Taxonomic informatics tools for the electronic nomenclator zoologicus

Author Posting. © Marine Biological Laboratory , 2006. This article is posted here by permission of Marine Biological Laboratory for personal use, not for redistribution. The definitive version was published in Biological Bulletin 210 (2006): 18-24.Given the current trends, it seems inevitable that all biological documents will eventually exist in a digital format and be distributed across the internet. New network services and tools need to be developed to increase retrieval rates for documents and to refine data recovery. Biological data have traditionally been well managed using taxonomic principles. As part of a larger initiative to build an array of names-based network services that emulate taxonomic principles for managing biological information, we undertook the digitization of a major taxonomic reference text, Nomenclator Zoologicus. The process involved replicating the text to a high level of fidelity, parsing the content for inclusion within a database, developing tools to enable expert input into the product, and integrating the metadata and factual content within taxonomic network services. The result is a high-quality and freely available web application (http://uio.mbl.edu/NomenclatorZoologicus/) capable of being exploited in an array of biological informatics services.This work was supported with funding from the Andrew W. Mellon Foundation and GBIF

Names are key to the big new biology

Author Posting. © The Author(s), 2010. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Trends in Ecology & Evolution 25 (2010): 686-691, doi:10.1016/j.tree.2010.09.004.Those who seek answers to big, broad questions about biology, especially questions emphasizing the organism (taxonomy, evolution, ecology), will soon benefit from an emerging names-based infrastructure. It will draw on the almost universal association of organism names with biological information to index and interconnect information distributed across the Internet. The result will be a virtual data commons, expanding as further data are shared, allowing biology to become more of a “big science”. Informatics devices will exploit this ‘big new biology’, revitalizing comparative biology with a broad perspective to reveal previously inaccessible trends and discontinuities, so helping us to reveal unfamiliar biological truths. Here, we review the first components of this freely available, participatory, and semantic Global Names Architecture.DJP thanks the NSF for support through the Data Conservancy project and the Alfred P. Sloan and John D. and Catherine T. MacArthur foundations for their support

Scientific names of organisms : attribution, rights, and licensing

© The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Research Notes 7 (2014): 79, doi:10.1186/1756-0500-7-79.As biological disciplines extend into the ‘big data’ world, they will need a names-based infrastructure to index and interconnect distributed data. The infrastructure must have access to all names of all organisms if it is to manage all information. Those who compile lists of species hold different views as to the intellectual property rights that apply to the lists. This creates uncertainty that impedes the development of a much-needed infrastructure for sharing biological data in the digital world. The laws in the United States of America and European Union are consistent with the position that scientific names of organisms and their compilation in checklists, classifications or taxonomic revisions are not subject to copyright. Compilations of names, such as classifications or checklists, are not creative in the sense of copyright law. Many content providers desire credit for their efforts. A ‘blue list’ identifies elements of checklists, classifications and monographs to which intellectual property rights do not apply. To promote sharing, authors of taxonomic content, compilers, intermediaries, and aggregators should receive citable recognition for their contributions, with the greatest recognition being given to the originating authors. Mechanisms for achieving this are discussed

UAS-SfM for coastal research : geomorphic feature extraction and land cover classification from high-resolution elevation and optical imagery

© The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Remote Sensing 9 (2017): 1020, doi:10.3390/rs9101020.The vulnerability of coastal systems to hazards such as storms and sea-level rise is typically characterized using a combination of ground and manned airborne systems that have limited spatial or temporal scales. Structure-from-motion (SfM) photogrammetry applied to imagery acquired by unmanned aerial systems (UAS) offers a rapid and inexpensive means to produce high-resolution topographic and visual reflectance datasets that rival existing lidar and imagery standards. Here, we use SfM to produce an elevation point cloud, an orthomosaic, and a digital elevation model (DEM) from data collected by UAS at a beach and wetland site in Massachusetts, USA. We apply existing methods to (a) determine the position of shorelines and foredunes using a feature extraction routine developed for lidar point clouds and (b) map land cover from the rasterized surfaces using a supervised classification routine. In both analyses, we experimentally vary the input datasets to understand the benefits and limitations of UAS-SfM for coastal vulnerability assessment. We find that (a) geomorphic features are extracted from the SfM point cloud with near-continuous coverage and sub-meter precision, better than was possible from a recent lidar dataset covering the same area; and (b) land cover classification is greatly improved by including topographic data with visual reflectance, but changes to resolution (when <50 cm) have little influence on the classification accuracy.This project was funded by the U.S. Geological Survey (USGS) Coastal and Marine Geology Program and the Department of the Interior Northeast Climate Science Center

Transient coastal landscapes : rising sea level threatens salt marshes

© The Author(s), 2018. This is the author's version of the work and is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Science of The Total Environment 640-641 (2018): 1148-1156, doi:10.1016/j.scitotenv.2018.05.235.Salt marshes are important coastal environments that provide key ecological services. As sea level rise has accelerated globally, concerns about the ability of salt marshes to survive submergence are increasing. Previous estimates of likely survival of salt marshes were based on ratios of sea level rise to marsh platform accretion. Here we took advantage of an unusual, long-term (1979-2015), spatially detailed comparison of changes in a representative New England salt marsh to provide an empirical estimate of habitat losses based on actual measurements. We show prominent changes in habitat mosaic within the marsh, consistent and coincident with increased submergence and coastal erosion. Model results suggest that at current rates of sea level rise, marsh platform accretion, habitat loss, and with the limitation of the widespread “coastal squeeze”, the entire ecosystem might disappear by the beginning of the next century, a fate that might be likely for many salt marshes elsewhere.Ivan Valiela and Elizabeth Elmstrom were supported by Woods Hole Sea Grant, NOAA grant no. NA14OAR4170074. Javier Lloret was supported by a Rosenthal Postdoctoral Fellowship Award from the Marine Biological Laboratory, and by a Northeast Climate Science Center Fellowship. Tynan Bowyer was supported by a Metcalf Research Fellowship of the University of Chicago. David Remsen was supported by MBL Cox and Bernstein funds.2020-06-0

Taxonomic indexing—extending the role of taxonomy

Author Posting. © Society of Systematic Biologists, 2006. This article is posted here by permission of Society of Systematic Biologists for personal use, not for redistribution. The definitive version was published in Systematic Biology 55 (2006): 367-373, doi: 10.1080/10635150500541680.Taxonomic indexing refers to a new array of taxonomically intelligent network services that use nomenclatural principles and elements of expert taxonomic knowledge to manage information about organisms. Taxonomic indexing was introduced to help manage the increasing amounts of digital information about biology. It has been designed to form a near basal layer in a layered cyberinfrastructure that deals with biological information. Taxonomic Indexing accommodates the special problems of using names of organisms to index biological material. It links alternative names for the same entity (reconciliation), and distinguishes between uses of the same name for different entities (disambiguation), and names are placed within an indefinite number of hierarchical schemes. In order to access all information on all organisms, Taxonomic indexing must be able to call on a registry of all names in all forms for all organisms. NameBank has been developed to meet that need. Taxonomic indexing is an area of informatics that overlaps with taxonomy, is dependent on the expert input of taxonomists, and reveals the relevance of the discipline to a wide audience

Location, location, location: utilizing pipelines and services to more effectively georeference the world's biodiversity data

Abstract Background Increasing the quantity and quality of data is a key goal of biodiversity informatics, leading to increased fitness for use in scientific research and beyond. This goal is impeded by a legacy of geographic locality descriptions associated with biodiversity records that are often heterogeneous and not in a map-ready format. The biodiversity informatics community has developed best practices and tools that provide the means to do retrospective georeferencing (e.g., the BioGeomancer toolkit), a process that converts heterogeneous descriptions into geographic coordinates and a measurement of spatial uncertainty. Even with these methods and tools, data publishers are faced with the immensely time-consuming task of vetting georeferenced localities. Furthermore, it is likely that overlap in georeferencing effort is occurring across data publishers. Solutions are needed that help publishers more effectively georeference their records, verify their quality, and eliminate the duplication of effort across publishers. Results We have developed a tool called BioGeoBIF, which incorporates the high throughput and standardized georeferencing methods of BioGeomancer into a beginning-to-end workflow. Custodians who publish their data to the Global Biodiversity Information Facility (GBIF) can use this system to improve the quantity and quality of their georeferences. BioGeoBIF harvests records directly from the publishers' access points, georeferences the records using the BioGeomancer web-service, and makes results available to data managers for inclusion at the source. Using a web-based, password-protected, group management system for each data publisher, we leave data ownership, management, and vetting responsibilities with the managers and collaborators of each data set. We also minimize the georeferencing task, by combining and storing unique textual localities from all registered data access points, and dynamically linking that information to the password protected record information for each publisher. Conclusion We have developed one of the first examples of services that can help create higher quality data for publishers mediated through the Global Biodiversity Information Facility and its data portal. This service is one step towards solving many problems of data quality in the growing field of biodiversity informatics. We envision future improvements to our service that include faster results returns and inclusion of more georeferencing engines

Local Extinction in the Bird Assemblage in the Greater Beijing Area from 1877 to 2006

Recent growth in industrialization and the modernization of agricultural activities, combined with human population growth, has greatly modified China’s natural environment, particularly in the vicinity of large cities. We compared avifauna checklists made between 1877 and 1938 with current checklists to determine the extent of local bird extinctions during the last century in the greater Beijing area. Our study shows that of the 411 bird species recorded from 1877–1938, 45 (10.9%) were no longer recorded from 2004–2006. Birds recorded as ‘rare’ in 1938 were more likely to have disappeared in subsequent years. Migrant status also influenced the probability of local bird extinction with winter migrants being the most affected class. Moreover, larger birds were more likely to have disappeared than smaller ones, potentially explained by differential ecological requirements and anthropogenic exploitation. Although our habitat descriptions and diet classification were not predictors of local bird extinction, the ecological processes driving local bird extinction are discussed in the light of historical changes that have impacted this region since the end of the 1930 s. Our results are of importance to the broader conservation of bird wildlife