Publications

@article{10.3897/biss.3.36106,
title = {Training Taxonomists for the Digital World: Are we prepared?},
author = {Boyko B Georgiev and Ana Casino and Catherina Voreadou},
url = {https://doi.org/10.3897/biss.3.36106},
doi = {10.3897/biss.3.36106},
year = {2019},
date = {2019-01-01},
journal = {Biodiversity Information Science and Standards},
volume = {3},
pages = {e36106},
publisher = {Pensoft Publishers},
abstract = {Digital knowledge and skills are rapidly becoming integral part of the work of the modern taxonomist. Their importance is further increased with the recent recognition of DiSSCo (Distributed System of Scientific Collections, https://dissco.eu). This new pan-European research infrastructure envisions placing European natural science collections at the centre of data-intensive scientific excellence and innovation for taxonomic and environmental research, food security, health and the bioeconomy. The mission of this ambitious project is to mobilise, unify and deliver bio- and geo-diversity information at the scale, form and precision required by scientific communities as well as to transform a fragmented landscape into a coherent and responsive research infrastructure.
An important step in improving the capacity of the research community underpinning DiSSCo is the COST Action MOBILISE (Mobilising Data, Policies and Experts in Scientific Collections, https://www.mobilise-action.eu). One of major capacity-building objectives is to facilitate implementation of common standards and newly-developed techniques by training and education. Its achievement is envisaged by standardised training modules such as training courses, workshops, webinars, online tutorials and short-term visits to other research units.
The first impression from surveying interests of candidates to be included into training events, demonstrates an uneven distribution of digital knowledge and skills across countries, institutions and generations. We advocate that a massive coordinated training programme may result in more efficient establishment of common standards and, consequently, better implementation of the forthcoming joint efforts in the development of the new pan-European research infrastricture.},
keywords = {capacity building, Digital knowledge, digital skills, DiSSCo, education, MOBILISE, natural history collections, research, taxonomy, training, young researchers},
pubstate = {published},
tppubtype = {article}
}

@article{10.3897/biss.3.37854,
title = {NaturalHeritage: Bridging Belgian natural history collections},
author = {Franck Theeten and Marielle Adam and Thomas Vandenberghe and Mathias Dillen and Patrick Semal and Serge Scory and Jean-Marc Herpers and Didier Van den Spiegel and Patricia Mergen and Larissa Smirnova and Henry Engledow and Ana Casino and Karsten Gödderz},
url = {https://doi.org/10.3897/biss.3.37854},
doi = {10.3897/biss.3.37854},
year = {2019},
date = {2019-01-01},
journal = {Biodiversity Information Science and Standards},
volume = {3},
pages = {e37854},
publisher = {Pensoft Publishers},
abstract = {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).},
keywords = {data analysis, data quality and cleaning, interoperable databases, natural history collections, search portal, standardisation, webservices},
pubstate = {published},
tppubtype = {article}
}