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CETAF-DiSSCo/COVID19-TAF biodiversity-related knowledge hub working group: indexed biotic interactions and review summary
<p>This data publication originated as part of developing a biodiversity-related knowledge hub on COVID-19 via COVID19-TAF - Communities Taking Action (https://cetaf.org/covid19-taf-communities-taking-action), a community-rooted initiative raised jointly by the Consortium of European Taxonomic Facilitaties (CETAF, https://cetaf.org) and Distributed Systems of Scientific Collections (DiSSCo, https://www.dissco.eu/).</p> <p>This archive contains the biodiversity datasets of interest identified in period 14 April-6 October 2020 through COVID19-TAF activities and subsequently indexed by Global Biotic Interactions (GloBI, https://globalbioticinteractions.org). GloBI provides open access to finding species interaction data (e.g., predator-prey, pollinator-plant, virus-host, parasite-host) by combining existing open datasets using open source software.</p> <p>These identified datasets (see references and reviews below) add to a growing collection of open species interaction datasets already indexed by GloBI. So, this data publication only includes a small subset of indexed datasets and include only datasets that were added as a direct consequence of COVID19-TAF activities of the biodiversity-related knowledge hub working group.</p> <p>If you have questions or comments about this publication, please open an issue at https://github.com/ParasiteTracker/tpt-reporting or contact the authors by email.</p> <p>Funding:<br> The creation of this archive was made possible in part by reporting software developed as part of the National Science Foundation award "Collaborative Research: Digitization TCN: Digitizing collections to trace parasite-host associations and predict the spread of vector-borne disease," Award numbers DBI:1901932 and DBI:1901926 . Also, this material is based upon work supported by the National Science Foundation under Grant No. DGE-1545433 .</p> <p>References:<br> Jorrit H. Poelen, James D. Simons and Chris J. Mungall. (2014). Global Biotic Interactions: An open infrastructure to share and analyze species-interaction datasets. Ecological Informatics. https://doi.org/10.1016/j.ecoinf.2014.08.005.</p> <p>GloBI Data Review Report</p> <p>Datasets under review:<br> - Geiselman, Cullen K. & Sarah Younger. 2020. Bat Eco-Interactions Database. www.batbase.org accessed via https://github.com/globalbioticinteractions/batbase/archive/9c65cfeee1a054f9db8cd8bf6892017fd1b3c840.zip on 2020-10-04T22:53:45.576Z<br> - Geiselman, Cullen K. and Tuli I. Defex. 2015. Bat Eco-Interactions Database. www.batplant.org accessed via https://github.com/globalbioticinteractions/batplant/archive/a2e1b57052244d5251d17e96ea61f58bea88975e.zip on 2020-10-04T22:54:28.727Z<br> - Daniel Becker, Gregory F Albery, Anna R Sjodin, Timothee Poisot, Tad Dallas, Evan A. Eskew, Maxwell J. Farrell, Sarah Guth, Barbara A Han, Nancy B Simmons, Colin J Carlson. 2020. Predicting wildlife hosts of betacoronaviruses for SARS-CoV-2 sampling prioritization. bioRxiv 2020.05.22.111344; doi: https://doi.org/10.1101/2020.05.22.111344 accessed via https://github.com/globalbioticinteractions/becker2020/archive/47c6ad28e1c5058f3c13ca69a59fdf21229e8d7f.zip on 2020-10-04T22:54:46.723Z<br> - Chen L, Liu B, Yang J, Jin Q, 2014. DBatVir: the database of bat-associated viruses. Database (Oxford). 2014:bau021. doi:10.1093/database/bau021 accessed via https://github.com/globalbioticinteractions/dbatvir/archive/a906d76e362484d3ca1edbe9683f672838ab70b0.zip on 2020-10-04T22:56:13.913Z<br> - Chen L, Liu B, Wu Z, Jin Q, Yang J, 2017. DRodVir: A resource for exploring the virome diversity in rodents. J Genet Genomics. 44(5):259-264. accessed via https://github.com/globalbioticinteractions/drodvir/archive/0346c0e8d4d66c6400e9965bd6a6aeed24cd7586.zip on 2020-10-04T23:06:04.368Z<br> - Agosti, Donat. 2020. Transcription of Linné, C. von, 1758. Systema naturae per regna tria naturae secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Available at: http://dx.doi.org/10.5962/bhl.title.542 . accessed via https://github.com/globalbioticinteractions/linnaeus1758/archive/a818060080fa04a88dac6df1ae5b897304ae8877.zip on 2020-10-05T00:46:04.852Z<br> - Mollentze, Nardus, & Streicker, Daniel G. (2019). Viral zoonotic risk is homogenous among taxonomic orders of mammalian and avian reservoir hosts (Version 1.0.0) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.3516613 accessed via https://github.com/globalbioticinteractions/mollentze2019/archive/ad12dc74d03c3d992618f16c37cafb7f7ffd9d01.zip on 2020-10-05T00:50:55.878Z<br> - Eneida L. Hatcher, Sergey A. Zhdanov, Yiming Bao, Olga Blinkova, Eric P. Nawrocki, Yuri Ostapchuck, Alejandro A. Schäffer, J. Rodney Brister, Virus Variation Resource – improved response to emergent viral outbreaks, Nucleic Acids Research, Volume 45, Issue D1, January 2017, Pages D482–D490, https://doi.org/10.1093/nar/gkw1065 . accessed via https://github.com/globalbioticinteractions/ncbi-virus/archive/531a8d743d7adcf1153a19087e5d3c5b76750e3e.zip on 2020-10-05T00:53:53.646Z<br> - Olival, K. J., Hosseini, P. R., Zambrana-Torrelio, C., Ross, N., Bogich, T. L., & Daszak, P. (2017). Host and viral traits predict zoonotic spillover from mammals. Nature, 546(7660), 646–650. doi:10.1038/nature22975 accessed via https://github.com/globalbioticinteractions/olival2017/archive/f61070a5339d0e6c6e76d7eb4e2102decb52317d.zip on 2020-10-05T00:56:43.356Z<br> - Pensoft Darwin Core Archives with associateTaxa columns accessed via https://github.com/globalbioticinteractions/pensoft-dwca/archive/ee8831a2a391203f4fa8c05a0ddd927202b234bf.zip on 2020-10-05T00:56:51.868Z<br> - Pensoft Darwin Core Archives available via Integrated Publication Toolkit accessed via https://github.com/globalbioticinteractions/pensoft-ipt/archive/4ad4b47978324681289e36f8c2b247b1bcc97b1a.zip on 2020-10-05T00:58:01.912Z<br> - De Rojas M, Doña J, Dimov I (2020) A comprehensive survey of Rhinonyssid mites (Mesostigmata: Rhinonyssidae) in Northwest Russia: New mite-host associations and prevalence data. Biodiversity Data Journal 8: e49535. https://doi.org/10.3897/BDJ.8.e49535 accessed via https://github.com/globalbioticinteractions/pensoft-table/archive/3488e0397ca4e083d5eca6949951e426a75713e3.zip on 2020-10-05T00:58:03.647Z<br> - Marcus Guidoti, Tatiana Ruschel, Donat Agosti. 2020. Corona virus related biotic associations manually extracted from literature. Plazi. accessed via https://github.com/globalbioticinteractions/plazi-covid19/archive/326578b0d9f974760dcd2e962d86636a6487a6c0.zip on 2020-10-05T00:58:08.025Z<br> - Shaw, LP, Wang, AD, Dylus, D, et al. The phylogenetic range of bacterial and viral pathogens of vertebrates. Mol Ecol. 2020; 29: 3361– 3379. https://doi.org/10.1111/mec.15463 accessed via https://github.com/globalbioticinteractions/shaw2020/archive/bb9ab857b7fdbb4e931752d01b43d37b3ada77cf.zip on 2020-10-05T01:05:23.554Z<br> - OpenBiodiv. 2020. Annotated biotic interaction tables from Pensoft publications. accessed via https://github.com/pensoft/pensoft-interaction-tables/archive/bb7d1dc9f2eba220a61502e06e6114053fd30788.zip on 2020-10-05T03:03:23.372Z<br> - Quentin J. Groom. 2020. Bat interation data manually extracted from literature. accessed via https://github.com/qgroom/batinterations/archive/70108945f9014aa0ac1db920191867f7e151c793.zip on 2020-10-05T03:04:11.533Z</p> <p>Generated on:<br> 2020-10-06</p> <p>by:<br> GloBI's Elton 0.10.2<br> (see https://github.com/globalbioticinteractions/elton).</p> <p> </p> <p>Note that all files ending with .tsv are files formatted<br> as UTF8 encoded tab-separated values files.</p> <p>https://www.iana.org/assignments/media-types/text/tab-separated-values</p> <p><br> Included in this review archive are:</p> <p>README:<br> This file.</p> <p>review_summary.tsv:<br> Summary across all reviewed collections of total number of distinct review comments.</p> <p>review_summary_by_collection.tsv:<br> Summary by reviewed collection of total number of distinct review comments.</p> <p>indexed_interactions_by_collection.tsv:<br> Summary of number of indexed interaction records by institutionCode and collectionCode.</p> <p>review_comments.tsv.gz:<br> All review comments by collection.</p> <p>indexed_interactions_full.tsv.gz:<br> All indexed interactions for all reviewed collections.</p> <p>indexed_interactions_simple.tsv.gz:<br> All indexed interactions for all reviewed collections selecting only sourceInstitutionCode, sourceCollectionCode, sourceCatalogNumber, sourceTaxonName, interactionTypeName and targetTaxonName.</p> <p>datasets_under_review.tsv:<br> Details on the datasets under review.</p> <p>elton.jar:<br> Program used to update datasets and generate the review reports and associated indexed interactions.</p> <p><br> datasets.zip:<br> source datasets collected by elton in process of executing the generate_report.sh script.</p> <p>generate_report.sh:<br> program used to generate the report</p> <p>generate_report.log:<br> log file generated as part of running the generate_report.sh script</p>
NICHE Flanders: reference values for the (a)biotic requirements of vegetation types in Flanders, Belgium
<p>This dataset contains site requirements/tolerance limits (or "reference values") for 28 vegetation types found in Flanders. It gives the lower and upper limits or the classes within which these vegetation types can occur, for 7 site factors that determine potential vegetation development. These reference values can be used to determine the potential distribution of the different vegetation types with the ecohydrological model NICHE Flanders (<a href="https://purews.inbo.be/ws/portalfiles/portal/5370206/Callebaut_etal_2007_NicheVlaanderen.pdf">Callebaut et al. 2007</a>, in Dutch).</p> <p>See the Technical info (available in English and Dutch) for more information.</p>
Supplementary material to: Long-term (bio)deterioration of Fe-containing and Fe-depleted sandstones: An experimental insight into biotic and abiotic interactions.
<p>This dataset includes: micorphotographs, scanning electron microscope images and related EDS spectra, thermal analysis (DSC-TG), grain size distribution. Abbreviations used in the supplementary file names refer to: GMB (growth medium inoculated with the bacteria, Pseudomonas fluorescens), GM (sterile growth medium), ARE (artificial root exudates), H2O (water), NR (Sample Nowa Ruda), Z (Sample Żerkowice ŻR).</p>
The Blue Carbon of Southern South West Atlantic salt marshes and their biotic and abiotic drivers
<p>Organic carbon stocks, salt marsh plant biomass, crab burrow abundances and diameters. This data was generated by sampling at 11 salt marsh sites along 3000 km of coastal line in southern SW Atlantic coast in South America. Organic carbon stocks and burial rates extarcted from other publications and used to update global estimates are also included with their respective references. Values of biotic and abiotic drivers included in the Structural Equation Model (SEM) to evaluate their roles in belowground organic carbon stocks.</p>
Bee Interaction Data from Global Biotic Interactions
<p>New versions of this dataset are found at: <a href="https://doi.org/10.5281/zenodo.16689326">https://doi.org/10.5281/zenodo.16689326</a></p> <p> </p> <p>This repository includes the following:</p> <ol> <li><strong>interactions-GloBI-September-14-2021.tsv.gz</strong>: a full version of the Global Biotic Interactions downloaded on September 14, 2021. No data transformations have occurred on this dataset after the download</li> <li><strong>globi_bee_data.sh</strong>: Shell script for extracting bee records using bee family names from the full version of Global Biotic Interactions</li> <li><strong>all_bee_data_unique.txt</strong>: a file that includes only bee interactions, based on extracting bee names from interactions-GloBI-September-14-2021.tsv.gz</li> </ol> <p>Global Biotic Interactions (GloBI - https://globalbioticinteractions.org) aims to simplify access to existing records of species interactions, such as predator-prey, plant-pollinator, and virus-host interactions. To achieve this, GloBI follows a process where existing, versioned datasets on species interactions are transformed into various aggregate formats, including tsv, csv, neo4j, rdf/nquad, and darwin core-ish archives, with applied name maps included for explicit taxonomic linking.</p> <p>GloBI owes its success to researchers, collections, projects, and institutions that openly share their datasets. Whenever you use this data, please credit the original data contributors, including citing the specific datasets used in derivative work. Each species interaction record in GloBI is linked to a reference and dataset citation. If you have any suggestions on how to make it easier to cite original datasets, you are welcome to join a discussion on https://globalbioticinteractions.org or related projects.</p> <p><strong>Introduction to Global Bee Interaction Data</strong></p> <p>The dataset available here includes all bee interactions recorded in the <a href="https://www.globalbioticinteractions.org/">Global Biotic Interactions</a> (GloBI; Poelen et al. 2014) index as of September 21, 2021. These interactions are gathered quarterly by the <a href="http://big-bee.net/">Big Bee Project </a>(Seltmann et al. 2021) from various sources, including natural history collections, community science observations (such as iNaturalist), and scientific literature. The dataset covers a wide range of bee interactions, including flower visitation, parasitic interactions (such as mite and viral interactions), and lecty, among others. The dataset is filtered for unique records based on interaction description and source citation to ensure accuracy and consistency. For other versions of the bee interaction dataset, please refer to <a href="https://zenodo.org/record/7315159">Seltmann, 2022</a>.</p> <p><strong>Data Description</strong><br>Please see the <a href="https://www.globalbioticinteractions.org/process">integration process page</a> to better understand how Global Biotic Interactions combines datasets from various sources. The complete interaction dataset for all species can be accessed via <a href="https://www.globalbioticinteractions.org/data">https://www.globalbioticinteractions.org/data</a> and the <a href="https://doi.org/10.5281/zenodo.3950589">GloBI Community Zenodo publication</a>.</p> <p><strong>Dataset column names</strong> definitions <a href="https://api.globalbioticinteractions.org/interactionFields">https://api.globalbioticinteractions.org/interactionFields</a> or <a href="https://api.globalbioticinteractions.org/interactionFields">https://api.globalbioticinteractions.org/interactionFields</a></p> <p><strong>References</strong></p> <p>Jorrit H. Poelen, James D. Simons and Chris J. Mungall. (2014). Global Biotic Interactions: An open infrastructure to share and analyze species-interaction datasets. Ecological Informatics. <a href="https://doi.org/10.1016/j.ecoinf.2014.08.005">https://doi.org/10.1016/j.ecoinf.2014.08.005</a></p> <p>Katja C. Seltmann. (2022). Global Bee Interaction Data (v2.02) [Data set]. Zenodo. <a href="https://doi.org/10.5281/zenodo.7315159">https://doi.org/10.5281/zenodo.7315159</a></p> <p>Seltmann KC, Allen J, Brown BV, Carper A, Engel MS, Franz N, Gilbert E, Grinter C, Gonzalez VH, Horsley P, Lee S, Maier C, Miko I, Morris P, Oboyski P, Pierce NE, Poelen J, Scott VL, Smith M, Talamas EJ, Tsutsui ND, Tucker E (2021) Announcing Big-Bee: An initiative to promote understanding of bees through image and trait digitization. Biodiversity Information Science and Standards 5: e74037. <a href="https://doi.org/10.3897/biss.5.74037">https://doi.org/10.3897/biss.5.74037</a></p>
Big Bee indexed biotic interactions and review summary
<p><strong>Extending Anthophila research through image and trait digitization (Big-Bee) indexed biotic interactions and review summary.</strong></p> <p>Declining populations of bees impact plant-pollinator interactions in both natural and agricultural systems. While bees and other insects pollinate most wild plants and are critical to sustaining a large proportion of global food production, they are decreasing in both numbers and diversity. Our understanding of the factors driving these declines is limited because we lack sufficient data on the distribution of bee species, and on the behavioral and anatomical traits that may make them either vulnerable or resilient to human-induced environmental changes, such as habitat loss and climate change. Fortunately, wild bees have been collected by researchers and deposited in natural history collections for over 100 years, retaining a wealth of associated attributes that can be extracted from specimen images. This project will digitally capture data and images from these historic specimens, develop tools to measure bee traits from these images and generate a comprehensive bee trait and image dataset to measure changes through time. This will increase our understanding of specific traits that put bee species at risk of decline - a critical need for both sustaining our agricultural economy and the conservation of our natural resources. In addition, the large image datasets created by this project can be used for new artificial intelligence identification tools that will help improve our future pollinator observation and monitoring efforts.</p> <p>The Big-Bee project began in 2021 and is funded by the National Science Foundation to mobilize data about worldwide bee species to data aggregators (e.g., iDigBio, GBIF). The Big-Bee Thematic Collection Network (Big-Bee) will create over one million high-resolution 2D and 3D images of bee specimens, representing over 5,000 worldwide bee species, including all of the major pollinating species of the United States. The Big-Bee network includes 13 institutions and partnerships with US government agencies. Novel mechanisms for sharing image datasets will be developed and datasets of bee traits will be available through an open data portal, the Bee Library, for research and education. The Big-Bee project will engage the general public in research through community science via crowdsourcing trait measurements and data transcription from images. In addition, training and professional development for natural history collection staff, researchers, and university students in data science will be provided through the creation and implementation of workshops focusing on bee traits and species identification. All data resulting from this award will be shared with and publicly available through the national digitized biocollections resource, iDigBio.org.</p> <p>This is the first archive of Big-Bee data indexed by Global Biotic Interactions (GloBI). GloBI provides open access to finding species interaction data (e.g., predator-prey, pollinator-plant, pathogen-host, parasite-host) by combining existing open datasets using open-source software. This version of the Big Bee dataset includes interactions that are not just bees. Also in this version, the datasets included in this publication are specifically those institutions in the Big Bee project network and do not represent all bee interaction data found at Global Biotic Interactions.</p> <p><strong>Bee Library Information - Statistics about Big Bee data providers</strong></p> <p>The specimens indexed by GloBI are also found in the <a href="https://library.big-bee.net/portal/">Bee Library</a>. To date, the number of specimens and images in the library are listed below. The Bee Library taxonomic backbone is not yet complete, so information regarding the number of species is not yet available. Further summary statistics are available in the Big Bee Metrics from the Bee Library and GloBI - July 24, 2023.pdf file.</p> <p><strong>From Bee Library (partner indexed records)</strong><br> 1,234,107 occurrence records<br> 993,692 (81%) georeferenced<br> 351,592 (28%) occurrences imaged<br> 986,323 (80%) identified to species<br> 9 families<br> 526 genera<br> 10,700 species<br> 11,386 total taxa (including subsp. and var.)</p> <p><strong>Statistics Per Collection</strong></p> <table> <tbody> <tr> <td>Collection</td> <td>Occurrences</td> <td>Georeferenced</td> <td>Imaged</td> <td>Interactions Indexed in GloBI (all)</td> <td>Interactions Indexed in GloBI (bees)</td> </tr> <tr> <td>ASU Hasbrouck Insect Collection - Bee<br> Records</td> <td>13223</td> <td>13221</td> <td>2352</td> <td>21300</td> <td>3834</td> </tr> <tr> <td>Bee Biology and Systematics Laboratory,<br> USDA-ARS Pollinating Insect-Biology,<br> Management, Systematics Research</td> <td>561820</td> <td>547461</td> <td>0</td> <td>0</td> <td>0</td> </tr> <tr> <td>California Academy of Sciences</td> <td>884</td> <td>300</td> <td>3</td> <td>16984</td> <td>117</td> </tr> <tr> <td>California Academy of Sciences - Type<br> Collection</td> <td>1838</td> <td>59</td> <td>83</td> <td>0</td> <td>0</td> </tr> <tr> <td>Essig Museum of Entomology, University<br> of California Berkeley</td> <td>58551</td> <td>55028</td> <td>0</td> <td> </td> <td>0</td> </tr> <tr> <td>Florida State Collection of Arthropods</td> <td>17134</td> <td>12349</td> <td>7816</td> <td>559</td> <td> </td> </tr> <tr> <td>Museum of Comparative Zoology, Harvard<br> University</td> <td>22020</td> <td>21099</td> <td>11595</td> <td>6777</td> <td>1535</td> </tr> <tr> <td>Natural History Museum of Los Angeles<br> County</td> <td>24685</td> <td>7421</td> <td>3480</td> <td>0</td> <td>0</td> </tr> <tr> <td>San Diego Natural History Museum<br> Entomology Department</td> <td>4065</td> <td>1690</td> <td>1982</td> <td>8688</td> <td>90</td> </tr> <tr> <td>University of California Santa Barbara<br> Invertebrate Zoology Collection</td> <td>8674</td> <td>8410</td> <td>2751</td> <td>1940</td> <td>660</td> </tr> <tr> <td>University of Colorado Museum of Natural<br> History, Entomology Collection</td> <td>18043</td> <td>18043</td> <td>0</td> <td>9589</td> <td>4723</td> </tr> <tr> <td>University of Kansas Natural History<br> Museum Entomology Division</td> <td>464927</td> <td>275200</td> <td>304415</td> <td>119963</td> <td>112677</td> </tr> <tr> <td>University of Michigan Museum of Zoology<br> Division of Insects</td> <td>17764</td> <td>15305</td> <td>15269</td> <td>53755</td> <td>4134</td> </tr> <tr> <td>University of New Hampshire, Donald S.<br> Chandler Entomological Collection</td> <td>17685</td> <td>17393</td> <td>0</td> <td>3137</td> <td>3137</td> </tr> <tr> <td>USGS Native Bee Inventory and Monitoring<br> Lab</td> <td>101</td> <td>101</td> <td>0</td> <td>0</td> <td>0</td> </tr> </tbody> </table> <p><strong>GloBI Data Review Report - Datasets in Review from Global Biotic Interactions</strong></p> <p>Datasets under review:<br> - UUniversity of Michigan Museum of Zoology, Division of Insects accessed via https://github.com/globalbioticinteractions/ummz-ummzi/archive/d9282e51f29f3157af2e5869a09ea8a111ddea34.zip on 2023-07-24T22:06:08.671Z<br> - Arizona State University Hasbrouck Insect Collection accessed via https://github.com/globalbioticinteractions/asu-asuhic/archive/4ed77cb9ca8e526269d4678692e2844c950022f8.zip on 2023-07-24T22:07:09.630Z<br> - California Academy of Sciences Entomology and Entomology Type Collection accessed via https://github.com/globalbioticinteractions/cas-ent/archive/47d385b73a63aa379cd5e6d3615005ba78b0ffc1.zip on 2023-07-24T22:08:13.753Z<br> - University of California Berkeley, Essig Museum of Entomology accessed via https://github.com/globalbioticinteractions/emec/archive/93b17a3db566baa001ce9190e6fbdb60fa99dda4.zip on 2023-07-24T22:08:24.495Z<br> - Florida State Collection of Arthropods accessed via https://github.com/globalbioticinteractions/fsca/archive/2cdcf9475b7e0ef2a728a96535608bc0ce2ac5ca.zip on 2023-07-24T22:08:49.972Z<br> - University of Kansas Natural History Museum accessed via https://github.com/globalbioticinteractions/ku-semc/archive/a9c7cb81050eef68b4428667206a219da458f517.zip on 2023-07-24T22:09:17.016Z<br> - Natural History Museum of Los Angeles County accessed via https://github.com/globalbioticinteractions/lacm-lacmec/archive/dafbf532c53fbadba126c81186c26d52677aa781.zip on 2023-07-24T22:11:11.442Z<br> - Harvard University M, Morris P J (2021). Museum of Comparative Zoology, Harvard University. Museum of Comparative Zoology, Harvard University. accessed via https://github.com/globalbioticinteractions/mcz/archive/b33635a9fc75fd7931ad968cbc11180e6467bfd7.zip on 2023-07-24T22:21:32.961Z<br> - San Diego Natural History Museum accessed via https://github.com/globalbioticinteractions/sdnhm-sdmc/archive/7238d8b804f543250eb487b43144e1125fb3688a.zip on 2023-07-24T22:26:25.503Z<br> - University of Colorado Museum of Natural History Entomology Collection accessed via https://github.com/globalbioticinteractions/ucm-ucmc/archive/60530dcc82d33c9675a4026ad60dc40bea8f2a91.zip on 2023-07-24T22:26:50.178Z<br> - University of California Santa Barbara Invertebrate Zoology Collection accessed via https://github.com/globalbioticinteractions/ucsb-izc/archive/66a4e39589d1dfa299d07985546c4be522ff60d8.zip on 2023-07-24T22:27:13.801Z<br> - University of New Hampshire Donald S. Chandler Entomological Collection accessed via https://github.com/globalbioticinteractions/unhc-unhc/archive/d7668a6bb4545dc4da0645ecc383169ba547b0f5.zip on 2023-07-24T22:27:28.670Z</p> <p>Generated on:<br> 2023-07-24</p> <p>by:<br> GloBI's Elton 0.12.6 <br> (see https://github.com/globalbioticinteractions/elton).</p> <p>Note that all files ending with .tsv are files formatted <br> as UTF8 encoded tab-separated values files.</p> <p>https://www.iana.org/assignments/media-types/text/tab-separated-values</p> <p><br> Included in this review archive are:</p> <p>README:<br> This file.</p> <p>review_summary.tsv:<br> Summary across all reviewed collections of total number of distinct review comments.</p> <p>review_summary_by_collection.tsv:<br> Summary by reviewed collection of total number of distinct review comments.</p> <p>indexed_interactions_by_collection.tsv: <br> Summary of number of indexed interaction records by institutionCode and collectionCode.</p> <p>review_comments.tsv.gz:<br> All review comments by collection.</p> <p>indexed_interactions_full.tsv.gz:<br> All indexed interactions for all reviewed collections.</p> <p>indexed_interactions_simple.tsv.gz:<br> All indexed interactions for all reviewed collections selecting only sourceInstitutionCode, sourceCollectionCode, sourceCatalogNumber, sourceTaxonName, interactionTypeName and targetTaxonName.</p> <p>datasets_under_review.tsv:<br> Details on the datasets under review.</p> <p>elton.jar: <br> Program used to update datasets and generate the review reports and associated indexed interactions.</p> <p>indexed_interactions_bees.tsv:<br> All indexed bee interactions <br> </p> <p>datasets.zip:<br> All datasets reviewed for this publication</p> <p> Big Bee Metrics from the Bee Library and GloBI - July 24, 2023.pdf:<br> Summary statistics from the Bee Library and GloBI about data partners</p> <p>If you have questions or comments about this publication, please open an issue at https://github.com/Big-Bee-Network/issues-observations-and-questions/discussions or contact the authors by email.</p> <p><strong>Funding:</strong><br> The creation of this archive was made possible by the National Science Foundation award Collaborative Research: Digitization TCN: Extending Anthophila research through image and trait digitization (Big-Bee). Award numbers: <a href="https://www.nsf.gov/awardsearch/showAward?AWD_ID=2102006">DBI:2102006</a>, DBI:2101929, DBI:2101908, DBI:2101876, DBI:2101875, DBI:2101851, DBI:2101345, DBI:2101913, DBI:2101891 and DBI:2101850.</p> <p>References:<br> Poelen JH, Simons JD and Mungall CH. (2014). Global Biotic Interactions: An open infrastructure to share and analyze species-interaction datasets. Ecological Informatics. <a href="https://doi.org/10.1016/j.ecoinf.2014.08.005">https://doi.org/10.1016/j.ecoinf.2014.08.005</a>.</p> <p>Seltmann KC, Allen J, Brown BV, Carper A, Engel MS, Franz N, Gilbert E, Grinter C, Gonzalez VH, Horsley P, Lee S, Maier C, Miko I, Morris P, Oboyski P, Pierce NE, Poelen J, Scott VL, Smith M, Talamas EJ, Tsutsui ND, Tucker E (2021) Announcing Big-Bee: An initiative to promote understanding of bees through image and trait digitization. Biodiversity Information Science and Standards 5: e74037. <a href="https://doi.org/10.3897/biss.5.74037">https://doi.org/10.3897/biss.5.74037</a></p> <p>Jorrit Poelen, Tobias Kuhn, & Katrin Leinweber. (2022). globalbioticinteractions/elton: 0.12.5 (0.12.5). Zenodo. https://doi.org/10.5281/zenodo.7267926</p>
Effects of biotic (shrimp) and abiotic (discharge) factors on the depositional environment quantified in a montane stream in Puerto Rico. (Shrimp/Algae/Can J. Fish Aquat. Sci. (1994))
Effects of biotic (shrimp) and abiotic (discharge) factors on the depositional environment were quantified in a montane stream in Puerto Rico. Electricity was used experimentally to exclude large (approximately >1cm in length) biota without artificially increasing sedimentation as in cage enclosure/exclosure experiments in stream systems. Shrimp (>1cm in length) were excluded from substrata by semicircular fence hooked up to battery-powered fence chargers which emitted continuous pulses of electricity. Unelectrified control substrata had natural high densities of atyid shrimp. Significantly greater masses of total sediment, fine and large organic particles, and algal biovolume occurred in shrimp exclusion treatments relative to controls. Shrimp exclusion treatments experienced slow and steady accumulation of sediments under base flow conditions and a large stepwise increase in sediment following a storm. No measurable sediment accrued in the presence of natural densities of shrimp under base flow conditions. Shrimp rapidly removed sediments that accrued during the storm (440-620 g*m2 dry mass-1), decreasing sediment mass in control treatments to near prestorm levels (5-13 g*m2 dry mass-1) within 30 h. Atyid shrimp can significantly affect the accumulation of organic and inorganic materials on rock substrata in stream pools between high-discharge events. Support for this work was provided by grants BSR-8811902, DEB-9411973, DEB-9705814 , DEB-0080538, DEB-0218039 , DEB-0620910 , DEB-1239764, DEB-1546686, and DEB-1831952 from the National Science Foundation to the University of Puerto Rico as part of the Luquillo Long-Term Ecological Research Program. Additional support provided by the University of Puerto Rico and the International Institute of Tropical Forestry, USDA Forest Service.
Soil biota counts from the Biotic Effects Experiment (BEE), McMurdo Dry Valleys, Antarctica (1999-2024, ongoing)
Increases in soil temperature and moisture may change the bioavailability of essential elements by altering solubility and diffusion rates in soils, or by changing the amounts of organic compounds. Long-term experiments in the Bonney, Hoare and Fryxell basins have been established with three treatments: 1) increased moisture, 2) soil warming (ITEX chambers), and 3) soil warming + increased moisture. The identification and abundance of soil biota are reported. Only control treatments have been measured since the 2014-2015 austral summer.
Background data 'Effect of biotic dependencies in species distribution models: The future distribution of Thymallus thymallus under consideration of Allogamus auricollis'
<p>Background data of the paper 'Effect of biotic dependencies in species distribution models: The future distribution of Thymallus thymallus under consideration of Allogamus auricollis'</p>
Global Biotic Interactions: Interpreted Data Products hash://md5/e76bf914309ad27dce6ab911d8854590 hash://sha256/ba79836caab5b7ba2d7d659123d27c89f4ad990bd50f97ded935edee9fbe9f87
<p>Global Biotic Interactions: Interpreted Data Products</p> <p>Global Biotic Interactions (GloBI, https://globalbioticinteractions.org, [1]) aims to facilitate access to existing species interaction records (e.g., predator-prey, plant-pollinator, virus-host). This data publication provides interpreted species interaction data products. These products are the result of a process in which versioned, existing species interaction datasets ([2]) are linked to the so-called GloBI Taxon Graph ([3]) and transformed into various aggregate formats (e.g., tsv, csv, neo4j, rdf/nquad, darwin core-ish archives). In addition, the applied name maps are included to make the applied taxonomic linking explicit. </p> <p>Citation<br>--------</p> <p>GloBI is made possible by researchers, collections, projects and institutions openly sharing their datasets. When using this data, please make sure to attribute these *original data contributors*, including citing the specific datasets in derivative work. Each species interaction record indexed by GloBI contains a reference and dataset citation. Also, a full lists of all references can be found in citations.csv/citations.tsv files in this publication. If you have ideas on how to make it easier to cite original datasets, please open/join a discussion via https://globalbioticinteractions.org or related projects.</p> <p>To credit GloBI for more easily finding interaction data, please use the following citation to reference GloBI:</p> <p>Jorrit H. Poelen, James D. Simons and Chris J. Mungall. (2014). Global Biotic Interactions: An open infrastructure to share and analyze species-interaction datasets. Ecological Informatics. https://doi.org/10.1016/j.ecoinf.2014.08.005.</p> <p>Bias and Errors<br>--------</p> <p>As with any analysis and processing workflow, care should be taken to understand the bias and error propagation of data sources and related data transformation processes. The datasets indexed by GloBI are biased geospatially, temporally and taxonomically ([5], [6]). Also, mapping of verbatim names from datasets to known name concept may contains errors due to synonym mismatches, outdated names lists, typos or conflicting name authorities. Finally, bugs may introduce bias and errors in the resulting integrated data product.</p> <p>To help better understand where bias and errors are introduced, only versioned data and code are used as an input: the datasets ([2]), name maps ([3]) and integration software ([6]) are versioned so that the integration processes can be reproduced if needed. This way, steps take to compile an integrated data record can be traced and the sources of bias and errors can be more easily found.</p> <p>This version was preceded by [7]. </p> <p>Contents<br>--------</p> <p>README:<br>this file</p> <p>citations.csv.gz:<br>contains data citations in a in a gzipped comma-separated values format.</p> <p>citations.tsv.gz:<br>contains data citations in a gzipped tab-separated values format.</p> <p>datasets.csv.gz:<br>contains list of indexed datasets in a gzipped comma-separated values format.</p> <p>datasets.tsv.gz:<br>contains list of indexed datasets in a gzipped tab-separated values format.</p> <p>verbatim-interactions.csv.gz<br>contains species interactions tabulated as pair-wise interaction in a gzipped comma-separated values format. Included taxonomic name are *not* interpreted, but included as documented in their sources.</p> <p>verbatim-interactions.tsv.gz<br>contains species interactions tabulated as pair-wise interaction in a gzipped tab-separated values format. Included taxonomic name are *not* interpreted, but included as documented in their sources. </p> <p>interactions.csv.gz:<br>contains species interactions tabulated as pair-wise interactions in a gzipped comma-separated values format. Included taxonomic names are interpreted using taxonomic alignment workflows and may be different than those provided by the original sources.</p> <p>interactions.tsv.gz:<br>contains species interactions tabulated as pair-wise interactions in a gzipped tab-separated values format. Included taxonomic names are interpreted using taxonomic alignment workflows and may be different than those provided by the original sources.</p> <p>refuted-interactions.csv.gz:<br>contains refuted species interactions tabulated as pair-wise interactions in a gzipped comma-separated values format. Included taxonomic names are interpreted using taxonomic alignment workflows and may be different than those provided by the original sources.</p> <p>refuted-interactions.tsv.gz:<br>contains refuted species interactions tabulated as pair-wise interactions in a gzipped tab-separated values format. Included taxonomic names are interpreted using taxonomic alignment workflows and may be different than those provided by the original sources.</p> <p>refuted-verbatim-interactions.csv.gz:<br>contains refuted species interactions tabulated as pair-wise interactions in a gzipped comma-separated values format. Included taxonomic name are *not* interpreted, but included as documented in their sources. </p> <p>refuted-verbatim-interactions.tsv.gz:<br>contains refuted species interactions tabulated as pair-wise interactions in a gzipped tab-separated values format. Included taxonomic name are *not* interpreted, but included as documented in their sources. </p> <p>interactions.nq.gz:<br>contains species interactions expressed in the resource description framework in a gzipped rdf/quads format.</p> <p>dwca-by-study.zip:<br>contains species interactions data as a Darwin Core Archive aggregated by study using a custom, occurrence level, association extension.</p> <p>dwca.zip:<br>contains species interactions data as a Darwin Core Archive using a custom, occurrence level, association extension.</p> <p>neo4j-graphdb.zip:<br>contains a neo4j v3.5.32 graph database snapshot containing a graph representation of the species interaction data.</p> <p>taxonCache.tsv.gz:<br>contains hierarchies and identifiers associated with names from naming schemes in a gzipped tab-separated values format.</p> <p>taxonMap.tsv.gz:<br>describes how names in existing datasets were mapped into existing naming schemes in a gzipped tab-separated values format.</p> <p>References<br>-----</p> <p>[1] Jorrit H. Poelen, James D. Simons and Chris J. Mungall. (2014). Global Biotic Interactions: An open infrastructure to share and analyze species-interaction datasets. Ecological Informatics. doi: 10.1016/j.ecoinf.2014.08.005.</p> <p>[2] Poelen, J. H. (2020) Global Biotic Interactions: Elton Dataset Cache. Zenodo. doi: 10.5281/ZENODO.3950557.</p> <p>[3] Poelen, J. H. (2021). Global Biotic Interactions: Taxon Graph (Version 0.3.28) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.4451472</p> <p>[4] Hortal, J. et al. (2015) Seven Shortfalls that Beset Large-Scale Knowledge of Biodiversity. Annual Review of Ecology, Evolution, and Systematics, 46(1), pp.523–549. doi: 10.1146/annurev-ecolsys-112414-054400.</p> <p>[5] Cains, M. et al. (2017) Ivmooc 2017 - Gap Analysis Of Globi: Identifying Research And Data Sharing Opportunities For Species Interactions. Zenodo. Zenodo. doi: 10.5281/ZENODO.814978.</p> <p>[6] Poelen, J. et al. (2022) globalbioticinteractions/globalbioticinteractions v0.24.6. Zenodo. doi: 10.5281/ZENODO.7327955.</p> <p>[7] GloBI Community. (2024). Global Biotic Interactions: Interpreted Data Products hash://md5/946f7666667d60657dc89d9af8ffb909 hash://sha256/4e83d2daee05a4fa91819d58259ee58ffc5a29ec37aa7e84fd5ffbb2f92aa5b8 (0.7) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.11552565</p> <p>Content References<br>-----</p> <p>hash://sha256/5f4906439eba61f936b3dd7455a62c51656a74206f82d3f654e330fda6fbbe45 citations.csv.gz<br>hash://sha256/c8100368dae39363b241472695c1ae197aaddc6e3d6c0a14f3f5ee704b37f3f6 citations.tsv.gz<br>hash://sha256/e6f4aa897c5b325e444315e021b246ffed07fef764b0de6c0f1b2688bbdf9d0f datasets.csv.gz<br>hash://sha256/e6f4aa897c5b325e444315e021b246ffed07fef764b0de6c0f1b2688bbdf9d0f datasets.tsv.gz<br>hash://sha256/f11dc825609cdb1d4a3e9ba8caca9bf93c90dd6f660c7f6a0c8aa01c035a5e1f dwca-by-study.zip<br>hash://sha256/7f16aacacae74e8b0cdef04c612ba776f508ff7ffe385abc57583e37aec8fe53 dwca.zip<br>hash://sha256/b65e4c9a3615f1386bb97e45fb907d053df55476149aa6d71e6f398351218d0d interactions.csv.gz<br>hash://sha256/0c28032392f82d753690be126805e6334ca46bdc4b5e2102a79b15ce0cc0ba90 interactions.nq.gz<br>hash://sha256/8a7031250c288ba0da3d5cdbedc19d54c2f16ba3aa70d49826a7369b6edeca04 interactions.tsv.gz<br>hash://sha256/d0c0fbf536cc63c004d057efc14600ba8cc5874f401b08f51837273b7854f1bb neo4j-graphdb.zip<br>hash://sha256/50e77636f8b58c040e38b6a70ba7cc8288b190ef252dc0d4eb2f12f4c541e82f README<br>hash://sha256/a74e2a39cfe133ae9de1eeea94f5dda8cbd58cfe61a8ccf91b7c540757719c74 refuted-interactions.csv.gz<br>hash://sha256/37b06e274e41ca749399763989816854101238ade9863365f384a2764c639e9d refuted-interactions.tsv.gz<br>hash://sha256/23315b6cd3fdc91f9c1d5d5bc39fa52cf1cef7a4e97d9d023d452751df13f30e refuted-verbatim-interactions.csv.gz<br>hash://sha256/ff82e40cee4f8a8852d0c241f5027f66157a2b8a9090ffa3a0a329a206828d96 refuted-verbatim-interactions.tsv.gz<br>hash://sha256/f072fbc7affb6e29978c7540af6cdccd3a219a23b0a4765b5bae56bd20df0d88 taxonCache.tsv.gz<br>hash://sha256/cd28c81bb2432646a81ad216bc11818f7568ce81826e0074d9a33579da2c1426 taxonMap.tsv.gz<br>hash://sha256/a1d14aa47806c624cf7e3a8c8236643dcf19ed1835c79c65958f7317ebfb9566 verbatim-interactions.csv.gz<br>hash://sha256/2284434219d5fdab1e2152955f04363852c132b76709c330d33e31517817a82e verbatim-interactions.tsv.gz</p> <p>hash://md5/d6ebf42729d988e15cb30adfa6112234 citations.csv.gz<br>hash://md5/42877ae68e51871b8eb7116e62f6b268 citations.tsv.gz<br>hash://md5/3e437580296fdeff3b6f35d1331db9d1 datasets.csv.gz<br>hash://md5/3e437580296fdeff3b6f35d1331db9d1 datasets.tsv.gz<br>hash://md5/fe88720fd992771bd64bfa220ad6a7d3 dwca-by-study.zip<br>hash://md5/cbe132a9288feaef2f3e0c0409b8dc2f dwca.zip<br>hash://md5/051f6db667c4b84616223c2776464dbf interactions.csv.gz<br>hash://md5/b66857f8750e56ba9abe484b1f72eac4 interactions.nq.gz<br>hash://md5/300839c346184b2fedc4e1fb31bcc29c interactions.tsv.gz<br>hash://md5/e79cf5ffee919672f99ea338f3661566 neo4j-graphdb.zip<br>hash://md5/898678f47561d7ef53722bc32957dcd9 README<br>hash://md5/65a185f19df304e53f92a7275f2de291 refuted-interactions.csv.gz<br>hash://md5/bc37a4354f8a2402e9335ae44f28cbd7 refuted-interactions.tsv.gz<br>hash://md5/42e817c31e2ca05e582be94e6ec283c5 refuted-verbatim-interactions.csv.gz<br>hash://md5/93639b70a1d8e47fd194b6384c0287a7 refuted-verbatim-interactions.tsv.gz<br>hash://md5/e32482b3697aa928a5fcb58a570191df taxonCache.tsv.gz<br>hash://md5/75251510925875d3fdc1952cc4b98043 taxonMap.tsv.gz<br>hash://md5/6a0c6224f4a4c3dca9994d70ad0b2fd2 verbatim-interactions.csv.gz<br>hash://md5/905acb49a700e5b5a292be02c917e710 verbatim-interactions.tsv.gz</p>
Global Biotic Interactions: Taxon Graph hash://sha256/0b58753e4ff5519442689d866c0f1d19ffa7d97f917144df1d1cd56ea756921d hash://md5/b23bd0210c88ca10c3e3253091f4fdfa
<p>Global Biotic Interactions: Taxon Cache and Taxon Map</p> <p>Global Biotic Interactions (GloBI) provides access to existing species interaction datasets (Poelen et al. 2014, http://globalbioticinteractions.org). As part of the dataset integration and aggregation, a best effort is made to resolve, match and link taxonomic names and associated vernacular/common names, hierarchies and thumbnails. </p> <p>The data archives included in this publication contain established taxonomic links (taxonMap.tsv.gz) and taxonomic information (taxonCache.tsv.gz) that GloBI retrieved and integrated from taxonomic name sources and web services associated with http://itis.gov, http://globalnames.org, http://eol.org and others open data services. </p> <p>While GloBI is not a naming authority and the primary goal of the name matching process is to detect incorrect or outdates names, the archives may serve as an example of how to publish denormalized taxonomic records and their interrelatioships in a pragmatic way.</p> <p>For related discussion threads, see https://github.com/globalbioticinteractions/globalbioticinteractions/issues/145 , https://github.com/globalbioticinteractions/globalbioticinteractions/issues/274 , https://github.com/globalbioticinteractions/globalbioticinteractions/issues/70 , https://github.com/EOL/tramea/issues/10 and https://github.com/globalbioticinteractions/globalbioticinteractions/issues/274 .</p> <p>Files<br> <br> README <br> this file</p> <p> taxonCache.tsv.gz <br> Taxonomic name, ids, hierarchies, common names and thumbnail associated to taxa known to GloBI. <br> <br> taxonCache.tsv.sha256<br> sha256 hash of taxonCache.tsv</p> <p> taxonCacheFirst10.tsv<br> Header and 10 following lines from taxonCache.tsv</p> <p> taxonCacheFirst10.tsv.sha256<br> sha256 hash of taxonCacheFirst10.tsv<br> <br> taxonMap.tsv.gz <br> Links between taxon name and ids across various taxon providers. </p> <p> taxonMap.tsv.sha256 <br> sha256 hash of taxonMap.tsv</p> <p> taxonMapFirst10.tsv<br> Header and 10 following lines from taxonMap.tsv<br> <br> taxonMapFirst10.tsv.sha256<br> sha256 hash of taxonMapFirst10.tsv</p> <p> prefixes.tsv<br> Term prefixes and their associated uri schemes. </p> <p> names.tsv.gz<br> Corpus of names used to resolve and link. Generated using https://github.com/globalbioticinteractions/elton .</p> <p> names.tsv.sha256<br> sha256 hash of names.tsv</p> <p> namesUnresolved.tsv.gz<br> Names that are not (yet) linked to name sources using https://github.com/globalbioticinteractions/nomer .</p> <p> namesUnresolved.tsv.sha256<br> sha256 hash of namesUnresolved.tsv </p> <p>Column Descriptions</p> <p> taxonCache.tsv.gz </p> <p> 1 | id<br> 2 | name<br> 3 | rank<br> 4 | commonNames<br> 5 | path<br> 6 | pathIds <br> 7 | pathNames<br> 8 | externalUrl<br> 9 | thumbnailUrl<br> <br> taxonMap.tsv.gz</p> <p> 1 | providedTaxonId<br> 2 | providedTaxonName<br> 3 | resolvedTaxonId<br> 4 | resolvedTaxonName</p> <p> names.tsv.gz</p> <p> 1 | providedTaxonId<br> 2 | providedTaxonName</p> <p> namesUnresolved.tsv.gz</p> <p> 1 | providedTaxonId<br> 2 | providedTaxonName</p> <p>References</p> <p>Jorrit H. Poelen, James D. Simons and Chris J. Mungall. (2014). Global Biotic Interactions: An open infrastructure to share and analyze species-interaction datasets. Ecological Informatics. https://doi.org/10.1016/j.ecoinf.2014.08.005.</p> <p>Updates</p> <p>org.globalbioticinteractions.taxon v0.3, 2018-03-02</p> <p>This taxon archive version was created by taking GloBI taxon v0.2 (Jan 2018) and appending a semi-automatically created WikiData taxon mapping and taxon cache.</p> <p>org.globalbioticinteractions.taxon v0.3.1, 2018-04-05</p> <p>This taxon archive version was created by taking GloBI taxon v0.2 (Jan 2018) and appending an automatically created WikiData taxon mapping and taxon cache using Apache Spark scripts at https://github.com/bio-guoda/guoda-datasets/tree/master/wikidata .</p> <p>org.globalbioticinteractions.taxon v0.3.2, 2018-05-21</p> <p>This taxon archive version includes the following:</p> <p>1. all lines in taxonMap.tsv.gz v0.3.1 that passed all validate-term-link tests defined in nomer v0.0.7 (see https://doi.org/10.5281/zenodo.1249964 or https://github.com/globalbioticinteractions/nomer/releases/tag/0.0.7).</p> <p>2. all lines in taxonCache.tsv.gz. v0.3.1 that passed all validate-term tests defined in nomer v0.0.7 </p> <p>3. all lines in 1. that did *not* pass the validate-term test, were re-resolved using nomer v0.0.7 commands "append globi-enrich" and "append globi-globalnames". Only SAME_AS and SYNONYM_OF matches were used to generate new entries for taxonCache and taxonMap.</p> <p>4. in addition, elton v0.4.5 (see https://doi.org/10.5281/zenodo.1212599 or https://github.com/globalbioticinteractions/elton/releases/tag/0.4.5) was used to generate an up-to-date names list by running the "update" and "names" commands on 18-19 May 2018. Of the resulting names, only id/names pairs that were unknown to the taxon graph were resolved using the "append globi-enrich" and "append globi-globalnames" commands of nomer v0.0.7. Only matches classified as SAME_AS and SYNONYM_OF were used to generate new entries for taxonCache and taxonMap.</p> <p>5. the updated versions of taxonMap.tsv.gz and taxonCache.tsv.gz were produced by appending result of 1., 2., 3. and 4. , removing duplicate lines and sorting the result. </p> <p>6. finally, the resulting taxonMap.tsv.gz. and taxonCache.tsv.gz files were validated using the nomer v0.0.7 validate-term-link and validate-term commands, respectively. The result indicated that all lines (other than the header) passed the validation tests.</p> <p>org.globalbioticinteractions.taxon v0.3.3, 2018-06-12</p> <p>This taxon archive version includes the following:</p> <p>1. normalizing taxonomic ranks using nomer's taxon rank matcher</p> <p>2. include more manual taxonomic name mappings provided by Brian Hayden and collaborators.</p> <p>3. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023 . </p> <p>4. remove mapping to NCBI taxa with name "Small" (and associated OTT).</p> <p><br>org.globalbioticinteractions.taxon v0.3.4, 2018-06-27</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023</p> <p>Please note that nomer and elton rely on web accessible apis like taxonomy resolution services and data portals. This dependence on external web-only accessible services might make reproduction of the results tricky due to network outages, server failures, upgrades, downgrades, data loss and/or abandonment of informatics projects/ datasets. </p> <p>org.globalbioticinteractions.taxon v0.3.5, 2018-06-28</p> <p>1. remove dubious provided name from taxon map. Names include "no name", "unidentified".<br>2. remove dubious mappings to Pavlova (e.g., Unidentified Amoebozoa -> Pavlova). Related to 1.<br>3. remove dubious mappings to resolve taxa that include names like "unidentified" or "organic species"<br>4. removed dubious mappings to "Boiga dendrophila"<br>5. removed dubious mappings from "Chaetognatha" (arrowworm) to a suspected homonym Lepidoptera GBIF:3257692 and IRMNG:1252651<br>6. removed dubious mappings from "small sharks" to multiple NCBI/OTT terms with name "Small"</p> <p>Please note that nomer and elton rely on web accessible apis like taxonomy resolution services and data portals. This dependence on external web-only accessible services might make reproduction of the results tricky due to network outages, server failures, upgrades, downgrades, data loss and/or abandonment of informatics projects/ datasets.</p> <p>org.globalbioticinteractions.taxon v0.3.6, 2018-09-10</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023</p> <p>org.globalbioticinteractions.taxon v0.3.7, 2018-10-18</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023<br>2. remove dubious mapping to Vertebrata (WORMS:370321 , http://www.marinespecies.org/aphia.php?p=taxdetails&id=370321). Also see https://github.com/globalbioticinteractions/globalbioticinteractions/issues/361 .<br>3. remove dubious mapping to NCBITaxon:1585532 (Beta vulgaris/Cercospora beticola mixed EST library). Also see https://github.com/globalbioticinteractions/globalbioticinteractions/issues/346 and https://github.com/Planteome/samara/issues/50 </p> <p>org.globalbioticinteractions.taxon v0.3.8, 2018-11-15</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023</p> <p>org.globalbioticinteractions.taxon v0.3.9, 2018-11-23</p> <p>1. label deprecated EOL ids by applying patches in http://doi.org/10.5281/zenodo.1495266 to taxonMap.tsv.gz and taxonCache.tsv.gz . Related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/383 .<br>2. remove all Encyclopedia of Life thumbnail urls from taxonCache. Related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/381 .<br>3. remove Encyclopedia of Life external urls associated with deprecated ids from taxonCache. </p> <p><br>org.globalbioticinteractions.taxon v0.3.10, 2018-11-26</p> <p>1. Remove suspicious name mappings related to Humpback scorpionfish (Scorpaenopsis gibbosa) by applying patch published in Poelen, Jorrit H. (2018). Global Biotic Interactions: Taxon Graph Patches (Version 0.2. [Data set]. Zenodo. http://doi.org/10.5281/zenodo.1560662 </p> <p>org.globalbioticinteractions.taxon v0.3.11, 2018-12-21</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023<br>2. remove suspicious name mappings using: ```zcat taxonMap.tsv.gz | grep -v -i -P "\tnone\t" | grep -v -P "(GBIF|IRMNG):.*\tBrachyura$" | grep -v -P "Gamarus" | grep -v -P "^EOL:1047365\ttrachurus trachurus" | grep -v -P "Loros\t.*Psittacidae" | grep -v -P "(GBIF|IRMNG).*Lucifer$" | grep -v -P "GBIF.*Diadema$" | gzip > taxonMapUpdated.tsv.gz```</p> <p>org.globalbioticinteractions.taxon v0.3.12, 2019-06-05</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p> <p>org.globalbioticinteractions.taxon v0.3.13, 2019-06-12</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p> <p>org.globalbioticinteractions.taxon v0.3.14, 2019-08-19</p> <p>1. revisit deprecated EOL ids by applying patches in http://doi.org/10.5281/zenodo.3371634 to taxonMap.tsv.gz and taxonCache.tsv.gz . Related to https://github.com/jhpoelen/eol-globi-data/issues/403 .</p> <p>org.globalbioticinteractions.taxon v0.3.15, 2019-08-26</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p> <p>org.globalbioticinteractions.taxon v0.3.16, 2019-09-22</p> <p>1. revisit deprecated EOL ids by applying patches in http://doi.org/10.5281/zenodo.3457626 to taxonMap.tsv.gz and taxonCache.tsv.gz of http://doi.org/10.5281/zenodo.3378125. Related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/408 .</p> <p>org.globalbioticinteractions.taxon v0.3.17, 2019-09-27</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p> <p>org.globalbioticinteractions.taxon v0.3.18, 2019-10-30</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p> <p>org.globalbioticinteractions.taxon v0.3.19, 2019-11-07</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p> <p>org.globalbioticinteractions.taxon v0.3.20, 2020-01-17</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p> <p>org.globalbioticinteractions.taxon v0.3.21, 2020-03-11</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p> <p>org.globalbioticinteractions.taxon v0.3.22, 2020-04-14</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p> <p>org.globalbioticinteractions.taxon v0.3.23, 2020-05-22</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p> <p>org.globalbioticinteractions.taxon v0.3.24, 2020-06-23</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p> <p>org.globalbioticinteractions.taxon v0.3.25, 2020-08-19</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p> <p>org.globalbioticinteraction.taxon v0.3.26, 2020-10-01</p> <p>1. adding links to Plazi treatment via nomer append plazi (see https://github.com/globalbioticinteractions/nomer/issues/23)<br>by applying patches available via https://doi.org/10.5281/zenodo.4062711 .</p> <p>org.globalbioticinteraction.taxon v0.3.27, 2020-10-22</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p> <p>org.globalbioticinteraction.taxon v0.3.28, 2021-01-19</p> <p>1. update taxonCache and taxonMap using patch 20210114-01 available via Poelen, Jorrit H. (2021). Global Biotic Interactions: Taxon Graph Patches (Version 0.6) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.4451462 .</p> <p>org.globalbioticinteractions.taxon v0.3.29, 2021-01-26</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p> <p>org.globalbioticinteractions.taxon v0.3.30, 2021-03-10</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p> <p>org.globalbioticinteractions.taxon v0.3.31, 2021-03-31</p> <p>1. update taxonCache and taxonMap using patch 20210331-01 available via Poelen, Jorrit H. (2021). Global Biotic Interactions: Taxon Graph Patches (Version 0.7) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.4655153 .</p> <p>org.globalbioticinteractions.taxon v0.3.32, 2021-05-12</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558<br>2. remove suspicious mappings from Fungal to some virus name described in https://www.gbif.org/species/4904189 Fungal see https://github.com/globalbioticinteractions/mangal/issues/1#issuecomment-833956239 .</p> <p>org.globalbioticinteractions.taxon v0.3.33, 2021-06-23</p> <p>1. remove suspicious viral name mappings as reported in https://github.com/globalbioticinteractions/globalbioticinteractions/issues/672 by updating taxonMap.tsv.gz using patch 20210623-01 available via Poelen, Jorrit H. (2021). Global Biotic Interactions: Taxon Graph Patches (Version 0.8) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.5021824 .</p> <p>org.globalbioticinteractions.taxon v0.3.34, 2021-09-24</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p> <p>org.globalbioticinteractions.taxon v0.3.35, 2021-11-19</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p> <p>org.globalbioticinteractions.taxon v0.3.36, 2022-03-29</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.6394931</p> <p>org.globalbioticinteractions.taxon v0.4.0, 2023-03-21</p> <p>1. update elton, nomer, and globi taxon graph versions<br>2. attempt to align all names, including those aligned previously. Replaced incremental name alignment. Incremental name alignment was a optimization needed because of web api performance. Now, no web apis are used, so the optimization is no longer needed.<br>take names from https://globalbioticinteractions.org/data verbatim-interactions.tsv.gz instead of parsing verbatim names from their sources</p> <p>org.globalbioticinteractions.taxon v0.4.1, 2023-03-23</p> <p>update taxon graph build script to fit into existing taxonMap/taxonCache schema<br>fix various bugs<br>remove internal validation until a more up-to-date validation method is available</p> <p>org.globalbioticinteractions.taxon v0.4.2, 2022-10-14</p> <p>update taxonCache and taxonMap using automated scripts available at globalbioticinteractions. (2023). globalbioticinteractions/taxon-graph-builder: 0.0.7 (0.0.7). Zenodo. https://doi.org/10.5281/zenodo.10037579</p> <p>org.globalbioticinteractions.taxon v0.4.3, 2022-10-26</p> <p>apply patch 20231026-01 to address https://github.com/globalbioticinteractions/globalwebdb/issues/1 and https://discuss.eol.org/t/questionable-link-in-trophic-web-for-white-tailed-jackrabbit/2296</p> <p>org.globalbioticinteractions.taxon v0.4.4, 2022-10-26</p> <p>apply patch 20231026-02 to continue to work towards addressing https://github.com/globalbioticinteractions/globalwebdb/issues/1 and https://discuss.eol.org/t/questionable-link-in-trophic-web-for-white-tailed-jackrabbit/2296</p> <p>org.globalbioticinteractions.taxon v0.4.5, 2022-10-26</p> <p>apply patch 20231026-03 to continue to work towards addressing https://github.com/globalbioticinteractions/globalwebdb/issues/1 and https://discuss.eol.org/t/questionable-link-in-trophic-web-for-white-tailed-jackrabbit/2296</p> <p>org.globalbioticinteractions.taxon v0.4.6, 2024-06-17</p> <p>apply patch 20240617 to work towards addressing suspicious Candidatus name mapping reported in https://github.com/globalbioticinteractions/globalbioticinteractions/issues/968</p> <p>org.globalbioticinteractions.taxon v0.5.0, 2024-07-05</p> <p>1. update taxonCache and taxonMap using automated scripts available via Taxon Graph Builder v0.1.0 https://github.com/globalbioticinteractions/taxon-graph-builder/releases/tag/0.1.0 and/or https://doi.org/10.5281/zenodo.1286023 . </p> <p>org.globalbioticinteractions.taxon v0.5.1, 2024-07-08</p> <p>1. update taxonCache and taxonMap using automated scripts available via Taxon Graph Builder v0.1.1 https://github.com/globalbioticinteractions/taxon-graph-builder/releases/tag/0.1.1 and/or https://doi.org/10.5281/zenodo.12687693 . </p> <p>org.globalbioticinteractions.taxon v0.5.2, 2024-07-11</p> <p>1. update taxonCache and taxonMap using automated scripts available via Taxon Graph Builder v0.1.2 https://github.com/globalbioticinteractions/taxon-graph-builder/releases/tag/0.1.2 and/or https://doi.org/10.5281/zenodo.12687693 . </p> <p>org.globalbioticinteractions.taxon v0.5.3, 2024-07-24</p> <p>1. update taxonCache and taxonMap using automated scripts available via Taxon Graph Builder v0.1.2 https://github.com/globalbioticinteractions/taxon-graph-builder/releases/tag/0.1.2 and/or https://doi.org/10.5281/zenodo.12687693 . </p> <p><br>org.globalbioticinteractions.taxon v0.5.4, 2025-02-12</p> <p>1. update taxonCache and taxonMap using automated scripts available via Taxon Graph Builder v0.1.2 https://github.com/globalbioticinteractions/taxon-graph-builder/releases/tag/0.1.2 and/or https://doi.org/10.5281/zenodo.12687693 . </p>
Raw metagenomic data from sweep net samples collected in 2016 as part of the Slikok Creek Watershed Biotic Inventory
<p>We set out to inventory vascular plants, bryophytes, lichens, birds, arthropods, and earthworms on a grid of sites in the portion of Slikok Creek watershed that is on the Kenai National Wildlife Refuge, Kenai Peninsula, Alaska. Occurrence data, images, and field data sheets from this project are available via an <a href="https://arctosdb.org/">Arctos</a> project page at <a href="http://arctos.database.museum/project/10002227">http://arctos.database.museum/project/10002227</a>.</p> <p>This dataset includes the raw FASTQ files from metagenomic processing and associated collection data. Of the 160 sweep net samples collected, 125 were selected for High Throughput Sequencing and shipped to RTL Genomics (<a href="http://rtlgenomics.com">http://rtlgenomics.com</a>) for extraction and sequencing steps. Sequencing was performed on an Illumina MiSeq platform and reads were processed using RTL Genomics’ standard methods with the mlCOIlintF/HCO2198 primer set of Leray et al. (2013), yielding a 313 bp region of the COI gene.</p> <p>Collection data are included in the file <code>ArctosData_43C6167EB1.csv</code> downloaded from Arctos. Extraction methods and sequencing methods provided by RTL Genomics are included in the files <code>Bowser 4869.pdf</code> and <code>Illumina MiSeq Two-Step Method 454 profile only.docx</code>. Primers used are provided in the file <code>Bowser_4869M.txt</code>. The archive <code>FASTQ.zip</code> contains all of the resulting FASTQ files.</p> <p>These sequence data have also been been published to GenBank's Sequence Read Archive in accessions <a href="http://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR10454582">SRR10454582</a>–<a href="http://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR10454706">SRR10454706</a> under BioProject <a href="http://www.ncbi.nlm.nih.gov/bioproject/PRJNA427721">PRJNA427721</a>.</p>
Soybean dependence on biotic pollination decreases with latitude - Data and Computer code
<p>Release of Datasets and R scripts needed to reproduce the analyses and figures published in the article <em>'Soybean dependence on biotic pollination decreases with latitude'</em>, published in Agriculture, Ecosystems & Environment, Volume 347, 1 May 2023, 108376. <a href="https://doi.org/10.1016/j.agee.2023.108376">https://doi.org/10.1016/j.agee.2023.108376</a></p> <p><strong>Highlights</strong></p> <ul> <li>In the absence of pollinators, soybean yield decreases between 0 and ~50%.</li> <li>Variation in pollinator dependence (PD) was found to be structured latitudinally.</li> <li>PD decreases at high latitudes due to an apparently higher incidence of autogamy.</li> <li>Temperature and photoperiod could play an important role in determining PD.</li> <li>Changes in cleistogamy and androsterility might explain the reported trends.</li> </ul> <p><strong>Abstract</strong></p> <p>Identifying large-scale patterns of variation in pollinator dependence (PD) in crops is important from both basic and applied perspectives. Evidence from wild plants indicates that this variation can be structured latitudinally. Individuals from populations at high latitudes may be more selfed and less dependent on pollinators due to higher environmental instability and overall lower temperatures, environmental conditions that may affect pollinator availability. However, whether this pattern is similarly present in crops remains unknown. Soybean (Glycine max), one of the most important crops globally, is partially self-pollinated and autogamous, exhibiting large variation in the extent of PD (from a 0 to ~50% decrease in yield in the absence of animal pollination). We examined latitudinal variation in soybean's PD using data from 28 independent studies distributed along a wide latitudinal gradient (4-43 degrees). We estimated PD by comparing yields between open pollinated and pollinator-excluded plants. In the absence of pollinators, soybean yield was found to decrease by an average of ~30%. However, PD decreases abruptly at high latitudes, suggesting a relative increase in autogamous seed production. Pollinator supplementation does not seem to increase seed production at any latitude. We propose that latitudinal variation in PD in soybean may be driven by temperature and photoperiod affecting the expression of cleistogamy and androsterility. Therefore, an adaptive mating response to an unpredictable pollinator environment apparently common in wild plants can also be imprinted in highly domesticated and genetically-modified crops.</p> <p><strong>Content</strong></p> <p>The dataset consists of two files</p> <p>1 - <a href="https://github.com/NERC-CEH/Soybean-dependence-on-biotic-pollination-decreases-with-latitude/blob/main/%5Bdata%5D%20Cunha%20et%20al.%20MS_soybean.xlsx">[data] Cunha et al. MS_soybean.xlsx</a> is an excel file with two sheets, <strong>data</strong> and <strong>data_map</strong>. These sheets contain the data used in the models defined in the R script <a href="https://github.com/NERC-CEH/Soybean-dependence-on-biotic-pollination-decreases-with-latitude/blob/main/%5BR%20script%5D%20Cunha%20et%20al.%20MS_soybean.R">[R script] Cunha et al. MS_soybean.R</a>.</p> <ul> <li> <p>1.1 The <strong>data</strong> sheet contains the variables:</p> <ul> <li>Value = log_ratios</li> <li>Lat = latitude in decimal degrees</li> <li>Variable = yield component</li> <li>Treatment = treatment type for comparing pollinator dependence</li> <li>Reference_Data_owner = study ID where the data was obtained</li> <li>Site = site within the study where each field experiment was performed</li> </ul> </li> <li> <p>1.2 The <strong>data_map</strong> sheet contains information used for plotting the geographical distribution of the used studies:</p> <ul> <li>Reference_Data_owner = study ID where the data was obtained</li> <li>Country = country where the study was performed</li> <li>Province = province where the study was performed</li> <li>Locality/Farm = locality where the study was performed</li> <li>Lat = latitude in decimal degrees</li> <li>Long = longitude in decimal degrees</li> </ul> </li> </ul> <p>2 - <a href="https://github.com/NERC-CEH/Soybean-dependence-on-biotic-pollination-decreases-with-latitude/blob/main/%5Bdata%5D%20Cunha%20et%20al.%20MS_soybean%20%5Bdate_photoperiod%5D.csv">[data] Cunha et al. MS_soybean [date_photoperiod].csv</a> is a comma-separated file that contains the information used in the R script <a href="https://github.com/NERC-CEH/Soybean-dependence-on-biotic-pollination-decreases-with-latitude/blob/main/%5BR%20script%5D%20Cunha%20et%20al.%20AGEE%20-%20gee_temp_ts_extract.R">[R script] Cunha et al. AGEE - gee_temp_ts_extract.R</a> and produces Figure S2.</p> <ul> <li> <p>2.1 The dataset contains the following variables:</p> <ul> <li>study_ID = study ID number where the data was obtained</li> <li>study_ref = study ID where the data was obtained</li> <li>latitude = latitude in decimal degrees</li> <li>longitude = longitude in decimal degrees</li> <li>date1 = date of the sowing or flowering when the experiment was done</li> <li>date2 = a second date, when available, of the sowing or flowering when the experiment was done</li> <li>event = if the date was related to the sowing of seeds or flowering of soybean.</li> </ul> </li> </ul>
Reproducibility package for Using root economics traits to predict biotic plant soil-feedbacks
<p>Using root economics space to predict biotic plant soil-feedbacks presents a novel framework linking below ground ecological theory to plant soil feedback effects. We show how to calculate root functional distance and location of two plant species in root economics space and how these measures can help to predict the strength and direction of the plant soil feedback between them. </p> <p>Contains data and scripts to reproduce analysis and figures for the manuscript (https://github.com/ggpmrutten/linkingRES-PSF)</p>
Global Biotic Interactions: Elton Dataset Cache iNaturalist
<p>Global Biotic Interactions: Elton Dataset Cache iNaturalist</p><p>The intended use of this archive/cache is to allow for offline-enabled access to versions of existing species interaction datasets provided by iNaturalist. The program "Elton" (https://doi.org/10.5281/zenodo.998263) was used to populate the content of elton-datasets.tar.gz . The same program can be used to extract information from the cache archive also. Global Biotic Interactions (https://globalbioticinteractions.org, https://doi.org/10.1016/j.ecoinf.2014.08.005) also uses these archives to create derived species interaction data archives, search indexes and APIs.</p><p>To get offline-enabled access to versions of other species interactions datasets, please see Global Biotic Interactions: Elton Dataset Cache at https://doi.org/10.5281/zenodo.2007418 .</p><p> </p><p>Contents</p><p>--------</p><p> </p><p>README: the first part of this file</p><p>elton-datasets.tar.gz:versioned archive with species interaction datasets</p><p>elton-datasets.tar.sha256:content signature of elton-datasets.tar</p><p>elton-datasets.tsv:list of included datasets</p><p>elton.jar:commandline program to help access the species interaction datasets</p><p> </p><p>Usage</p><p>-----</p><p> </p><p>To install, extract elton-datasets.tar.gz into a directory of choice using:</p><p> </p><p>tar xfz elton-dataset.tar.gz</p><p> </p><p>To use, download elton.jar included this publication and execute the following to get a list of available datasets:</p><p>java -Xmx4G -jar elton.jar datasets</p><p>on a system that has java v8+ installed.</p><p>If all goes well, you should be able to regenerate the included file elton-dataset.tsv .</p><p>For more information on how to use elton.jar, execute:</p><p>java -jar elton.jar usage</p><p>or visit https://github.com/globalbioticinteractions/elton for more available commands.</p><p>Alternatively, without using Elton, you can access the data by inspecting the access.tsv files in the various directories of the datasets directory.</p><p>When using these datasets in a publication or product, please cite the *original* data providers and publications. You can find the citations in the data.</p><p>Included datasets:</p><p>globalbioticinteractions/inaturalist https://github.com/globalbioticinteractions/inaturalist/archive/db6545f3d7afd88f48064dddb9f4692603545a44.zip 2023-10-14T00:29:47.032Z application/globi</p><p>globalbioticinteractions/inaturalist https://github.com/globalbioticinteractions/inaturalist/archive/db6545f3d7afd88f48064dddb9f4692603545a44.zip 9a1342936d3abd508a039b4216a9c3b18b6d135160338c966f40a6fee3191731 2023-10-14T00:29:49.693Z</p><p>globalbioticinteractions/inaturalist https://www.inaturalist.org/observations/globi-observations-resource-relationships-dwca.zip 32642cd31854c4e4c93e40ed2e0117819be2397b736bff12bee32e5045204df2 2023-10-14T00:30:04.130Z</p><p>globalbioticinteractions/inaturalist https://github.com/globalbioticinteractions/inaturalist/archive/db6545f3d7afd88f48064dddb9f4692603545a44.zip 9a1342936d3abd508a039b4216a9c3b18b6d135160338c966f40a6fee3191731 2023-10-14T00:34:30.397Z</p><p>globalbioticinteractions/inaturalist https://www.inaturalist.org/taxa/inaturalist-taxonomy.dwca.zip b3355c65d28c3dc7a4e9b66d6e20bf603d91c68e6c392473be93ed43e680055c 2023-10-14T00:34:40.679Z</p><p>globalbioticinteractions/inaturalist https://github.com/globalbioticinteractions/inaturalist/archive/db6545f3d7afd88f48064dddb9f4692603545a44.zip 9a1342936d3abd508a039b4216a9c3b18b6d135160338c966f40a6fee3191731 2023-10-14T00:35:17.450Z</p>
Biotic cover in crescentic gouges of New England 2021
In this study, I tested the hypothesis that crescentic gouges – conspicuous, crescent-shaped troughs on recently glaciated granite domes – are important microsites of alpine and subalpine biomat development and plant establishment, and thus can be used to augment montane ecosystem conservation and restoration efforts. To test my hypothesis, in September 2021, I quantified biotic percent cover in crescentic gouges and measured gouge proximity to upslope, established biomat and plant assemblages (i.e., presumed propagule sources), proximity to established hiking trails (i.e., distance from disturbance), and gouge sizes at four mid-elevation granite balds in NH, VT, and ME, USA. I used distance-based linear regression modeling (DISTLMv.5) to evaluate the effects of these predictor variables on biotic cover in the gouges. At all sites, all three predictor variables (proximity to upslope, well-developed assemblage, proximity to hiking trail, and gouge size) together explained a statistically significant proportion of the variation in total biotic cover in crescentic gouges. At one site (Speckled Mountain, ME), all three predictors explained 71% of the variation in biotic cover; the proportion of variance explained at other sites was lower but still statistically significant. When I evaluated the effects of predictor variables individually, each significantly affected biotic cover in crescentic gouges at all sites. My data suggest that crescentic gouges, particularly larger gouges not overlain by pine canopy, support strong biomat and plant colonization, and thus should be considered in alpine and subalpine plant conservation and restoration initiatives. Cordoning off crescentic gouges at mid-elevation sites would be a novel, inexpensive, and relatively straightforward way to augment existing alpine and subalpine conservation and restoration efforts.
Figure 3 in Biotic components of dung beetles (Insecta: Coleoptera: Scarabaeidae: Scarabaeinae) from Pantanal - Cerrado Border and its implications for Chaco regionalization
Figure 3. Generalized tracks (GT A–L) of dung beetles, different biotic components observed in the Pantanal–Cerrado Border.
Data from: Biotic interactions help explain variation in elevational range limits of birds among Bornean mountains
Aim <p>Physiological tolerances and biotic interactions along habitat gradients are thought to influence species occurrence. Distributional differences caused by such forces are particularly noticeable on tropical mountains, where high species turnover along elevational gradients occurs over relatively short distances and elevational distributions of particular species can shift among mountains. Such shifts are interpreted as evidence of the importance of spatial variation in interspecific competition and habitat or climatic gradients. To assess the relative importance of competition and compression of habitat and climatic zones in setting range limits, we examined differences in elevational ranges of forest bird species among four Bornean mountains with distinct features.</p> Location <p>Bornean mountains Kinabalu, Mulu, Pueh and Topap Oso.</p> Taxon <p>Rain forest bird communities along elevational gradients.</p> Methods <p>We surveyed the elevational ranges of rain forest birds on four mountains in Borneo to test which environmental variables—habitat zone compression or presence of likely competitors—best predicted differences in elevational ranges of species among mountains. For this purpose, we used two complementary tests: a comparison of elevational range limits between pairs of mountains, and linear mixed models with naïve occupancy as the response variable.</p> Results <p>We found that lowland species occur higher in elevation on two small mountains compared to Mt. Mulu. This result is inconsistent with the expectation that distributions of habitats are elevationally compressed on small mountains, but is consistent with the hypothesis that a reduction in competition (likely diffuse) on short mountains, which largely lack montane specialist species, allows lowland species to occur higher in elevation. The relative influence of competition changes with elevation, and the correlation between lower range limits of montane species and the distribution of their competitors was weaker than in lowland species.</p> Main conclusions <p>These findings provide support for the importance of biotic interactions in setting elevational range limits of tropical bird species, although abiotic gradients explain the majority of distribution patterns. Thus, models predicting range shifts under climate change scenarios must include not only climatic variables, as is currently most common, but also information on potentially resulting changes in species interactions, especially for lowland species.</p>
Accompanying dataset for: Predicting Species Emergence in Simulated Complex Pre-Biotic Networks
<p>This is the accompanying data and code for the publication [Markovitch & Krasnogor: Predicting Species Emergence in Simulated Complex Pre-Biotic Networks] containing the full set of 10,000 lognormal networks studied, their network communities and the compotype species observed during simulations with the GARD model. Details are given in the aforementioned paper. Please see also: http://ico2s.org/</p> <p>This work was funded by the UK's Engineering and Physical Sciences Research Council (EPSRC) under projects (EP/J004111/2) "Towards a Universal Biological-Cell Operating System (AUdACiOuS)" and (EP/N031962/1) "Synthetic Portabolomics: Leading the way at the crossroads of the Digital and the Bio Economies"</p> <p> </p>
Fig. 10 in A new assessment of the Late Devonian antiarchan fish Bothriolepis leptocheira from South Timan (Russia) and the biotic crisis near the Frasnian-Famennian boundary
Fig. 10. Antiarchan fish Bothriolepis leptocheira jeremejevi (Rohon, 1900), Sosnogorsk locality, Sosnogorsk Formation, lowermost Famennian, anterior dorso-lateral (A–D, F, left; E, right) and left mixilateral (G–I, right) plates of the trunk armour. A. IG KSC 155/116 in dorsal (A1) and visceral (A2) views. B. IG KSC 155/111. C. IG KSC 155/61. D. IG KSC 155/60. E. IG KSC 155/136. F. IG KSC 155/112. G. IG KSC 155/110. H. Incomplete IG KSC 155/144. I. IG KSC 155/115. B–E, G–I, in dorsal views; F, in lateral view. Abbreviations: ADL, anterior ventro-lateral plate; AMD, anterior median dorsal plate; AVL, anterior ventro-lateral plate; cf.AMD, area overlapping AMD; dlg2, posterior oblique dorsal sensory line groove; dlr, dorso-lateral ridge of trunk armour; dxp, dorso-ventral pit-line groove; lcg, main lateral line groove; oa.ADL, oa.AMD, oa.AVL, oa.PMD, area overlapped by ADL, AMD, AVL or PMD respectively; PMD, posterior median dorsal plate; pnoa, postnuchal ornamented corner of ADL; pro, processus obstans of trunk armour.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.