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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
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
Inproceedings Reference Early dispersal for quadrupedal cetaceans: an amphibious whale from the middle Eocene of the southeastern Pacific
Located in Library / RBINS Staff Publications 2019
Inproceedings Reference New fossils of paroxyclaenids (Placentalia, Mammalia) from the early Eocene of France shed light on the origin and evolution of these endemic European mammals
Paroxyclaenidae is an enigmatic archaic group of middle size placental mammals. They are known only from Europe, and are recorded from the early Eocene (Ypresian) to the middle Eocene (Bartonian). Paroxyclaenids are divided into two distinct subfamilies: Paroxyclaeninae and Merialinae. They have been variously placed by different authors in Carnivora, Creodonta, ‘Condylarthra’, and Insectivora, but are considered since 1970’s as members of Pantolesta. The dentition of paroxyclaenids is complete (4 premolars, 3 molars); it is highly specialized, with relatively enlarged posterior premolars, spaced out cheek teeth, but primitive, for instance, in the absence of hypocone on upper molars. The molars decrease in size from M1/m1 to M3/m3; the M3 and m3 are sometimes well reduced. A particularity of the dentition of some paroxyclaenids is the tendency to enlargement and molarisation of the third and fourth upper and lower premolars, generally exceeding the succeeding molars in size. We recently studied unpublished fossils from the first half of the Ypresian: these fossils originate from the French localities of Le Lien (Hérault), Pourcy, Mutigny, Avenay (Marne), and Condé-en-Brie (Aisne). They allow to describe new specimens of Merialus martinae (the oldest paroxyclaenid) and three new species – the oldest paroxyclaenine and two merialines. Their study is the opportunity to review the evolution of this family – the last extensive and comprehensive review of the paroxyclaenids has been published in 1988. The two paroxyclaenid subfamilies – Paroxyclaeninae and Merialinae – are rarely recorded together: this case only occurs in the Paris Basin during the early Eocene (Mutigny, Avenay, Condé-en-Brie). Half of the merialines are present in the Southern European Province, while the paroxyclaenines are only recorded in Northern European Province. The two subfamilies reach their maximum size (+/- 3-4 kg) (e.g., Spaniella, Kopidodon) around the early/middle Eocene boundary (47.8 Myr). However, some smaller paroxyclaenids (body mass around 1 kg) have co-existed together with the larger ones. The small middle Eocene paroxyclaenids, which are as small as the taxa found in the early Eocene, have been the last representatives of the group (Bartonian). The maximum of diversity of the Paroxyclaenids occurred during the Lutetian (middle Eocene). Finally, because the new fossils provide information on the morphology of the earliest paroxyclaenids, their study is the opportunity to question the origin of this group and its relationships among Placentalia. Grant Information: This abstract is a contribution to the project BR/121/A3/PALEURAFRICA funded by the Belgian Science Policy Office.
Located in Library / RBINS Staff Publications 2017
Inproceedings Reference Platychelone emarginata gigantic Cretaceous marine turtle from Belgium
Platychelone emarginata Dollo, 1909 is a large turtle from the Late Cretaceous (Maastrichtian) chalk sediments of Limburg, Belgium. Hitherto, only the name was given to this turtle without describing details or providing figures. A single well articulated carapace (IRScNB. Reg. 1681), lacking nuchal, peripherals, and pygal plates, is preserved. The distance from the first costal to the distal end of the eighth costal is 180 cm, indicating that the original carapace was about 210 cm long. Its gigantic size, flattened shell, reduction of distal half of costals, and loss of scute sulcus, indicate that Platychelone is a member of true marine turtles (superfamily Chelonioidea). Neurals are rectangular shape and inclination of the first thoracic vertebra is almost vertical, suggesting this turtle belongs to either Protostegidae or Dermochelyidae. Seventh and eighth costals are medially meeting due to the loss of neurals; this condition is shared with the genus Mesodermochelys from the Late Cretaceous (Santonian to Maastrichtian) of Japan. Thus, it seems most probable that Platychelone is a closest relative of Mesodermochelys among basal dermochelyids. Platychelone has presumed autoapomorphic characters such as very thickened distal ends of thoracic ribs and irregular sculptures on carapace, not seen in any other chelonioids. This genus is only known by the holotype, whereas Allopleuron hoffmanni, a very common cheloniid marine turtle from in the Maastrichtian deposits of Belgium and Netherland, is known from some hundred specimens. So far, there is no ancestral or related taxon of Platychelone from the Campanian deposits of Belgium. The occurrence of Platychelone is very rare but evokes a high taxonomic diversity of gigantic chelonioids in the Cretaceous Tethys.
Located in Library / RBINS Staff Publications 2017
Inproceedings Reference The small-mammal assemblage from Caverne Marie-Jeanne (Hastière-Lavaux, Belgium): environmental and climatic approach of the marine isotope stage 3 in North-Western Europe
Small mammal faunas from the Pleistocene of Belgium are not well-known. Some have been studied from the second half of the Late Pleistocene and the Early Holocene. However, only a few sites from the first half of the Late Pleistocene (Marine Isotope Stage 3, MIS 3, ca. 60-30 ka) have yielded small mammal assemblages. Among them is the Marie-Jeanne Cave that is situated in the southeast of Belgium, in the Ardennes region. It is formed in the Early Carboniferous limestone deposits above the Meuse River, near the town of Hastière-Lavaux. The excavated deposits evidenced ten different layers but only the layers 6 to 2 yieldeda large collection of faunal remains. Recent dating of the stratigraphic sequence of the Marie-Jeanne Cave shows that these layers have a chronological range pertaining to MIS 3 (about 50-40 ka BP). During the first field campaign in 1943, about 40 m3 of sedimentswereextracted recovering a large collection of disarticulated bone fragments and several plant, mollusc and archaeological remains housed at the RBINS. A first study of this material underlined the presence of 29 taxa of insectivores, bats and rodents. The recent revision of the material revealed 9897 identified specimens, corresponding to a minimum of 4980 individuals. This permitted us to add to the previous list two vole species, the steppe lemming Lagurus lagurus and the European pine vole Microtus (Terricola) subterraneus. We also undertook new paleoenvironmental and paleoclimatic reconstructions based on alternative methods from those previously used for the MIS 3 sequence of the Marie-Jeanne Cave. Our results indicate that MIS 3 is characterized by dynamic alternations of forest expansion with semiarid area expansion in accordance with the warming and cooling, respectively, of the sea-surface temperatures. It was in this context of rapid fluctuations that the terrestrial sequence of the Marie-Jeanne Cave in north-western Europe was formed. The fossiliferous layers underwent cold and dry environmental and climatic conditions. This is indicated by lower temperatures and slightly higher precipitation than today, together with an environment dominated by open woodland formations and open dry meadows. Our results are consistent with the available chronological, large-mammal, herpetofaunal, and mollusc datasets for this lower part of the sequence. They are also consistent with regional loess studies in Belgium and with previous work performed on small mammals from MIS 3 in Belgium and elsewhere in Europe. Grant Information: Generalitat de Catalunya projects, Synthesis Grants, PhD grant of the Erasmus Mundus Programme - International Doctorate in Quaternary and Prehistory.
Located in Library / RBINS Staff Publications 2017
Inproceedings Reference Climate change impact on wind, waves and surges
Located in Library / RBINS Staff Publications 2019