Ana Casino's research while affiliated with Consortium of European Taxonomic Facilities and other places

Publications (17)

Article
Full-text available
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...
Preprint
Full-text available
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(...
Article
Full-text available
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...
Article
Full-text available
In an effort to characterise the various dimensions of activity within the biodiversity informatics landscape, we developed a framework to survey these dimensions for ten major organisations*1 relative to both their current activities and long-term strategic ambitions. This survey assessed the contact between these infrastructure organisations by c...
Article
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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...
Article
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The Distributed System of Scientific Collections (DiSSCo) Research Infrastructure (RI) is presently in its preparatory phase. DiSSCo is developing a new distributed RI to operate as a one-stop-shop for the envisaged European Natural Science Collection (NSC) and all its derived information. Through mass digitisation, DiSSCo will transform the fragme...
Article
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Results are presented of a study investigating solutions and procedures to incorporate private natural history collections into the international collections data infrastructure. Results are based on pilot projects carried out in three European countries aimed at approaches on how to best motivate and equip citizen collectors for digitisation: 1) I...
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
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...
Conference Paper
Full-text available
With digitisation of natural history collections over the past decades, their traditional roles — for taxonomic studies and public education — have been greatly expanded into the fields of biodiversity assessments, climate change impact studies, trait analyses, sequencing, 3D object analyses etc. (Nelson and Ellis 2019; Watanabe 2019). Initial esti...
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...
Conference Paper
Full-text available
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...
Article
Full-text available
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...
Technical Report
Full-text available
There is a growing need to set data-driven priorities when planning for the digitisation of European natural history collections. Currently, there is no single location where the required information is gathered and where it can be easily consulted and used by decision-makers and scientists. In particular, the information on digitised and non-digit...
Technical Report
Full-text available
Anno 2017 the task of mobilizing data from biocollections ahead of us is still enormous (data of 90% of the biocollections still needs to be mobilized). It is imperative for stakeholders, individual keepers of natural science collections, the community at large, and even for funding agencies, not only to tackle this backlog as quickly as possible,...
Article
Full-text available
A simple, permanent and reliable specimen identifier system is needed to take the informatics of collections into a new era of interoperability. A system of identifiers based on HTTP URI (Uniform Resource Identifiers), endorsed by the Consortium of European Taxonomic Facilities (CETAF), has now been rolled out to 14 member organisations (Güntsch et...
Article
Full-text available
With biodiversity research activities being increasingly shifted to the web, the need for a system of persistent and stable identifiers for physical collection objects becomes increasingly pressing. The Consortium of European Taxonomic Facilities agreed on a common system of HTTP-URI-based stable identifiers which is now rolled out to its member or...

Citations

... Integrative and multiscale approaches are required to mitigate biodiversity loss. Techniques involving various molecular markers, combined with the rapid development of biodiversity informatics, have allowed an impressive progress in the accumulation, harmonisation, management, use and dissemination of data and information on the world's biota, especially during the last two decades (Gadelha et al., 2021, Smith et al., 2022, Waterhouse et al., 2022. Molecular biodiversity can be further considered as the "connecting tissue" of the wider biodiversity structure, ensuring that the common aspects are linked across the various levels of complexity and granularity. ...
... These collections are daily updated for the first two, punctually for the third. Additional collections regrouping supplementary data files from PMC as well as taxonomic treatments from Plazi [Naderi et al. 2022, Penev et al. 2022] are planned. A parsing task is done to split each document in distinct fields, for example title, abstract, keywords, which are then pushed into a MongoDB database. ...
... Building on the extended specimen concept (Webster 2017), the BCoN vision for the future of collections includes transparent annotation of the underlying data and the linking of disparate specimen records; ecological and environmental data; and derivative items such as gene sequences and isotope readings, through voucher-tissue, predator-prey, and host-parasite type relationships-all enabled by continued growth of physical and digital collections. The European program for a Distributed System of Scientific Collections (DiSSCo), which began planning in 2018 under the European Commission Horizon 2020 project on innovation and consolidation for large scale digitization of natural heritage (ICEDIG; Hardisty et al. 2020), aims for digital unification of all European natural science assets under common policies for curation, access, and use. As such, DiSSCo enables the fragmented landscape of the extensive European natural science collections to be transformed into an integrated digital specimen knowledge base that provides interconnected hard evidence about the natural world. ...
... As part of SYNTHESYS+, the NHM has been building the Specimen Data Refinery (SDR) ( Smith et al. 2019) -a workflow engine for chaining ML models, each performing one atomic task in the data extraction process. The SDR is now in public beta, and we present evaluation metrics from our initial testing. ...
... We are witnessing a new era of rapid development and improvement of methods and technologies for herbarium data gathering and management, and we now encourage the academic community to facilitate the conception of ways for the conservation community to learn about and utilize these advancements. Ongoing digitization, online publishing of specimens, collaborative networks for data management and cross-validation, and dataset building are the initial steps (Wang et al., 2009;Matsunaga et al., 2013;Dugenie et al., 2017;Yagui et al., 2017;Dormontt et al., 2018;Theeten et al., 2019), and these are followed by the development of scoring and data-sharing protocols (Yost et al., 2018), the addition of non-traditional digitized data fields, user annotation capabilities, and born-digital field data collection, including citizen-science applications (Heberling & Isaac, 2018;James et al., 2018;Powell et al., 2019). These advancements will make machine learning increasingly user-friendly (e.g. ...
... The DiSSCo 45 (biodiversity), ELIXIR 46 (biomedical research), E-RIHS 47 (cultural heritage), and EISCAT 48 (atmospheric research) initiatives provide excellent examples of the challenges and needs which many scientific disciplines are faced with [26,27]. At the bottom layer of the scientific knowledge space are the digital representations of large numbers of physical objects such as, for example, biological specimens [28], or observations of phenomena such as caused by, for example, diseases, treatments of diseases, chemical processes in the atmosphere, and many others. ...
... 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). ...
... On the other hand, it is preferable to adjust the existing infrastructure of established repositories rather than create new ones and to streamline the submission process of diverse data via user-friendly submission portals. The key lies in linking the data to a single specimen for which a specimen identifier will be required (Güntsch et al. 2018). ...
... Essential specimen information can now be retrieved easily from hyperlinks; for example, CETAF (The Consortium of European Taxonomic Facilities) member organisations have implemented a system of persistent identifi ers for objects in collections (Güntsch et al. 2017). These Uniform Resource Identifi ers follow a defi ned syntax and are potentially human readable, following a logical grammar. ...