Mathias Dillen

Mathias Dillen
Ghent University | UGhent · Department of Environment

About

39
Publications
3,160
Reads
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162
Citations
Citations since 2016
38 Research Items
160 Citations
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20162017201820192020202120220102030

Publications

Publications (39)
Article
Full-text available
The paper summarises many years of discussions and experience of biodiversity publishers, organisations, research projects and individual researchers, and proposes recommendations for implementation of persistent identifiers for article metadata, structural elements (sections, subsections, figures, tables, references, supplementary materials and ot...
Preprint
Abstract: Tens of millions of images from biological collections have become available online in the last two decades. In parallel, there has been a dramatic increase in the capabilities of image analysis technologies, especially those involving machine learning and computer vision. Whilst image analysis has become mainstream in consumer applicatio...
Article
The BiCIKL project is born from a vision that biodiversity data are most useful if they are presented as a network of data that can be integrated and viewed from different starting points. BiCIKL’s goal is to realise that vision by linking biodiversity data infrastructures, particularly for literature, molecular sequences, specimens, nomenclature a...
Article
Full-text available
Scientific collections have been built by people. For hundreds of years, people have collected, studied, identified, preserved, documented and curated collection specimens. Understanding who those people are is of interest to historians, but much more can be made of these data by other stakeholders once they have been linked to the people’s identit...
Article
People are involved with the collection and curation of all biodiversity data, whether they are researchers, members of the public, taxonomists, conservationists, collection managers or wildlife managers. Knowing who those people are and connecting their biographical information to the biodiversity data they collect helps us contextualise their sci...
Article
Full-text available
Natural history specimens constitute physical evidence for past observations of nature. They hold further value as the backbone of taxonomy and as historical samples that can be subjected to further analysis. Yet, as physical objects scattered across collections around the world, their scientific use cases are limited by an overall lack of FAIRness...
Article
Full-text available
Semantic segmentation has been proposed as a tool to accelerate the processing of natural history collection images. However, developing a flexible and resilient segmentation network requires an approach for adaptation which allows processing different datasets with minimal training and validation. This paper presents a cross-validation approach de...
Article
Full-text available
Natural history collection data available digitally on the web have so far only made limited use of the potential of semantic links among themselves and with cross-disciplinary resources. In a pilot study, botanical collections of the Consortium of European Taxonomic Facilities (CETAF) have therefore begun to semantically annotate their collection...
Article
Full-text available
The natural history specimens of the world have been documented on paper labels, often physically attached to the specimen itself. As we transcribe these data to make them digital and more useful for analysis, we make interpretations. Sometimes these interpretations are trivial, because the label is unambiguous, but often the meaning is not so clea...
Preprint
When sequencing molecules from an organism it is standard practice to create voucher specimens. This ensures that the results are repeatable and that the identification of the organism can be verified. It also means that the sequence data can be linked to a whole host of other data related to the specimen, including traits, other sequences, environ...
Article
We compare different approaches to transcribing natural history data and summarise the advantages and disadvantages of each approach using six case studies from four different natural history collections. We summarise the main cost considerations when planning a transcription project and discuss the limitations we current have in understanding the...
Article
Full-text available
DiSSCo, the Distributed System of Scientific Collections, is a pan-European Research Infrastructure (RI) mobilising, unifying bio- and geo-diversity information connected to the specimens held in natural science collections and delivering it to scientific communities and beyond. Bringing together 120 institutions across 21 countries and combining e...
Article
Full-text available
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 mana...
Article
Full-text available
The LinBi project aims to enhance the discoverability of digitized objects from natural history collections hosted by institutes all over Europe. This enhancement is achieved by publishing new and enriched content to the Europeana collections platform. The use of simple vocabularies and machine-readable metadata encourages reuse and has the additio...
Article
Full-text available
Distributed Systems of Scientific Collections (DiSSCo) a pan-European Research Infrastructure will facilitate the production of tens of millions of digital images of natural history specimens each year. The labels of these specimens contain valuable information for research, but their transcription can be difficult and time-consuming, with often ha...
Article
Full-text available
Zenodo (https://zenodo.org) is an open-access repository operated by CERN (European Organization for Nuclear Research), which provides researchers with an easy and stable platform to archive and publish their data and other output, such as software tools, manuals and project reports. In the context of the ICEDIG (Innovation and Consolidation for La...
Article
Full-text available
The rapid development and refinement of digital technologies in the last two decades has spearheaded a wave of digitization in natural history collections. This has generated a massive number of digitized images and many more are expected with the planned European Distributed Systems of Scientific Collections (DiSSCo) infrastructure. Many of these...
Article
Full-text available
Digitisation of Natural History Collections (NHC) has evolved from transcription of specimen catalogues in databases to web portals providing access to data, digital images, and 3D models of specimens. These portals increase global accessibility to specimens and help preserve the physical specimens by reducing their handling. The size of the NHC re...
Article
Full-text available
Being able to connect together the specimens collected and determined by a person is key to understanding the origins, history, identity and ownership of a collection. Yet making these connections is difficult because people’s names change, are not unique and are written in many different ways. Semantic annotation of people names with stable identi...
Article
Full-text available
More and more herbaria are digitising their collections. Images of specimens are made available online to facilitate access to them and allow extraction of information from them. Transcription of the data written on specimens is critical for general discoverability and enables incorporation into large aggregated research datasets. Different methods...
Data
R script used to map data from FinBIF API to DwC
Data
Python script to upload the dataset to Zenodo
Data
Taxonomic coverage (interactive HTML file)
Article
Full-text available
There are more than 1.2 billion biological specimens in the world’s museums and herbaria. These objects are particularly important forms of biological sample and observation. They underpin biological taxonomy but the data they contain have many other uses in the biological and environmental sciences. Nevertheless, from their conception they are alm...
Article
Full-text available
Recent research has suggested that increasing neighbourhood tree species diversity may mitigate the impact of pests or pathogens by supporting the activities of their natural enemies and/or reducing the density of available hosts. In this study, we attempted to assess these mechanisms in a multitrophic study system of young oak (Quercus), oak powde...
Data
Data (including metadata) collected in this study. (XLSX)
Data
Results of the full model for the choice feeding experiment. (DOCX)
Data
Parameter estimates for the identity models of the field experiment. (DOCX)
Article
In light of global biodiversity loss, the influence of species composition on ecosystem functioning has attracted increasing attention. However, questions remain whether neighbourhood species richness or identity is more important and what mechanisms drive these composition effects. We investigated the role of local species richness and identity on...

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