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Article Reference Species turnover between the northern and southern part of the South China Sea in the Elaphropeza Macquart Mangrove fly communities of Hong Kong and Singapore (Insecta: Diptera: Hybotidae)
Located in Library / No RBINS Staff publications
Article Reference Gene Tree Estimation Error with Ultraconserved Elements: An Empirical Study on Pseudapis Bees
Located in Library / RBINS Staff Publications 2021
Article Reference North American Branchiobdellida (Annelida: Clitellata) or Crayfish Worms in France: the most diverse distribution of these exotic ectosymbionts in Europe
Located in Library / RBINS Staff Publications 2020
Article Reference Re-description of the type species of the genera Ganesella Blanford, 1863 and Globotrochus Haas, 1935; with description of a new Ganesella species from Thailand (Eupulmonata, Camaenidae)
Located in Library / RBINS Staff Publications 2019
Article Reference Octet Stream CETAF Collection Dashboard: Mapping natural history collections diversity
Several initiatives aim to map the diversity of Natural History (NH) collections and standardise their descriptions. The Global Registry of Biodiversity Repositories (GRBio) is the most recent global registry. Unfortunately the server has been down since mid-2018 but the Global Biodiversity Information Facility (GBIF) recently "rescued" this data. In addition to this, the One World Collection exercise is a set of high-level collection descriptors (size, group coverage and geographic distribution) supporting a common strategy between the largest world institutions. Despite these efforts, a large part of the NH collections remains digitally unavailable and digitisation at the specimen level will take several decades. A new NH collections dashboard is needed in order to harmonise the efforts of the institutions. The Consortium of European Taxonomic Facilities (CETAF) is a good place to introduce this excercise. CETAF’s members hold over half of the world’s NH collections, representing 80% of the world's bio- and geo-diversity. Most of these collections are now engaged in the preparation for the common process of the Distributed System of Scientific Collections (DiSSCo, European Strategy Forum on Research Infrastructure). Additionally in Belgium, the Royal Belgian Institute of Natural Sciences (RBINS), Royal Museum of Central Africa (RMCA), Meise Botanic Garden (MBG) and CETAF have joined efforts to set up a common research portal (Natural Heritage, BRAIN-be project). The goal is to link together several collection management systems (CMS) and to (re)create links between isolated collection items. The CETAF collections dashboard splits the information into small metadata units related to topics relevant to the collections (taxonomy, geographic distribution, digitisation strategy and coverage, stratigraphy, etc.). The model allows for the creation of new units without a complete modification of the database structure. All units are defined by the Dublin Core and by fields derived from the Innovation and consolidation for large scale digitisation of natural heritage (ICEDIG) d2.3 deliverable (van Egmond et al. 2019). The object hierarchy allows for the creation of sub-collections and preserves the unity of the information. The CMS has an internal object database with a full index and a faceted search interface. It also has web services and XLS (Microsoft® Excel®) import/export functionalities. The collection dashboard also includes a complete workflow and access rights management at the object level. This is important for the information that is protected by the EU General Data Protection Regulation (GDPR). The dashboard is now being evaluated with the collections hosted by the partners of Natural Heritage. The system will be proposed to CETAF members and connections will be established with the international portals such as the GBIF or the future DiSSCo portal.
Located in Library / RBINS Staff Publications 2019
Article Reference Octet Stream DaRWIN: An open source natural history collections data management system
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).
Located in Library / RBINS Staff Publications 2019
Article Reference Octet Stream NaturalHeritage: Bridging Belgian natural history collections
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).
Located in Library / RBINS Staff Publications 2019
Article Reference Octet Stream Combined High-Throughput Imaging and Sequencing: Addressing the collections on demand requirement in SYNTHESYS+ project
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 community’s 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.
Located in Library / RBINS Staff Publications 2019
Article Reference Note sur la présence de Berginnus tamarisci Wollaston, 1854 en Belgique (Insecta: Coleoptera: Mycetophagidae)
Located in Library / RBINS Staff Publications 2018
Inproceedings Reference A diverse Miocene toothed whale (Odontoceti) fauna from Calvert Cliffs, Atlantic Coastal Plain, U.S.A.
Located in Library / RBINS Staff Publications 2019