Deborah Paul

Deborah Paul
University of Illinois, Urbana-Champaign | UIUC · Illinois Natural History Survey

Master of Education

About

60
Publications
12,425
Reads
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509
Citations
Citations since 2016
53 Research Items
493 Citations
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2016201720182019202020212022020406080100120140
Additional affiliations
October 2011 - present
Florida State University
Position
  • Technology Specialist

Publications

Publications (60)
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
Full-text available
Biodiversity informatics workbenches and aggregators that make their data externally accessible via application programming interfaces (APIs) facilitate the development of customized applications that fit the needs of a diverse range of communities. In the past, the technical skills required to host web-facing applications placed constraints on man...
Article
All organizations need clear and succinct mission and vision statements to communicate the purpose and overall goals of the group. These products provide the foundation for development of long(er) term strategic planning including communication plans. Logos offer us another way to highlight and brand what we do and why we do it. Periodically, for a...
Article
Full-text available
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...
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
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Recent global events reinforce the need for local to global coalitions to address a variety of socio-environmental challenges such as the current COVID-19 pandemic (Cook et al. 2020) and biodiversity loss in general. Scientists reviewing data and fitness for current and future use note urgent necessary changes needed in data collection, specimen co...
Article
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Connecting basic data about bats and other potential hosts of SARS-CoV-2 with their ecological context is crucial to the understanding of the emergence and spread of the virus. However, when lockdowns in many countries started in March, 2020, the world's bat experts were locked out of their research laboratories, which in turn impeded access to lar...
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...
Article
Full-text available
International collaboration between collections, aggregators, and researchers within the biodiversity community and beyond is becoming increasingly important in our efforts to support biodiversity, conservation and the life of the planet. The social, technical, logistical and financial aspects of an equitable biodiversity data landscape – from work...
Preprint
Full-text available
Connecting basic data about bats and other potential mammal hosts of SARS-CoV-2 with their ecological context is now critical for understanding the emergence and spread of COVID-19. However, when global lockdown started in March 2020, the world’s bat experts were locked out of their research laboratories, which, in turn, locked up large volumes of...
Article
Full-text available
Despite being nearly 10 months into the COVID-19 (coronavirus disease 2019) pandemic, the definitive animal host for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the causal agent of COVID-19, remains unknown. Unfortunately, similar problems exist for other betacoronaviruses, and no vouchered specimens exist to corroborate host spec...
Article
Full-text available
Natural history collections constitute an enormous wealth of information of Life on Earth. It is estimated that over 2 billion specimens are preserved at institutions worldwide, of which less than 10% are accessible via biodiversity data aggregators such as GBIF. Moreover, they are a very important resource for eco‐evolutionary research, which grea...
Article
North America has more than 4000 bee species, yet we have little information on the health, distribution, and population trends of most of these species. In the United States, what information is available is distributed across multiple institutions, and efforts to track bee populations are largely uncoordinated on a national scale. An overarching...
Article
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...
Article
Full-text available
Data standards allow us to aggregate, compare, compute and communicate data from a wide variety of origins. However, for historical reasons, data are most likely to be stored in many different formats and conform to different models. Every data set might contain a huge amount of information, but it becomes tremendously difficult to compare them wit...
Article
Full-text available
The COVID-19 pandemic has disrupted all aspects of our lives, but has also spawned new opportunities. Months of multidisciplinary, global collaboration have explored the connections between natural history collections and COVID-19. Museums have unrivalled (and still largely untapped) potential to contribute data, methods, and expertise to predictio...
Article
Full-text available
Information about natural history collections helps to map the complex landscape of research resources and assists researchers in locating and contacting the holders of specimens. Collection records contribute to the development of a fully interlinked biodiversity knowledge graph (Page 2016), showcasing the existence and importance of museums and h...
Article
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A deep irony of COVID-19 likely originating from a bat-borne coronavirus (Boni et al. 2020) is that the global lockdown to quell the pandemic also locked up physical access to much basic knowledge regarding bat biology. Digital access to data on the ecology, geography, and taxonomy of potential viral reservoirs, from Southeast Asian horseshoe bats...
Article
Full-text available
Genomic evidence suggests that the causative virus of COVID-19 (SARS-CoV-2) was introduced to humans from horseshoe bats (family Rhinolophidae) (Andersen et al. 2020) and that species in this family as well as in the closely related Hipposideridae and Rhinonycteridae families are reservoirs of several SARS-like coronaviruses (Gouilh et al. 2011). S...
Article
Full-text available
https://www.researchgate.net/deref/https%3A%2F%2Facademic.oup.com%2Fbioscience%2Farticle%2Fdoi%2F10.1093%2Fbiosci%2Fbiaa064%2F5857068
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
Research collections are an important tool for understanding the Earth, its systems, and human interaction. Despite the importance of collections, many are not maintained or curated as thoroughly as we would like. Part of the reason for this is the lack of professional reward for collection, curation, or maintenance. To address this gap in attribut...
Book
Proceedings of the Biodiversity_Next Conference, Leiden 2019
Article
Full-text available
Integrated Digitized Biocollections (iDigBio) is the United States’ (US) national resource and coordinating center for biodiversity specimen digitization and mobilization. It was established in 2011 through the US National Science Foundation’s (NSF) Advancing Digitization of Biodiversity Collections (ADBC) program, an initiative that grew from a wo...
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...
Conference Paper
Full-text available
For the last 15 years, Biodiversity Information Standards (TDWG) has recognized two competing standards for organism occurrence data, ABCD (Access to Biological Collections Data; Holetschek et al. 2012) and DarwinCore (Wieczorek et al. 2012). These two representations emerged from contrasting strategies for mobilizing information about organism occ...
Conference Paper
Full-text available
Aggregating content of museum and scientific collections worldwide offers us the opportunity to realize a virtual museum of our planet and the life upon it through space and time. By mapping specimen-level data records to standards and publishing this information, an increasing number of collections contribute to a digitally accessible wealth of kn...
Article
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Canadensys is an associate GBIF node in Canada, officially established as a node in 2014, but publishing data on GBIF since 2011. Since then, Canadensys has grown from nine institutions to a network of nearly 25 institutions that publish biodiversity data and we have migrated from an in-house explorer, to a Living Atlases (LA) framework. Canadensys...
Article
Full-text available
Research collections are an important tool for understanding the Earth, its systems, and human interaction. Despite the importance of collections, many are not maintained or curated as thoroughly as we would like. Part of the reason for this is the lack of professional reward for collection, curation, or maintenance. To address this gap in attribut...
Article
Full-text available
The expanding availability of access to data about museum specimens, species occurrences, trait data, genetics, and landscapes is revolutionizing biodiversity research. But mobilizing, evaluating, and synthesizing these data to address research questions requires domain-specific computing skills and knowledge. The Carpentries is a global non-profit...
Article
Full-text available
The last 250 years of biodiversity research have produced a wealth of information on the natural world. First locked up in museum drawers or printed publications, in isolated desktop computers or in incompatible digital formats, and in multiple human languages, an increasing proportion is now digitally accessible, thanks to a number of organisation...
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...
Article
Full-text available
Georeferencing is the process of aligning a text description of a geographic location with a spatial location based on a geographic coordinate system. Training aids are commonly created around the georeferencing process to disseminate community standards and ideas, guide accurate georeferencing, inform users about new tools, and help users evaluate...
Article
Full-text available
Much data quality (DQ) feedback is now available to data providers from aggregators of collections specimen and related data. Similarly, transcription centres and crowdsourcing platforms also provide data that must be assessed and often manipulated before uploading to a local database and subsequently published with aggregators. In order to facilit...
Article
Full-text available
Connecting biodiversity data across databases is not as easy as one might think. Different databases use different identifiers and taxonomies and connecting these data often results in loss of information and precision. Here we present some of the challenges we faced with integrating multiple biodiversity data sets, including specimen data from the...
Article
Full-text available
Building on centuries of research based on herbarium specimens gathered through time and around the globe, a new era of discovery, synthesis, and prediction using digitized collections data has begun. This paper provides an overview of how aggregated, open access botanical and associated biological, environmental, and ecological data sets, from gen...
Article
Full-text available
The digitization of biocollections is a critical task with direct implications for the global community who use the data for research and education. Recent innovations to involve citizen scientists in digitization increase awareness of the value of biodiversity specimens; advance science, technology, engineering, and math literacy; and build sustai...
Conference Paper
Full-text available
In this era of global change, early recognition of change in Earth's biota is vital to prevent the loss of biodiversity and ecological health. Biological outliers (e.g., in phenology, distribution, morphology, etc.) may indicate early stages of significant, transformative change that merit immediate attention. As active naturalists, collectors of b...
Article
Full-text available
To access a full text version of this paper plus supplementary materials, navigate to: http://www.bioone.org/toc/apps/3/9 Effective workflows are essential components in the digitization of biodiversity specimen collections. To date, no comprehensive, community-vetted workflows have been published for digitizing flat sheets and packets of plants,...
Article
Full-text available
A goal of the biodiversity research community is to digitize the majority of the one billion specimens in US collections by 2020. Meeting this ambitious goal requires increased collaboration and technological innovation and broader engagement beyond the walls of universities and museums. Engaging the public in digitization promises to both serve th...
Conference Paper
Full-text available
There are an estimated 2 – 3 billion museum specimens world – wide (OECD 1999, Ariño 2010). In an effort to increase the research value of their collections, institutions across the U. S. have been seeking new ways to cost effectively transcribe the label information associated with these specimen collections. Current digitization methods are still...
Conference Paper
The Augmenting OCR Working Group (A-OCR WG) at Integrated Digitized Biocollections (iDigBio) seeks to improve community OCR strategies and algorithms for faster, better parsing of OCR output derived from valuable data on natural history collection specimen labels. This task is exceedingly difficult because museum labels are often annotated, and var...
Article
Full-text available
This paper describes and illustrates five major clusters of related tasks (herein referred to as task clusters) that are common to efficient and effective practices in the digitization of biological specimen data and media. Examples of these clusters come from the observation of diverse digitization processes. The staff of iDigBio (The U.S. Nationa...

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Projects

Projects (2)
Project
ICEDIG – “Innovation and consolidation for large scale digitisation of natural heritage” - is an EU-funded project that aims at supporting the implementation phase of the new Research Infrastructure DiSSCo (“Distributed System of Scientific Collections”) by designing and addressing the technical, financial, policy and governance aspects necessary to operate such a large distributed initiative for natural sciences collections across Europe. more at www.icedig.eu