Biodiversity Informatics https://journals.ku.edu/jbi <p>This electronic journal focuses on the emerging field of biodiversity informatics - the creation, integration, analysis, and understanding of information regarding biological diversity.</p> The University of Kansas en-US Biodiversity Informatics 1546-9735 <p>Copyright for articles published in this journal is retained by the authors, with first publication rights granted to the journal. All articles are licensed under a <a href="https://creativecommons.org/licenses/by-nc/4.0/" target="_blank">Creative Commons Attribution Non-Commercial</a> license.</p> An open-access platform for camera-trapping data https://journals.ku.edu/jbi/article/view/6975 <p>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 (<em>Odocoileus</em> <em>virginianus</em>). 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.</p> Mario César Lavariega ##submission.copyrightStatement## http://creativecommons.org/licenses/by-nc/4.0 2018-02-02 2018-02-02 13 10.17161/bi.v13i0.6975 A metric to quantify analogous conditions and rank environmental layers https://journals.ku.edu/jbi/article/view/6744 <p>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 (<em>y</em> ∝ <em>x</em><sup>-1</sup>), 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 <em>vs. </em>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 <em>ad hoc</em> 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.</p> Peter Lowenberg Neto ##submission.copyrightStatement## http://creativecommons.org/licenses/by-nc/4.0 2018-02-06 2018-02-06 13 10.17161/bi.v13i0.6744 Assessment of biodiversity data holdings and user data needs for Ghana https://journals.ku.edu/jbi/article/view/7108 <p>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.<em></em></p> Alex Asase Gladys O Schwinger ##submission.copyrightStatement## http://creativecommons.org/licenses/by-nc/4.0 2018-03-16 2018-03-16 13 10.17161/bi.v13i0.7108 From theory to practice: a photographic inventory of museum collections to optimize collection management https://journals.ku.edu/jbi/article/view/7036 <p class="p1">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<span class="Apple-converted-space"> </span><em><span class="s1">Calligrapha </span></em>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<span class="Apple-converted-space"> </span><em><span class="s1">Calligrapha </span></em>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.</p> Jonas Merckx Martijn Van Roie Jesús Gómez-Zurita Wouter Dekoninck ##submission.copyrightStatement## http://creativecommons.org/licenses/by-nc/4.0 2018-07-19 2018-07-19 13 10.17161/bi.v13i0.7036 Sample data and training modules for cleaning biodiversity information https://journals.ku.edu/jbi/article/view/7600 <p>Large-scale biodiversity databases have become crucial information sources in many analyses in biogeography, macroecology, and conservation biology, often involving development of empirical models of species’ ecological niches and predictions of their geographic distributions. These analyses, however, can be impaired by the presence of errors, particularly as regards taxonomic identifications and accurate geographic coordinates. Here, we present a detailed data-cleaning exercise based on two contrasting datasets; we link these example data with a step-by-step guide to overcoming these problems and improving data quality for analyses based on these data.</p> Marlon E Cobos Laura Jiménez Claudia Nuñez-Penichet Daniel Romero-Alvarez Marianna Simoes ##submission.copyrightStatement## http://creativecommons.org/licenses/by-nc/4.0 2018-10-24 2018-10-24 13 49 50 10.17161/bi.v13i0.7600