Wouter Addink

Naturalis Biodiversity Center | NCB

Tens of millions of images from biological collections have become available online over 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. While image analysis has become mainstream in consumer applications, it is...

The Distributed System of Scientific Collections (DiSSCo) is a new world-class Research Infrastructure (RI) for Natural Science Collections. The DiSSCo RI aims to create a new business model for one European collection that digitally unifies all European natural science assets under common access, curation, policies and practices that ensure that a...

The Minimum Information about a Digital Specimen (MIDS) standard is being developed within Biodiversity Information Standards (TDWG) to provide a framework for organisations, communities and infrastructures to define, measure, monitor and prioritise the digitisation of specimen data to achieve increased accessibility and scientific use. MIDS levels...

With the rise of Artificial Intelligence (AI), a large set of new tools and services is emerging that supports specimen data mapping, standards alignment, quality enhancement and enrichment of the data. These tools currently operate in isolation, targeted to individual collections, collection management systems and institutional datasets. To addres...

The Biodiversity Digital Twin (BioDT) project (2022-2025) aims to create prototypes that integrate various data sets, models, and expert domain knowledge enabling prediction capabilities and decision-making support for critical issues in biodiversity dynamics. While digital twin concepts have been applied in industries for continuous monitoring of...

Thanks to substantial support for biodiversity data mobilization in recent decades, billions of occurrence records are openly available, documenting life on Earth and enabling timely research, awareness raising, and policy-making. Initiatives across local to global scales have been separately funded to serve different, yet often overlapping audienc...

Digital specimens are new information objects on the internet, which act as digital surrogates of the physical objects they represent. They are designed to be extended with data derived from the specimen like genetic, morphological and chemical data, and with data that puts the specimen in context of its gathering event and the environment it was d...

The Biodiversity Knowledge Hub (BKH) is a web platform acting as an integration point and broker of an open, FAIR (Findable, Accessible, Interoperable, Reusable) and interlinked corpora of biodiversity data, services and knowledge. It serves the entire biodiversity research cycle, from specimens and observations to sequences, taxon names and finall...

The Distributed System of Scientific Collections (DiSSCo) is a new world-class Research Infrastructure (RI) for Natural Science Collections. The DiSSCo RI aims to create a new business model for one European collection that digitally unifies all European natural science assets under common access, curation, policies and practices that ensure that a...

United and coordinated efforts of biodiversity data infrastructures are needed to bring together various data forms from many different scientific areas. Biodiversity data are considered of great importance and use when they form a network of knowledge that can be seamlessly integrated and presented to various audiences, promoting both research and...

Persistent Identifier (PID) systems are the foundation for achieving the FAIR Guiding Principles (“findable, accessible, interoperable and reusable”). As FAIR data and connecting different data classes (i.e. specimens, genomics, observations, taxonomy and publications) are essential aspects of the BiCIKL project, we need a PID system at least at th...

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...

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...

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...

The landscape of biodiversity data infrastructures and organisations is complex and fragmented. Many occupy specialised niches representing narrow segments of the multidimensional biodiversity informatics space, while others operate across a broad front, but differ from others by data type(s) handled, their geographic scope and the life cycle phase...

Natural science collections are vast repositories of bio- and geodiversity specimens. These collections, originating from natural history cabinets or expeditions, are increasingly becoming unparalleled sources of data facilitating multidisciplinary research (Meineke et al. 2018, Heberling et al. 2019, Cook et al. 2020, Thompson et al. 2021). Due to...

Working together is key in terms of knowledge exchange and in the Biodiversity Community Integrated Knowledge Library project (BiCIKL), infrastructures involved in the biodiversity data landscape are working together to connect data from their different but related data domains. This will be key to connecting the dots towards the development of glo...

The early twenty-first century has witnessed massive expansions in availability and accessibility of digital data in virtually all domains of the biodiversity sciences. Led by an array of asynchronous digitization activities spanning ecological, environmental, climatological, and biological collections data, these initiatives have resulted in a ple...

One of the most desired (and still missing) elements to enable the concept of Digital Extended (Webster et al. 2021) Specimens is a persistent identifier (PID) for the new digital specimen object. Digital Specimens are created to act as a digital surrogate of the physical objects. Digital Specimens contain all data relevant to the specimens as well...

Threats to global biodiversity are increasingly recognised by scientists and the public as a critical challenge. Molecular sequencing technologies offer means to catalogue, explore, and monitor the richness and biogeography of life on Earth. However, exploiting their full potential requires tools that connect biodiversity infrastructures and resour...

The landscape of biodiversity data infrastructures and organisations is complex and fragmented. Many occupy specialised niches representing narrow segments of the multidimensional biodiversity informatics space, while others operate across a broad front but differ from others by data type(s) handled, their geographic scope and the life cycle phase(...

BiCIKL is an European Union Horizon 2020 project that will initiate and build a new European starting community of key research infrastructures, establishing open science practices in the domain of biodiversity through provision of access to data, associated tools and services at each separate stage of and along the entire research cycle. BiCIKL wi...

Threats to global biodiversity are increasingly recognised by scientists and the public as a critical challenge. Molecular sequencing technologies offer means to catalogue, explore, and monitor the richness and biogeography of life on Earth. However, exploiting their full potential requires tools that connect biodiversity infrastructures and resour...

International mass digitization efforts through infrastructures like the European Distributed System of Scientific Collections (DiSSCo), the US resource for Digitization of Biodiversity Collections (iDigBio), the National Specimen Information Infrastructure (NSII) of China, and Australia’s digitization of National Research Collections (NRCA Digital...

The BiCIKL Project is born from a vision that biodiversity data are most useful if they are viewed as a network of data that can be integrated and viewed from different starting points. BiCIKL’s goal is to realize that vision by linking biodiversity data infrastructures, particularly for literature, molecular sequences, specimens, nomenclature and...

The Horizon 2020 project Bi odiversity C ommunity I ntegrated K nowledge L ibrary (BiCIKL) (started 1st of May 2021, duration 3 years) will build a new European community of key research infrastructures, researchers, citizen scientists and other stakeholders in biodiversity and life sciences. Together, the BiCIKL 14 partners will solidify open scie...

DiSSCo (Distributed System of Scientific Collections) is a research infrastructure (RI) under development, which will provide services for the global research community to support and enhance physical and digital access to the natural history collections in Europe. These services include training, support, documentation and e-services. This talk wi...

Persistent identifiers (PID) to identify digital representations of physical specimens in natural science collections (i.e., digital specimens) unambiguously and uniquely on the Internet are one of the mechanisms for digitally transforming collections-based science. Digital Specimen PIDs contribute to building and maintaining long-term community tr...

To support future research based on natural sciences collection data, DiSSCo (Distributed System of Scientific Collections) – the European Research Infrastructure for Natural Science Collections – adopts Digital Object Architecture as the basis for its planned data infrastructure. Using the outputs of one Research Data Alliance (RDA) interest group...

Digitisation and publication of museum specimen data is happening worldwide, but far from complete. Museums can start by sharing what they know about their holdings at a higher level, long before each object has its own record. Information about what is held in collections worldwide is needed by many stakeholders including collections managers, fun...

In a Biodiversity_Next 2019 symposium, a vision of Digital Specimens based on the concept of a Digital Object Architecture (Kahn and Wilensky 2006) (DOA) was discussed as a new layer between data infrastructure of natural science collections and user applications for processing and interacting with information about specimens and collections. This...

European natural history collections are a critical infrastructure for meeting the most important challenge humans face over the next 30 years – creating a sustainable future for ourselves and the natural systems on which we depend – and for answering fundamental scientific questions about ecological, evolutionary, and geological processes. Since 2...

The collaboration between LifeWatch ERIC and DiSSCo (Distributed System of Scientific Collections), both pan-European research infrastructures focusing on biodiversity, can be achieved in a number of ways. The direct initiation of this collaboration can be carried out through their joint support to GBIF (Global Biodiversity Information Facility). T...

DiSSCo – the Distributed System of Scientific Collections – will mobilise, unify and deliver bio- and geo-diversity information at the scale, form and precision required by scientific communities, and thereby transform a fragmented landscape into a coherent and responsive research infrastructure. At present DiSSCo has 115 partners from 21 countries...

Natural Science Collections (NSCs) contain specimen-related data from which we extract valuable information for science and policy. Openness of those collections facilitates development of science. Moreover, virtual accessibility to physical containers by means of their digitization will allow an exponential increase in the level of available infor...

European Natural Science Collections (NSC) are part of the global natural and cultural capital and represent 80% of the world bio-and geo-diversity. Data derived from these collections underpin thousands of scholarly publications and official reports (used to support legislative and regulatory processes relating to health, food, security, sustainab...

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 y...

Preserved specimens in natural science collections have lifespans of many decades and often, several hundreds of years. Specimens must be unambiguously identifiable and traceable in the face of changes in physical location, changes in organisation of the collection to which they belong, and changes in classification. When digitizing museum collecti...

Many biogeographical, macroecological and biodiversity studies rely on digitized and georeferenced specimen data from natural history musea and herbaria. Currently, GBIF, the most important data portal for biodiversity data holds 149 million records of preserved specimens. Within Europe, however, it is estimated that all collection institutes colle...

In 2015, the global biodiversity information initiatives Biodiversity Heritage Library (BHL), Barcode of Life Data systems (BoLD), Catalogue of Life (CoL), Encyclopedia of Life (EOL), and the Global Biodiversity Information Facility (GBIF) took the first step to work on the idea for building a single shared authoritative nomenclature and taxonomic...

DiSSCo (The Distributed System of Scientific Collections) is a Research Infrastructure (RI) aiming at providing unified physical (transnational), remote (loans) and virtual (digital) access to the approximately 1.5 billion biological and geological specimens in collections across Europe. DiSSCo represents the largest ever formal agreement between n...

Biodiversity informatics plays a central enabling role in the research community's efforts to address scientific conservation and sustainability issues. Great strides have been made in the past decade establishing a framework for sharing data, where taxonomy and systematics has been perceived as the most prominent discipline involved. To some exten...

i4Life provides linkages between the Catalogue of Life, an expert based knowledge portal for living species on earth, and global partners (IUCN, GBIF, ENA at EBI, BOLD, EoL, and Life Watch) providing data portals for distribution, genetic diversity and conservation information. This novel e-infrastructure offers the only single global consensus lis...

Version 2.06 at: https://abcd.tdwg.org/xml/documentation/primer/2.06/ Archived version in Github: https://github.com/tdwg/wiki-archive/blob/master/twiki/data/ABCD/AbcdPrimer.txt

Present distributed systems consist of loosely coupled fully autonomous databases on which only distributed search and retrieval of data is possible. This may develop into distributed database systems: a set of databases on multiple computers that appear to applications as one single database. An application may simultaneously access and modify the...