Biodiversity Informatics最新文献

{"title":"From theory to practice: a photographic inventory of museum collections to optimize collection management","authors":"Jonas Merckx, Martijn Van Roie, J. Gómez‐Zurita, W. Dekoninck","doi":"10.17161/BI.V13I0.7036","DOIUrl":"https://doi.org/10.17161/BI.V13I0.7036","url":null,"abstract":"The digitization of museum specimens is a key priority in the Digital Era. Digital databases help to avoid unnecessary manipulation hazards to delicate collections, increase their accessibility to third party researchers, and contribute to the ongoing documentation of global biodiversity. Time, workforce and the need of specialized infrastructures limit the processing of the vast number of specimens in natural history collections. Cheaper, easy-to-use methods and volunteer programs are developing quickly to help bridge the gap. We present the results of combining citizen science for the digitization of an entomological collection in conjunction with the cooperation of a taxonomic expert for the remote identification of samples. In addition, we provide an assessment of the avoided monetary costs and the time needed for each step of the process. A photographic inventory of specimens belonging to the leaf beetle genus Calligrapha was compiled by volunteers using a low-cost compact camera and the species were identified using these images. Using digital photographs allowed for a rapid screening of specimens in the collection and resulted in an updated taxonomic identification of the Calligrapha collection at the Royal Belgian Institute of Natural Sciences. The pictures of the specimens and their original labels, as well as the new information from this endeavor were placed in an online public catalogue. This study demonstrates a worked example of how digitization has led to a practical, useful outcome through cooperation with an end user and highlights the value of museum collection digitization projects.","PeriodicalId":269455,"journal":{"name":"Biodiversity Informatics","volume":"20 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129512450","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assessment of biodiversity data holdings and user data needs for Ghana","authors":"A. Asase, Gladys Schwinger","doi":"10.17161/BI.V13I0.7108","DOIUrl":"https://doi.org/10.17161/BI.V13I0.7108","url":null,"abstract":"Data on biodiversity are important to addressing the challenges of sustainable development, and for decision-making about natural resources and environments. Biodiversity information, when mobilized and shared openly, has the potential to impact science and conservation positively. However, biodiversity data mobilization is expensive, such that data mobilization and sharing activities must be prioritized to meet the needs of the user community. In this study, we undertook a detailed assessment of biodiversity data holdings and user needs in Ghana through semi-structured questionnaire interviews, and focus-group discussions in the form of a workshop. Most biodiversity data-holding organizations were at preliminary stages of digital biodiversity data mobilization and sharing. Taxonomic, checklist, and geographic data on plants and animals were identified as most needed. Priority thematic needs were as regards protected areas, invasive alien species, threatened species, economic species (timber and non-timber forest products), and pathogens and diseases. Human and infrastructural capacities, and sustainable coordination were identified as the major challenges to biodiversity data management. This study provides a detailed case study of how assessing biodiversity data holdings and user data needs can be used to strategize biodiversity data mobilization, data publication, and data use activities.","PeriodicalId":269455,"journal":{"name":"Biodiversity Informatics","volume":"30 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129293849","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A metric to quantify analogous conditions and rank environmental layers","authors":"Peter Lowenberg Neto","doi":"10.17161/bi.v13i0.6744","DOIUrl":"https://doi.org/10.17161/bi.v13i0.6744","url":null,"abstract":"Analogous conditions in environmental variables are expected because environments are spatially autocorrelated and often present similar combinations over geographic space. That similar environmental combinations may be found at different localities provides a crucial basis for correlative species distribution modeling. An absolutely analogous variable is constant, while a non-analogous variable has no-repeating values, yet no current method allows researchers to quantify intermediate degrees of analogous conditions and rank environmental layers. I approached this issue from the perspective of dual-space correspondence, in which (a) variable range and modal frequency have a theoretical inverse relationship ( y ∝ x -1 ), and (b) modal values of frequency are limited by the number of pixels in a given raster layer. For two geographic extents and two resolutions (2.5’ and 10’), I obtained range and modal frequency of 19 bioclimatic variables and 5 reference variables. Then, I measured Euclidean distances from candidate variables to the non-analogous variable as a metric for degree of analogous conditions, which were used to rank variables. Bioclimatic layers were plotted in log-log scatterplots of range vs. modal frequency; variables were located inside the upper-right triangle (except for one set), and no layer fit the inverse model. Temperature variables presented higher degrees of analogous conditions than precipitation for South America and the Araucaria Moist Forests ecoregion. Geographic extent and pixel resolution changed the degree of analogous conditions of derived variables (quarterly and monthly); however, a pattern of change was not observed, which suggested ad hoc hypotheses on geographic and temporal idiosyncrasies. Variables with high contribution in previous SDM/ENM studies (e.g., temperature seasonality and annual precipitation) showed low degree of analogous conditions. It is expected that heterogeneous layers would generate better correlational geographic distributional predictions than analogous variables, even though this hypothesis remains untested. Ranking layers can provide grounds for selecting variables in distribution and niche modeling, particularly as regards interpreting spatial projection and transferability. Alternatively, ranking can be used to compare degrees of analogous conditions of the same layer in different time spans.","PeriodicalId":269455,"journal":{"name":"Biodiversity Informatics","volume":"6 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129960530","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An open-access platform for camera-trapping data","authors":"M. Lavariega","doi":"10.17161/BI.V13I0.6975","DOIUrl":"https://doi.org/10.17161/BI.V13I0.6975","url":null,"abstract":"In southern Mexico, local communities have been playing important roles in the design and collection of wildlife data through camera-trapping in community-based monitoring of biodiversity projects. However, the methods used to store the data have limited their use in matters of decision-making and research. Thus, we present the Platform for Community-based Monitoring of Biodiversity (PCMB), a repository, which allows storage, visualization, and downloading of photographs captured by community-based monitoring of biodiversity projects in protected areas of southern Mexico. The platform was developed using agile software development with extensive interaction between computer scientists and biologists. System development included gathering data, design, built, database and attributes creation, and quality control. The PCMB currently contains 28,180 images of 6478 animals (69.4% mammals and 30.3% birds). Of the 32 species of mammals recorded in 18 PA since 2012, approximately a quarter of all photographs were of white-tailed deer ( Odocoileus virginianus ). Platforms permitting access to camera-trapping data are a valuable step in opening access to data of biodiversity; the PCMB is a practical new tool for wildlife management and research with data generated through local participation. Thus, this work encourages research on the data generated through the community-based monitoring of biodiversity projects in protected areas, to provide an important information infrastructure for effective management and conservation of wildlife.","PeriodicalId":269455,"journal":{"name":"Biodiversity Informatics","volume":"264 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129177472","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Botanical Sampling Gaps Across the Cameroon Mountains","authors":"M. Sainge, J. Onana, F. Nchu, D. Kenfack, A. Peterson","doi":"10.17161/BI.V12I0.6707","DOIUrl":"https://doi.org/10.17161/BI.V12I0.6707","url":null,"abstract":"With the emergence of a new field, biodiversity informatics, an important task has been to evaluate completeness of biodiversity information that is existing and available for various countries and regions. This paper offers a first and very basic assessment of sampling gaps and inventory completeness across the Cameroon Mountains. Because digital accessible knowledge is severely limited for the region, we relied on qualitative evaluations of inventory completeness, supplemented by large amounts of data from the National Herbarium of Cameroon (YA) database. Detailed botanical inventories have been developed for Mt Cameroon, the Kupe-Mwanenguba Mountains, Mt Oku, and the Mambila Plateau, leaving substantial geographic and environmental coverage gaps corresponding to Rumpi Hills, Mt Nlonako, Kimbi Fungom National Park, Bali and Bafut Ngemba, Mt Bamboutos, Kagwene, and Tchabal Mbabo. This paper provides a roadmap for a comprehensive botanical survey for this region. Completing this survey plan, the resulting data will allow researchers to track changes in biodiversity and identify priority areas for conservation on the various mountain ranges that make up this important biodiversity hotspot.","PeriodicalId":269455,"journal":{"name":"Biodiversity Informatics","volume":"24 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115645445","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Crowdsourcing Natural History Archives: Tools for Extracting Transcriptions and Data","authors":"Katherine Mika, J. D. Veer, Constance A. Rinaldo","doi":"10.17161/BI.V12I0.6646","DOIUrl":"https://doi.org/10.17161/BI.V12I0.6646","url":null,"abstract":"This paper is a survey of the landscape of current, successful, and innovative platforms for extracting full text transcriptions and structured data using crowdsourcing as a tool. Archival manuscript items are the key case studies reviewed to develop a set of tools for the Biodiversity Heritage Library for use in enhancing access to and extraction information from items in scientific and natural history collections.","PeriodicalId":269455,"journal":{"name":"Biodiversity Informatics","volume":" 21","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132158324","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"IRMNG 2006–2016: 10 Years of a Global Taxonomic Database","authors":"Anthony J. J. (Tony) Rees, L. Vandepitte, W. Decock, B. Vanhoorne","doi":"10.17161/BI.V12I0.6522","DOIUrl":"https://doi.org/10.17161/BI.V12I0.6522","url":null,"abstract":"IRMNG, the Interim Register of Marine and Nonmarine Genera, was commenced in 2006 as an initiative of the Australian OBIS Node (OBIS Australia) following an analysis of the taxonomic names management needs of the Ocean Biogeographic Information System (OBIS). The main objectives were to produce a hierarchical classification of all life, both extant and fossil, to at least generic level (and to species as data were readily available) and to provide a tool to distinguish marine from nonmarine, and extant from fossil taxa. Over its first 10 years of operation IRMNG has acquired almost 487,000 of an estimated 510,000 published genus names (including both valid names and synonyms) in addition to almost 1.8 million species names, of which 1.3 million are considered valid. Throughout this time IRMNG data have been available for public query via a dedicated web interface based at CSIRO in Australia, as well as being supplied as bulk downloads for use by a range of global biodiversity projects. Over the period 2014-2016 responsibility for the system has been passed to the Data Centre Division of the Flanders Marine Institute (VLIZ) in Belgium, which is continuing the maintenance and development of IRMNG at its new web location, www.irmng.org . With its present estimated holdings of >95% of all published genus names (plus associated authorities and years of publication) across all taxonomic domains, including fossil as well as extant taxa, within an internally consistent taxonomic hierarchy, IRMNG is at present uniquely placed to provide an overview of “all life” to at least generic level, to permit the discovery of trends in publication of genera through time, to provide preliminary information on the marine vs. nonmarine and extant vs. fossil status of the taxa concerned, and to generate lists of both unique and non-unique names (homonyms sensu lato ) for the benefit of users of biodiversity data.","PeriodicalId":269455,"journal":{"name":"Biodiversity Informatics","volume":"98 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127281672","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Introducción a los Análisis Espaciales con Énfasis en Modelos de Nicho Ecológico","authors":"Angela P. Cuervo-Robayo, L. Escobar, Luis Osorio-Olvera, Javier Nori, Sara Varela, E. Martínez-Meyer, J. Velásquez-Tibatá, Clarita Rodríguez-Soto, M. Munguía, Nora P. Castañeda-Álvarez, A. Lira-Noriega, Mariano Soley-Guardia, Josep M. Serra-Diaz, A. Peterson","doi":"10.17161/BI.V12I0.6507","DOIUrl":"https://doi.org/10.17161/BI.V12I0.6507","url":null,"abstract":"En 2016 implementamos un sistema de seminarios de ensenanza, en formato de videos libres y accesibles desde internet, con la finalidad de dar a conocer de forma sencilla y en castellano, las bases conceptuales y aplicaciones de los modelos de nicho ecologico en estudios de ecologia, conservacion biologica, epidemiologia y agrobiodviersidad, asi como su implementacion para el diseno de politicas publicas de los recursos naturales. Cada seminario fue desarrollado por uno o varios expertos discutiendo conceptos, metodos y diferentes herramientas disponibles para elaborar modelos de distribucion de especies. Este manuscrito reune los resumenes de cada uno de los seminarios en linea, dando referencias clave para cada tema y el enlace al video correspondiente. Los videos estan disponibles de forma libre en YouTube o en formato .mp4 bajo solicitud.","PeriodicalId":269455,"journal":{"name":"Biodiversity Informatics","volume":"55 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131507265","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rescuing and Sharing Historical Vegetation Data for Ecological Analysis: The California Vegetation Type Mapping Project","authors":"M. Kelly","doi":"10.17161/BI.V11I1.5886","DOIUrl":"https://doi.org/10.17161/BI.V11I1.5886","url":null,"abstract":"Research efforts that synthesize historical and contemporary ecological data with modeling approaches improve our understanding of the complex response of species, communities, and landscapes to changing biophysical conditions through time and in space. Historical ecological data are particularly important in this respect. There are remaining barriers that limit such data synthesis, and technological improvements that make multiple diverse datasets more readily available for integration and synthesis are needed. This paper presents one case study of the Wieslander Vegetation Type Mapping project in California and highlights the importance of rescuing, digitizing and sharing historical datasets. We review the varied ecological uses of the historical collection: the vegetation maps have been used to understand legacies of land use change and plan for the future; the plot data have been used to examine changes to chaparral and forest communities around the state and to predict community structure and shifts under a changing climate; the photographs have been used to understand changing vegetation structure; and the voucher specimens in combination with other specimen collections have been used for large scale distribution modeling efforts. The digitization and sharing of the data via the web has broadened the scope and scale of the types of analysis performed. Yet, additional research avenues can be pursued using multiple types of VTM data, and by linking VTM data with contemporary data. The digital VTM collection is an example of a data infrastructure that expands the potential of large scale research through the integration and synthesis of data drawn from numerous data sources; its journey from analog to digital is a cautionary tale of the importance of finding historical data, digitizing it with best practices, linking it with other datasets, and sharing it with the research community.","PeriodicalId":269455,"journal":{"name":"Biodiversity Informatics","volume":"299 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132718918","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Completeness of Digital Accessible Knowledge of Plants of Benin and Priorities for Future Inventory and Data Discovery","authors":"J. Ganglo, Sunday Berlioz Kakpo","doi":"10.17161/BI.V11I0.5053","DOIUrl":"https://doi.org/10.17161/BI.V11I0.5053","url":null,"abstract":"Discovery of and access to primary biodiversity data are critical components in informed decision-making regarding sustainable use of biological resources and conservation of biodiversity. Primary biodiversity data are increasingly available from Benin, but information about completeness of this information across the country is still lacking for most groups. This study analyzed the Digital Accessible Knowledge regarding the plants of Benin to identify gaps in both geographic and environmental dimensions. Many gaps exist in plant data for Benin, particularly in the northern most departments; central and southern Benin are better known, but some gaps remain even there. The resulting view of Beninese Digital Accessible Knowledge can guide future inventory and data discovery efforts.","PeriodicalId":269455,"journal":{"name":"Biodiversity Informatics","volume":"65 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130967127","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}