognitive deterioration and multifocal neurologic signs should raise the attention to curable autoimmune diseases. Although the cause of ADEM is still unclear, immune suppression is the mainstay of treatment. Most patients improve on high-dose glucocorticoids and eventually immune globulin treatment or plasma exchange if steroid-unresponsive.
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http://dx.doi.org/10.1080/17843286.2020.1784613DOI Listing
February 2022

Watervogels - Wintering waterbirds in Flanders, Belgium.

Zookeys 2020 24;915:127-135. Epub 2020 Feb 24.

Research Institute for Nature and Forest (INBO), Brussels, Belgium Research Institute for Nature and Forest Brussels Belgium.

"Watervogels - Wintering waterbirds in Flanders, Belgium" is a sampling event dataset published by the Research Institute for Nature and Forest (INBO). It contains more than 94,000 sampling events (site counts), covering over 710,000 species observations (and zero counts when there is no associated occurrence) and 36 million individual birds for the period 1991-2016. The dataset includes information on 167 different species in nearly 1,100 wetland sites. The aim of these bird counts is to gather information on the size, distribution, and long-term trends of wintering waterbird populations in Flanders. These data are also used to assess the importance of individual sites for waterbirds, using quantitative criteria. Furthermore, the waterbird counts contribute to international monitoring programs, such as the International Waterbird Census (coordinated by Wetlands International) and fulfil some of the objectives of the European Bird Directive, the Ramsar Convention, and the Agreement on the Conservation of African-Eurasian Migratory Waterbirds (AEWA). Here the dataset is published as a standardized Darwin Core Archive and includes for each event: a stable event ID, date and location of observation and a short description of the sampling protocol, effort and conditions (in the event core), supplemented with specific information for each occurrence: a stable occurrence ID, the scientific name and higher classification of the observed species, the number of recorded individuals, and a reference to the observer of the record (in the occurrence extension). Issues with the dataset can be reported at https://github.com/inbo/data-publication/issues. The following information is not included in this dataset and available upon request: roost site counts, counts from historical (inactive) locations and counts from before 1991. We have released this dataset to the public domain under a CC0 1.0 Universal (CC0 1.0) Public Domain Dedication (https://creativecommons.org/publicdomain/zero/1.0/). We would appreciate it if you follow the INBO norms for data use (https://www.inbo.be/en/norms-data-use) when using the data. If you have any questions regarding this dataset, do not hesitate to contact us via the contact information provided in the metadata or via [email protected]
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http://dx.doi.org/10.3897/zookeys.915.38265DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7052018PMC
February 2020

A database of threat statuses and life-history traits of Red List species in Flanders (northern Belgium).

Biodivers Data J 2019 5;7:e34089. Epub 2019 Apr 5.

Research Institute for Nature and Forest (INBO), Brussels, Belgium Research Institute for Nature and Forest (INBO) Brussels Belgium.

Background: Red Lists estimate the extinction risk of species at global or regional levels and are important instruments in conservation policies. Global Red List assessments are readily available via the IUCN website (https://www.iucnredlist.org) and are regularly updated by (taxonomic) experts. Regional Red Lists, however, are not always easy to find and often use local criteria to assess the local extinction risk of species.

New Information: Here, we publish a database with the outcome of 38 Red List assessments in Flanders (northern Belgium) between 1994 and 2018. In total, the database contains 6,224 records of 5,039 unique taxa pertaining to 24 different taxonomic groups. Using a quality control procedure, we evaluated the criteria used, the number of records, the temporal and spatial distribution of the data and the up-to-dateness of the Red Lists. This way, nineteen Red Lists were approved as being of sufficient high quality (i.e. validated) and nineteen others were not. Once validated, Red Lists are approved by the regional Minister of Environment and published in the Belgian Official Gazette acquiring legal status. For the validated Red Lists, we additionally compiled (life-history) traits that are applicable to a wide variety of species groups (taxonomic kingdom, environment, biotope, nutrient level, dispersal capacity, lifespan and cuddliness). The publication of this dataset allows comparison of Red List statuses with other European regions and countries and permits analyses about how certain (life-history) traits can explain the Red List status of species. The dataset will be regularly updated by adding new Red List (re)assessments and/or additional (life-history) traits.
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http://dx.doi.org/10.3897/BDJ.7.e34089DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6477847PMC
April 2019

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

PhytoKeys 2017 8(85):1-10. Epub 2017 Aug 8.

Natuurpunt Studie, Coxiestraat 11, 2800 Mechelen, Belgium.

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.
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http://dx.doi.org/10.3897/phytokeys.85.14925DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5624210PMC
August 2017

Innovative Visualizations Shed Light on Avian Nocturnal Migration.

PLoS One 2016 24;11(8):e0160106. Epub 2016 Aug 24.

Computational Geo-Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands.

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.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0160106PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4996449PMC
July 2017

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

Zookeys 2016 26(585):143-56. Epub 2016 Apr 26.

Vlinderwerkgroep Natuurpunt, Coxiestraat 11, B-2800 Mechelen, Belgium.

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).
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http://dx.doi.org/10.3897/zookeys.585.8019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4857040PMC
May 2016

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

Zookeys 2016 20(555):115-24. Epub 2016 Jan 20.

Terrestrial Ecology Unit (TEREC), Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium.

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).
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http://dx.doi.org/10.3897/zookeys.555.6173DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4740824PMC
February 2016

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

Zookeys 2015 22(475):119-45. Epub 2015 Jan 22.

Research Institute for Nature and Forest (INBO), Kliniekstraat 25, 1070, Brussels, Belgium.

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.
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http://dx.doi.org/10.3897/zookeys.475.8556DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4311703PMC
February 2015

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

PLoS One 2014 6;9(8):e102623. Epub 2014 Aug 6.

Research Institute for Nature and Forest (INBO), Brussels, Belgium.

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.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0102623PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4123864PMC
April 2015

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

PhytoKeys 2013 24(25):55-67. Epub 2013 Jul 24.

Université de Montréal Biodiversity Centre, 4101 rue Sherbrooke est, H1X2B2, Montreal, Canada.

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.
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http://dx.doi.org/10.3897/phytokeys.25.3100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3819130PMC
November 2013
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