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Sawflies from northern Ecuador and a checklist for the country (Hymenoptera: Argidae, Orussidae, Pergidae, Tenthredinidae, Xiphydriidae)
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RBINS Staff Publications 2018
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Historical DNA metabarcoding of the prey and microbiome of trematomid fishes using museum samples.
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RBINS Staff Publications 2018
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Finding the data you need to support your Southern Ocean science
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RBINS Staff Publications 2018
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Environmental Impacts of Offshore Wind Farms in the Belgian Part of the North Sea: Getting ready for offshore wind farm expansion in the North Sea.
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RBINS Staff Publications 2022
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Turbine size impacts the number of seabird collisions per installed megawatt and offers possibilities for mitigation.
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As the offshore wind energy technology is rapidly progressing and because wind turbines at sea have a relatively short life span, repowering scenarios are already being discussed for the oldest wind farms. Ongoing developments result in larger wind turbines and an increased open airspace between turbines. Despite taller towers having larger rotor swept zones and therefore a higher collision risk area compared to smaller-sized turbines, there is increasing evidence that fewer but larger, more power-efficient turbines may have a lower collision rate per installed megawatt. As such, turbine size can offer an opportunity to mitigate seabird fatalities by increasing the clearance below the lower rotor tip. We assessed the seabird collision risk for a hypothetical repowering scenario of the first offshore wind farm zone in Belgian waters with larger turbines and the effect of an additional increase in hub height on that theoretical collision risk. For all species included in this exercise, the estimated collision risk decreased in a repowering scenario with 15 MW turbines (40.4% reduction on average) because of higher clearance between the lower tip of the turbine rotor and the sea level, and the need for a lower number of turbines per km². Increasing the hub height of those 15 MW turbines with 10 m, further decreases the expected number of seabird collisions with another 37% on average. However, terrestrial birds and bats also migrate at sea and the effect of larger turbines on these taxa is less clear. Possibly even more terrestrial birds and bats are at risk of collision compared to the current turbines. So, while larger turbines and increasing the hub height can be beneficial for seabirds, this likely needs to be applied in combination with curtailment strategies, which stop the turbines during heavy migration events, to reduce the impact on other species groups.
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RBINS Staff Publications 2022
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Revision of the Neogene stratigraphy of Belgium – Discussion document Version 1.0 1/05/2022
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RBINS Staff Publications 2022
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Integrative taxonomy resuscitates two species in the Lasioglossum villosulum complex (Kirby, 1802) (Hymenoptera: Apoidea: Halictidae)
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RBINS Staff Publications 2018
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DaRWIN: An open source natural history collections data management system
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DaRWIN (Data Research Warehouse Information Network) is an in-house solution developed by the Royal Belgian Institute of Natural Sciences (RBINS), as a Natural History collections management system for biological and geological samples in collections. In 2014, the Royal Museum for Central Africa (RMCA) adopted this system for its collections and started to take part in new developments. The DaRWIN database currently manages information on more than 600,000 records (about 4 million specimens) housed at the RBINS and more than 650,000 records (more than 1 million specimens) at the RMCA. DaRWIN is an open source system, consisting of a PostgreSQL database and a customizable web-interface based on the Symfony framework (https://symfony.com). DaRWIN is divided into 2 parts: one public section that gives a “read-only” access to digitised specimens, one section for registered users, with different levels of access rights (user, encoder, conservator and administrator), customizable for each collection and allowing update of specimens and collections, daily management of collections, and the potential for dealing with sensitive information. DaRWIN stores sample data and related information such as place and date of collection, missions and collectors, identifiers, technicians involved, taxonomy, identification information (type, stage, state, etc.), bibliography, related files, storage, etc. Other features that deal with day-to-day curation operations are available: loans, printing of labels for storage, statistics and reporting. DaRWIN features its own JSON (JavaScript Object Notation) webservice for specimens and scientific names and can export data in tab-delimited, Excel, PDF and GeoJSON formats. More recently, a procedure for importing batches of data has been developed, based on tab-delimited files, making integration of data from (old/historical) databases faster and more controlled. Additional improvements of$~$the$~$user interface and database model have been made. For example, parallel taxonomical hierarchies can be created, allowing users to work with temporary taxonomies, old scientific names (basionyms and synonyms) and document the history of type specimens. Finally, quality control and data cleaning on several tables have been implemented, e.g. mapping of locality names with vocabularies like Geonames, adding ISO 3166 two-letter country codes (https://www.iso.org/iso-3166-country-codes.html), cleaning duplicates from people/institutions and taxonomy catalogues. A tool for checking taxonomical names on GBIF (Global Biodiversity Information Facility), WoRMS (World Register of Marine Species) and DaRWIN itself, based on webservices and tab-delimited files, has been developed. Last year, RBINS, RMCA and Meise Botanic Garden (MBG) defined a new framework of collaboration in the NaturalHeritage project (http://www.naturalheritage.be), in order to foster interoperability among their collection data sources. This new framework presents itself as one common research portal$~$for$~$data on natural history collections (from DaRWIN and other existing collection databases) of the three partnered institutions and makes data compliant to a standard agreed by the partners. See Poster "NaturalHeritage: Bridging Belgian Natural History Collections" for more information. DaRWIN is accessible online (http://darwin.naturalsciences.be). A Github repository is also available (https://github.com/naturalsciences/natural\_heritage\_darwin).
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RBINS Staff Publications 2019
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NaturalHeritage: Bridging Belgian natural history collections
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The Royal Belgian Institute of Natural Sciences (RBINS), the Royal Museum for Central Africa (RMCA) and Meise Botanic Garden house more than 50 million specimens covering all fields of natural history. While many different research topics have their own specificities, throughout the years it became apparent that with regards to collection data management, data publication and exchange via community standards, collection holding institutions face similar challenges (James et al. 2018, Rocha et al. 2014). In the past, these have been tackled in different ways by Belgian natural history institutions. In addition to local and national collaborations, there is a great need for a joint structure to share data between scientific institutions in Europe and beyond. It is the aim of large networks and infrastructures such as the Global Biodiversity Information Facility (GBIF), the Biodiversity Information Standards (TDWG), the Distributed System of Scientific collections (DiSSCo) and the Consortium of European Taxonomic Facilities (CETAF) to further implement and improve these efforts, thereby gaining ever increasing efficiencies. In this context, the three institutions mentioned above, submitted the NaturalHeritage project (http://www.belspo.be/belspo/brain-be/themes\_3\_HebrHistoScien\_en.stm) granted in 2017 by the Belgian Science Policy Service, which runs from 2017 to 2020. The project provides links among databases and services. The unique qualities of each database are maintained, while the information can be concentrated and exposed in a structured way via one access point. This approach aims also to link data that are unconnected at present (e.g. relationship between soil/substrate, vegetation and associated fauna) and to improve the cross-validation of data. (1) The NaturalHeritage prototype (http://www.naturalheritage.be) is a shared research portal with an open access infrastructure, which is still in the development phase. Its backbone is an ElasticSearch catalogue, with Kibana, and a Python aggregator gathering several types of (re)sources: relational databases, REpresentational State Transfer (REST) services of objects databases and bibliographical data, collections metadata and the GBIF Internet Publishing Toolkit (IPT) for observational and taxonomical data. Semi-structured data in English are semantically analysed and linked to a rich autocomplete mechanism. Keywords and identifiers are indexed and grouped in four categories (“what”, “who”, “where”, “when”). The portal can act also as an Open Archives Initiatives Protocol for Metadata Harvesting (OAI-PMH) service and ease indexing of the original webpage on the internet with microdata enrichment. (2) The collection data management system of DaRWIN (Data Research Warehouse Information Network) of RBINS and RMCA has been improved as well. External (meta)data requirements, i.e. foremost publication into or according to the practices and standards of GBIF and OBIS (Ocean Biogeographic Information System: https://obis.org) for biodiversity data, and INSPIRE (https://inspire.ec.europa.eu) for geological data, have been identified and evaluated. New and extended data structures have been created to be compliant with these standards, as well as the necessary procedures developed to expose the data. Quality control tools for taxonomic and geographic names have been developed. Geographic names can be hard to confirm as their lack of context often requires human validation. To address this a similarity measure is used to help map the result. Species, locations, sampling devices and other properties have been mapped to the World Register of Marine Species and DarwinCore (http://www.marinespecies.org), Marine Regions and GeoNames, the AGRO Agronomy and Vertebrate trait ontologies and the British Oceanographic Data Centre (BODC) vocabularies (http://www.obofoundry.org/ontology/agro.html). Extensive mapping is necessary to make use of the ExtendedMeasurementOrFact Extension of DarwinCore (https://tools.gbif.org/dwca-validator/extensions.do).
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RBINS Staff Publications 2019
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Combined High-Throughput Imaging and Sequencing: Addressing the collections on demand requirement in SYNTHESYS+ project
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Imagine you are a scientist, working on collections. You have your pet taxon and you need information which is distributed in a number of books and publications but also in the specimens deposited in$~$Museums or Herbaria. Instead of paying visits to these establishments, around the world, you wish there was a means to transform all the information you need into a digitized form of the physical objects, you can reach from the screen of your laptop, tablet or cell phone. You dream you were able to watch, inspect and even dissect the type material you need online but also to compare it with others they way sequences are blasted against large databases, these days. You plan to make global research on this taxon and try to derive patterns from both the molecular and organismal level of the biological organization and to link the patterns resulting to the drivers of change for this taxon.$~$This is the vision of the Virtual Museum of Natural History and one of the ways to achieve this vision is to address the “collections on demand” requirement. One of the possible means to address this requirement is the digitization through the use of the micro-ct technology. The micro-CT virtual laboratory (vLab), developed by LifeWatchGreece research infrastructure (RI), makes it possible the online exploration and dissemination of micro-CT datasets, which are only rarely made available to the public due to their large size and a lack of dedicated online platforms for the interactive manipulation of 3D data. This presentation shows the development of such a “collections on demand” function, implemented by the SYNTHESYS+ project (DiSSCo RI), which combines such high-throughput technologies, that is micro-ct and genomics, to address the scientific communityʼs requirements. We show that this approach to combine patterns deriving from the application of novel techniques, which represent different kinds of observations is possible and we propose certain case studies as examples. The innovation aspects of this function include: Expansion and development of cost models for Collections on Demand; Development of standards and guidelines for exchange of collection-derived imaging data; Construction of new data pipelines and standard workflows, enabling access to complex digital content such as 3D scans; Development of novel molecular lab protocols, workflows and informatics pipelines, to enable large scale; DNA sequencing of NH collections.
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RBINS Staff Publications 2019