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Doctoral thesis
Automating the construction of higher order data representations from heterogeneous biodiversity datasets
Datasets created from large-scale specimen digitisation drive biodiversity research, but these are often heterogeneous: incomplete and fragmented. As aggregated data volumes increase, there have been calls to develop a “biodiversity knowledge graph” to better interconnect the data and support meta-analysis, particularly relating to the process of species description. This work...Nicolson, Nicky
Clustering, Specimen digitisation, Biodiversity informatics, Machine learning, and Record linkage
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Journal article
Global access to nomenclatural botanical resources: Evaluating open access availability.
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Abstract
Connecting the Dots: Aligning human capacity through networks toward a globally interoperable Digital Extended Specimen (DES) infrastructure.
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 audiences of data users,...Ellwood, Elizabeth R. ; Addink, Wouter ; Bates, John ; Bentley, Andrew ; Buschbom, Jutta …
Collaboration, Biodiversity, Digital Extended Specimen (DES), International partners, and Roadmap
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Journal article
Open science tools: Supporting hands-on creation of the "digital extended specimen".
As a biodiversity informatics community, we have mobilised and interconnected a wide array of information, including specimen collections, published literature and metadata resources, which compile facts about collections and the people that work with them. We have defined data standards to facilitate data interoperability and tools development. Along with colleagues...Nicolson, Nicky ; Lucas, Eve
Document production, Open science, Research tools, Digital specimens, and Record linkage
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Journal article
Recommendations for interoperability among infrastructures.
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,...Meeus, Sofie ; Addink, Wouter ; Agosti, Donat ; Arvanitidis, Christos ; Balech, Bachir …
Hackathon, Wikidata, Biodiversity informatics, Cloud computing, Linking, Data standards, API, and FAIR data
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Journal article
Plant and fungal collections: Current status, future perspectives.
Societal Impact Statement Plant and fungal specimens provide the auditable evidence that a particular organism occurred at a particular place, and at a particular point in time, verifying past occurrence and distribution. They also document the aspects of human exploration and culture. Collectively specimens form a global asset with significant... -
Conference paper (published)
Identifying Novel Features from Specimen Data for the Prediction of Valuable Collection Trips.
Primary biodiversity data provide “what, where, and when” data points: the assertion that a species occurred at a particular point in space and time. These are most valuable when associated with specimens stored in natural history museums and herbaria, which evidence the assertions with reference to a physical specimen. The...Nicolson, Nicky ; Tucker, Allan
Collecting trip, Identification, Specimen data, Data-mining, Collectors, and Metadata
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Journal article
Harnessing Large-Scale Herbarium Image Datasets Through Representation Learning.
The mobilization of large-scale datasets of specimen images and metadata through herbarium digitization provide a rich environment for the application and development of machine learning techniques. However, limited access to computational resources and uneven progress in digitization, especially for small herbaria, still present barriers to the wide adoption of these...Walker, Barnaby E. ; Tucker, Allan ; Nicolson, Nicky
Machine learning, Natural history collections, Digitized herbarium specimens, Deep learning, and Computer vision
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Journal article
People are essential to linking biodiversity data.
People are one of the best known and most stable entities in the biodiversity knowledge graph. The wealth of public information associated with people and the ability to identify them uniquely open up the possibility to make more use of these data in biodiversity science. Person data are almost always...Groom, Quentin ; Güntsch, Anton ; Huybrechts, Pieter ; Kearney, Nicole ; Leachman, Siobhan …
Natural history collections, Specimen data, Biodiversity data, Collectors, and Metadata