David J. Patterson
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View article: NewsPanda: Media Monitoring for Timely Conservation Action
NewsPanda: Media Monitoring for Timely Conservation Action Open
Non-governmental organizations for environmental conservation have a significant interest in monitoring conservation-related media and getting timely updates about infrastructure construction projects as they may cause massive impact to ke…
View article: A concept for application of integrated digital technologies to enhance future smart agricultural systems
A concept for application of integrated digital technologies to enhance future smart agricultural systems Open
View article: NewsPanda: Media Monitoring for Timely Conservation Action
NewsPanda: Media Monitoring for Timely Conservation Action Open
Non-governmental organizations for environmental conservation have a significant interest in monitoring conservation-related media and getting timely updates about infrastructure construction projects as they may cause massive impact to ke…
View article: Restoring Asia’s roar: Opportunities for tiger recovery across the historic range
Restoring Asia’s roar: Opportunities for tiger recovery across the historic range Open
Wildlife conservation in the Anthropocene requires bold conservation solutions including restoration of ecosystems and species. The recovery of large carnivore populations is a conservation goal which can generate significant benefits in t…
View article: A global assessment of the prevalence of current and potential future infrastructure in Key Biodiversity Areas
A global assessment of the prevalence of current and potential future infrastructure in Key Biodiversity Areas Open
Infrastructure development is a major threat to biodiversity, leading to habitat loss and fragmentation, increased accessibility and pollution. Key Biodiversity Areas represent the most comprehensive network of important areas for biodiver…
View article: Geology and mineralization at Renison Bell, western Tasmania
Geology and mineralization at Renison Bell, western Tasmania Open
Cassiterite mineralization at Renison Bell, Western Tasmania, is spatially and temporally related to the Upper Devonian Pine Hill Granite, and occurs in dolomites and associated elastic sediments of ?Proterozoic to Cambrian age. The sedime…
View article: The scope and scale of the life sciences (‘Nature’s envelope’)
The scope and scale of the life sciences (‘Nature’s envelope’) Open
The extension of biology with a more data-centric component offers new opportunities for discovery. To enable investigations that rely on third-party data, the infrastructure that retains data and allows their re-use should, arguably, enab…
View article: <i>Kinopus chlorellivorus</i> gen. nov., sp. nov. (Vampyrellida, Rhizaria), a New Algivorous Protist Predator Isolated from Large-Scale Outdoor Cultures of <i>Chlorella sorokiniana</i>
<i>Kinopus chlorellivorus</i> gen. nov., sp. nov. (Vampyrellida, Rhizaria), a New Algivorous Protist Predator Isolated from Large-Scale Outdoor Cultures of <i>Chlorella sorokiniana</i> Open
The vampyrellids (Vampyrellida, Rhizaria) are a major group of predatory amoebae that have attracted significant attention because of their diversity of feeding strategies. The crucial roles they play in important processes such as suppres…
View article: Improving the discoverability of biodiversity data using the Global Names Finder
Improving the discoverability of biodiversity data using the Global Names Finder Open
The majority of biodiversity data is not findable, accessible, integratable, or reusable, partially because of a lack of metadata. Taxonomic names as metadata are useful, but not sufficient because these names may be updated as knowledge p…
View article: The scope and scale of the life sciences (‘Nature’s envelope’)
The scope and scale of the life sciences (‘Nature’s envelope’) Open
The extension of biology with a more data-centric component offers new opportunities for discovery. To enable investigations that rely on third-party data, the infrastructure that retains data and allows their re-use should, ideally, enabl…
View article: The Emerging Threat of Extractives Sector to Intact Forest Landscapes
The Emerging Threat of Extractives Sector to Intact Forest Landscapes Open
As demand for commodities increases globally, resource-rich countries are focal areas for industrial expansion. The extractives sector is driving unprecedented growth of infrastructure (e.g., roads, railways and pipelines) into sparsely po…
View article: From Reductionism to Reintegration: Solving society’s most pressing problems requires building bridges between data types across the life sciences
From Reductionism to Reintegration: Solving society’s most pressing problems requires building bridges between data types across the life sciences Open
Decades of reductionist approaches in biology have achieved spectacular progress, but the proliferation of subdisciplines, each with its own technical and social practices regarding data, impedes the growth of the multidisciplinary and int…
View article: Reintegrating biology: A data-centric approach
Reintegrating biology: A data-centric approach Open
Decades of reductionist scientific approaches have led to spectacular progress and the proliferation of biological sub-disciplines, each spawning its own technical and social practices regarding data. This fragmented landscape poses substa…
View article: Acknowledgments
Acknowledgments Open
am grateful to my colleagues at the University of Southampton, especially Mark Everist, for their support during the fi nal preparation of the manuscript.Thanks also to Carol Oja for help with permissions, and to Fred Frith for surrenderin…
View article: Finding scientific names in Biodiversity Heritage Library, or how to shrink Big Data
Finding scientific names in Biodiversity Heritage Library, or how to shrink Big Data Open
The Biodiversity Heritage Library contains 57 million pages of biological information. The majority of this information is a scanned and digitized non-structured text. This "raw" text is hard to access by computers or humans, without the a…
View article: Unifying Biology Through Informatics (UBTI) a new programme of the International Union of Biological Sciences
Unifying Biology Through Informatics (UBTI) a new programme of the International Union of Biological Sciences Open
Biological information, both new and old, is increasingly available in thousands of on-line sites. Biological information relates to elements as small as subatomic particles, and as large as the entire biosphere, and to processes that last…
View article: Beyond the “Code”: A Guide to the Description and Documentation of Biodiversity in Ciliated Protists (Alveolata, Ciliophora)
Beyond the “Code”: A Guide to the Description and Documentation of Biodiversity in Ciliated Protists (Alveolata, Ciliophora) Open
Recent advances in molecular technology have revolutionized research on allaspects of the biology of organisms, including ciliates, and created unprece-dented opportunities for pursuing a more integrative approach to investigationsof biodi…
View article: “gnparser”: a powerful parser for scientific names based on Parsing Expression Grammar
“gnparser”: a powerful parser for scientific names based on Parsing Expression Grammar Open
View article: Copyright and the Use of Images as Biodiversity Data
Copyright and the Use of Images as Biodiversity Data Open
Taxonomy is the discipline responsible for charting the world’s organismic diversity, understanding ancestor/descendant relationships, and organizing all species according to a unified taxonomic classification system. Taxonomists document …
View article: Beyond the “Code”: A Guide to the Description and Documentation of Biodiversity in Ciliated Protists (Alveolata, Ciliophora)
Beyond the “Code”: A Guide to the Description and Documentation of Biodiversity in Ciliated Protists (Alveolata, Ciliophora) Open
Recent advances in molecular technology have revolutionized research on all aspects of the biology of organisms, including ciliates, and created unprecedented opportunities for pursuing a more integrative approach to investigations of biod…
View article: Additional file 1 of â gnparserâ : a powerful parser for scientific names based on Parsing Expression Grammar
Additional file 1 of â gnparserâ : a powerful parser for scientific names based on Parsing Expression Grammar Open
Includes a full and formal explanation of all parser fields as a JSON schema. (JSON 9 kb)
View article: Additional file 4 of â gnparserâ : a powerful parser for scientific names based on Parsing Expression Grammar
Additional file 4 of â gnparserâ : a powerful parser for scientific names based on Parsing Expression Grammar Open
Extensive test suite that describes the parserâ s behavior. It is also a source of examples of parser functionality and output format. Test suite consists of a pipe delimited input (scientific name) and parsed output in JSON format. (TXT 2…
View article: Additional file 3 of â gnparserâ : a powerful parser for scientific names based on Parsing Expression Grammar
Additional file 3 of â gnparserâ : a powerful parser for scientific names based on Parsing Expression Grammar Open
1,000 name-strings randomly selected from GNI and used to determine Accuracy, Precision and Recall data (Table 1). (TXT 32 kb)
View article: Additional file 2 of â gnparserâ : a powerful parser for scientific names based on Parsing Expression Grammar
Additional file 2 of â gnparserâ : a powerful parser for scientific names based on Parsing Expression Grammar Open
README.rst file that is converted to HTML format. It is also available at project home page [44]. (ZIP 7 kb)
View article: Copyright and the Use of Images as Biodiversity Data [Forum paper]
Copyright and the Use of Images as Biodiversity Data [Forum paper] Open
Taxonomy is the discipline responsible for charting the world’s organismic diversity, understanding ancestor/descendant relationships, and organizing all species according to a unified taxonomic classification system. Taxonomists document …
View article: Copyright and the Use of Images as Biodiversity Data
Copyright and the Use of Images as Biodiversity Data Open
1. Abstract Taxonomy is the discipline responsible for charting the world’s organismic diversity, understanding ancestor/descendant relationships, and organizing all species according to a unified taxonomic classification system. Taxonomis…
View article: Report of the Special Committee on Registration of Algal and Plant Names (including fossils)
Report of the Special Committee on Registration of Algal and Plant Names (including fossils) Open
The Special Committee on Registration of Algal and Plant Names (including fossils) was established at the XVIII International Botanical Congress (IBC) in Melbourne in 2011, its mandate being to consider what would be involved in registerin…
View article: (276–279) Proposals to provide for registration of new names and nomenclatural acts
(276–279) Proposals to provide for registration of new names and nomenclatural acts Open
The Melbourne Congress of 2011 authorized a Special Committeeon Registration of Algal and Plant Names (including fossils), whichwas established the following year (Wilson in Taxon 61: 878–879.2012). Its explicit mandate was “to consider wh…
View article: Challenges with using names to link digital biodiversity information
Challenges with using names to link digital biodiversity information Open
The need for a names-based cyber-infrastructure for digital biology is based on the argument that scientific names serve as a standardized metadata system that has been used consistently and near universally for 250 years.As we move toward…
View article: Data Policy Recommendations for Biodiversity Data. EU BON Project Report
Data Policy Recommendations for Biodiversity Data. EU BON Project Report Open
Data Policy Recommendations for Biodiversity Data. EU BON Project Report