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1. Terrestrial Parasite Tracker indexed biotic interactions and review summary

   https://doi.org/10.5281/zenodo.7194486  

   Poelen, Jorrit H; Seltmann, Katja C; Campbell, Mariel; Orlofske, Sarah A; Light, Jessica E; Tucker, Erika M; Demboski, John R; McElrath, Tommy; Grinter, Christopher C; Diaz-Bastin, Rachel; et al (January 2022, Zenodo)

   {"Abstract":["PLEASE CONTACT AUTHORS IF YOU CONTRIBUTED AND WOULD LIKE TO BE LISTED AS A CO-AUTHOR. Terrestrial Parasite Tracker indexed biotic interactions and review summary. The Terrestrial Parasite Tracker (TPT) project began in 2019 and is funded by the National Science foundation to mobilize data from vector and ectoparasite collections to data aggregators (e.g., iDigBio, GBIF) to help build a comprehensive picture of arthropod host-association evolution, distributions, and the ecological interactions of disease vectors which will assist scientists, educators, land managers, and policy makers. Arthropod parasites often are important to human and wildlife health and safety as vectors of pathogens, and it is critical to digitize these specimens so that they, and their biotic interaction data, will be available to help understand and predict the spread of human and wildlife disease. This data publication contains versioned TPT associated datasets and related data products that were tracked, reviewed and indexed by Global Biotic Interactions (GloBI) and associated tools. 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. 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. Funding: The creation of this archive was made possible by 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 References: 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. GloBI Data Review Report Datasets under review: - University of Michigan Museum of Zoology Insect Division. Full Database Export 2020-11-20 provided by Erika Tucker and Barry Oconner. accessed via https://github.com/EMTuckerLabUMMZ/ummzi/archive/6731357a377e9c2748fc931faa2ff3dc0ce3ea7a.zip on 2022-10-12T18:43:37.491Z - Academy of Natural Sciences Entomology Collection for the Parasite Tracker Project accessed via https://github.com/globalbioticinteractions/ansp-para/archive/5e6592ad09ec89ba7958266ad71ec9d5d21d1a44.zip on 2022-10-12T18:45:13.893Z - Bernice Pauahi Bishop Museum, J. Linsley Gressitt Center for Research in Entomology accessed via https://github.com/globalbioticinteractions/bpbm-ent/archive/c085398dddd36f8a1169b9cf57de2a572229341b.zip on 2022-10-12T18:47:33.370Z - Texas A&M University, Biodiversity Teaching and Research Collections accessed via https://github.com/globalbioticinteractions/brtc-para/archive/f0a718145b05ed484c4d88947ff712d5f6395446.zip on 2022-10-12T18:49:42.688Z - Brigham Young University Arthropod Museum accessed via https://github.com/globalbioticinteractions/byu-byuc/archive/4a609ac6a9a03425e2720b6cdebca6438488f029.zip on 2022-10-12T18:50:01.049Z - California Academy of Sciences Entomology accessed via https://github.com/globalbioticinteractions/cas-ent/archive/562aea232ec74ab615f771239451e57b057dc7c0.zip on 2022-10-12T18:50:25.480Z - Clemson University Arthropod Collection accessed via https://github.com/globalbioticinteractions/cu-cuac/archive/6cdcbbaa4f7cec8e1eac705be3a999bc5259e00f.zip on 2022-10-12T18:50:53.662Z - Denver Museum of Nature and Science (DMNS) Parasite specimens (DMNS:Para) accessed via https://github.com/globalbioticinteractions/dmns-para/archive/2a15f657d5e2d7a6ee6359ee30e630bde8fea2ee.zip on 2022-10-12T18:52:36.684Z - Field Museum of Natural History IPT accessed via https://github.com/globalbioticinteractions/fmnh/archive/6bfc1b7e46140e93f5561c4e837826204adb3c2f.zip on 2022-10-12T19:19:24.919Z - Illinois Natural History Survey Insect Collection accessed via https://github.com/globalbioticinteractions/inhs-insects/archive/38692496f590577074c7cecf8ea37f85d0594ae1.zip on 2022-10-12T19:21:30.100Z - UMSP / University of Minnesota / University of Minnesota Insect Collection accessed via https://github.com/globalbioticinteractions/min-umsp/archive/3f1b9d32f947dcb80b9aaab50523e097f0e8776e.zip on 2022-10-12T19:22:18.235Z - Milwaukee Public Museum Biological Collections Data Portal accessed via https://github.com/globalbioticinteractions/mpm/archive/9f44e99c49ec5aba3f8592cfced07c38d3223dcd.zip on 2022-10-12T19:22:42.835Z - Museum for Southwestern Biology (MSB) Parasite Collection accessed via https://github.com/globalbioticinteractions/msb-para/archive/f13bfa0d5493057198639d566f744379c05179f3.zip on 2022-10-12T20:46:06.063Z - The Albert J. Cook Arthropod Research Collection accessed via https://github.com/globalbioticinteractions/msu-msuc/archive/38960906380443bd8108c9e44aeff4590d8d0b50.zip on 2022-10-12T21:02:26.320Z - Ohio State University Acarology Laboratory accessed via https://github.com/globalbioticinteractions/osal-ar/archive/876269d66a6a94175dbb6b9a604897f8032b93dd.zip on 2022-10-12T21:02:46.553Z - Frost Entomological Museum, Pennsylvania State University accessed via https://github.com/globalbioticinteractions/psuc-ento/archive/30b1f96619a6e9f10da18b42fb93ff22cc4f72e2.zip on 2022-10-12T21:02:57.714Z - Purdue Entomological Research Collection accessed via https://github.com/globalbioticinteractions/pu-perc/archive/e0909a7ca0a8df5effccb288ba64b28141e388ba.zip on 2022-10-12T21:03:17.696Z - Texas A&M University Insect Collection accessed via https://github.com/globalbioticinteractions/tamuic-ent/archive/f261a8c192021408da67c39626a4aac56e3bac41.zip on 2022-10-12T21:03:56.509Z - University of California Santa Barbara Invertebrate Zoology Collection accessed via https://github.com/globalbioticinteractions/ucsb-izc/archive/4d997dbe8e86398f9f7f4d7851013e788073ae9c.zip on 2022-10-12T21:05:27.222Z - University of Hawaii Insect Museum accessed via https://github.com/globalbioticinteractions/uhim/archive/53fa790309e48f25685e41ded78ce6a51bafde76.zip on 2022-10-12T21:05:40.778Z - University of New Hampshire Collection of Insects and other Arthropods UNHC-UNHC accessed via https://github.com/globalbioticinteractions/unhc/archive/f72575a72edda8a4e6126de79b4681b25593d434.zip on 2022-10-12T21:05:59.319Z - Scott L. Gardner and Gabor R. Racz (2021). University of Nebraska State Museum - Parasitology. Harold W. Manter Laboratory of Parasitology. University of Nebraska State Museum. accessed via https://github.com/globalbioticinteractions/unl-nsm/archive/6bcd8aec22e4309b7f4e8be1afe8191d391e73c6.zip on 2022-10-12T21:06:07.054Z - Data were obtained from specimens belonging to the United States National Museum of Natural History (USNM), Smithsonian Institution, Washington DC and digitized by the Walter Reed Biosystematics Unit (WRBU). accessed via https://github.com/globalbioticinteractions/usnmentflea/archive/ce5cb1ed2bbc13ee10062b6f75a158fd465ce9bb.zip on 2022-10-12T21:06:43.102Z - US National Museum of Natural History Ixodes Records accessed via https://github.com/globalbioticinteractions/usnm-ixodes/archive/c5fcd5f34ce412002783544afb628a33db7f47a6.zip on 2022-10-12T21:06:51.935Z - Price Institute of Parasite Research, School of Biological Sciences, University of Utah accessed via https://github.com/globalbioticinteractions/utah-piper/archive/43da8db550b5776c1e3d17803831c696fe9b8285.zip on 2022-10-12T21:07:03.317Z - University of Wisconsin Stevens Point, Stephen J. Taft Parasitological Collection accessed via https://github.com/globalbioticinteractions/uwsp-para/archive/f9d0d52cd671731c7f002325e84187979bca4a5b.zip on 2022-10-12T21:07:14.513Z - Giraldo-Calderón, G. I., Emrich, S. J., MacCallum, R. M., Maslen, G., Dialynas, E., Topalis, P., … Lawson, D. (2015). VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases. Nucleic acids research, 43(Database issue), D707–D713. doi:10.1093/nar/gku1117. accessed via https://github.com/globalbioticinteractions/vectorbase/archive/00d6285cd4e9f4edd18cb2778624ab31b34b23b8.zip on 2022-10-12T21:07:22.543Z - WIRC / University of Wisconsin Madison WIS-IH / Wisconsin Insect Research Collection accessed via https://github.com/globalbioticinteractions/wis-ih-wirc/archive/34162b86c0ade4b493471543231ae017cc84816e.zip on 2022-10-12T21:07:52.105Z - Yale University Peabody Museum Collections Data Portal accessed via https://github.com/globalbioticinteractions/yale-peabody/archive/43be869f17749d71d26fc820c8bd931d6149fe8e.zip on 2022-10-12T21:16:57.226Z Generated on: 2022-10-12 by: GloBI's Elton 0.12.4 (see https://github.com/globalbioticinteractions/elton). Note that all files ending with .tsv are files formatted as UTF8 encoded tab-separated values files. https://www.iana.org/assignments/media-types/text/tab-separated-values Included in this review archive are: README: This file. review_summary.tsv: Summary across all reviewed collections of total number of distinct review comments. review_summary_by_collection.tsv: Summary by reviewed collection of total number of distinct review comments. indexed_interactions_by_collection.tsv: Summary of number of indexed interaction records by institutionCode and collectionCode. review_comments.tsv.gz: All review comments by collection. indexed_interactions_full.tsv.gz: All indexed interactions for all reviewed collections. indexed_interactions_simple.tsv.gz: All indexed interactions for all reviewed collections selecting only sourceInstitutionCode, sourceCollectionCode, sourceCatalogNumber, sourceTaxonName, interactionTypeName and targetTaxonName. datasets_under_review.tsv: Details on the datasets under review. elton.jar: Program used to update datasets and generate the review reports and associated indexed interactions. datasets.zip: Source datasets used by elton.jar in process of executing the generate_report.sh script. generate_report.sh: Program used to generate the report generate_report.log: Log file generated as part of running the generate_report.sh script"]} 

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2. Big Bee indexed biotic interactions and review summary

   https://doi.org/10.5281/zenodo.8184843  

   Seltmann, Katja C; Poelen, Jorrit H; Allen, Julie; Eldredge, K Taro; Engel, Michael; Gonzalez, Victor; Knowles, L Lacey; Horsley, Pam (January 2023, Zenodo)

   {"Abstract":["Extending Anthophila research through image and trait digitization (Big-Bee) indexed biotic interactions and review summary. 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. 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. 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. Bee Library Information - Statistics about Big Bee data providers The specimens indexed by GloBI are also found in the Bee Library. 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. From Bee Library (partner indexed records) 1,234,107 occurrence records 993,692 (81%) georeferenced 351,592 (28%) occurrences imaged 986,323 (80%) identified to species 9 families 526 genera 10,700 species 11,386 total taxa (including subsp. and var.) Statistics Per Collection Collection Occurrences Georeferenced Imaged Interactions Indexed in GloBI (all) Interactions Indexed in GloBI (bees) ASU Hasbrouck Insect Collection - Bee Records 13223 13221 2352 21300 3834 Bee Biology and Systematics Laboratory, USDA-ARS Pollinating Insect-Biology, Management, Systematics Research 561820 547461 0 0 0 California Academy of Sciences 884 300 3 16984 117 California Academy of Sciences - Type Collection 1838 59 83 0 0 Essig Museum of Entomology, University of California Berkeley 58551 55028 0 0 Florida State Collection of Arthropods 17134 12349 7816 559 Museum of Comparative Zoology, Harvard University 22020 21099 11595 6777 1535 Natural History Museum of Los Angeles County 24685 7421 3480 0 0 San Diego Natural History Museum Entomology Department 4065 1690 1982 8688 90 University of California Santa Barbara Invertebrate Zoology Collection 8674 8410 2751 1940 660 University of Colorado Museum of Natural History, Entomology Collection 18043 18043 0 9589 4723 University of Kansas Natural History Museum Entomology Division 464927 275200 304415 119963 112677 University of Michigan Museum of Zoology Division of Insects 17764 15305 15269 53755 4134 University of New Hampshire, Donald S. Chandler Entomological Collection 17685 17393 0 3137 3137 USGS Native Bee Inventory and Monitoring Lab 101 101 0 0 0 GloBI Data Review Report - Datasets in Review from Global Biotic Interactions Datasets under review: - 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 - Arizona State University Hasbrouck Insect Collection accessed via https://github.com/globalbioticinteractions/asu-asuhic/archive/4ed77cb9ca8e526269d4678692e2844c950022f8.zip on 2023-07-24T22:07:09.630Z - 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 - 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 - Florida State Collection of Arthropods accessed via https://github.com/globalbioticinteractions/fsca/archive/2cdcf9475b7e0ef2a728a96535608bc0ce2ac5ca.zip on 2023-07-24T22:08:49.972Z - University of Kansas Natural History Museum accessed via https://github.com/globalbioticinteractions/ku-semc/archive/a9c7cb81050eef68b4428667206a219da458f517.zip on 2023-07-24T22:09:17.016Z - 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 - 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 - San Diego Natural History Museum accessed via https://github.com/globalbioticinteractions/sdnhm-sdmc/archive/7238d8b804f543250eb487b43144e1125fb3688a.zip on 2023-07-24T22:26:25.503Z - 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 - 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 - 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 Generated on: 2023-07-24 by: GloBI's Elton 0.12.6 (see https://github.com/globalbioticinteractions/elton). Note that all files ending with .tsv are files formatted as UTF8 encoded tab-separated values files. https://www.iana.org/assignments/media-types/text/tab-separated-values Included in this review archive are: README: This file. review_summary.tsv: Summary across all reviewed collections of total number of distinct review comments. review_summary_by_collection.tsv: Summary by reviewed collection of total number of distinct review comments. indexed_interactions_by_collection.tsv: Summary of number of indexed interaction records by institutionCode and collectionCode. review_comments.tsv.gz: All review comments by collection. indexed_interactions_full.tsv.gz: All indexed interactions for all reviewed collections. indexed_interactions_simple.tsv.gz: All indexed interactions for all reviewed collections selecting only sourceInstitutionCode, sourceCollectionCode, sourceCatalogNumber, sourceTaxonName, interactionTypeName and targetTaxonName. datasets_under_review.tsv: Details on the datasets under review. elton.jar: Program used to update datasets and generate the review reports and associated indexed interactions. indexed_interactions_bees.tsv: All indexed bee interactions datasets.zip: All datasets reviewed for this publication Big Bee Metrics from the Bee Library and GloBI - July 24, 2023.pdf: Summary statistics from the Bee Library and GloBI about data partners 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. Funding: 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: DBI:2102006, DBI:2101929, DBI:2101908, DBI:2101876, DBI:2101875, DBI:2101851, DBI:2101345, DBI:2101913, DBI:2101891 and DBI:2101850. References: Poelen JH, Simons JD and Mungall CH. (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. 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. https://doi.org/10.3897/biss.5.74037 Jorrit Poelen, Tobias Kuhn, & Katrin Leinweber. (2022). globalbioticinteractions/elton: 0.12.5 (0.12.5). Zenodo. https://doi.org/10.5281/zenodo.7267926"],"Other":["{"references": ["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. https://doi.org/10.3897/biss.5.74037", "Poelen JH, Simons JD and Mungall CH. (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.", "Jorrit Poelen, Tobias Kuhn, & Katrin Leinweber. (2022). globalbioticinteractions/elton: (0.12.4). Zenodo. https://doi.org/10.5281/zenodo.6385185"]}"]} 

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3. Big Bee indexed biotic interactions and review summary

   https://doi.org/10.5281/zenodo.7865367  

   Seltmann, Katja C; Poelen, Jorrit H; Allen, Julie; Eldredge, K Taro; Engel, Michael; Gonzalez, Victor; Knowles, L Lacey; Horsley, Pam (January 2023, Zenodo)

   {"Abstract":["Extending Anthophila research through image and trait digitization (Big-Bee) indexed biotic interactions and review summary. 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. 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. 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. Bee Library Information - Statistics about Big Bee data providers The specimens indexed by GloBI are also found in the Bee Library. 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 27 2022.pdf file. From Bee Library (partner indexed records) 1,218,256 occurrence records 992,776 (81%) georeferenced 350,105 (29%) occurrences imaged 1,004,491 (82%) identified to species 9 families 523 genera 10,808 species 11,492 total taxa (including subsp. and var.) Statistics per Collection (partner collections) Collection Occurrences Georeferenced Imaged Interactions Indexed in GloBI (all) Interactions Indexed in GloBI (bees) ASU Hasbrouck Insect Collection - Bee Records 13219 13217 2047 19774 3834 Bee Biology and Systematics Laboratory, USDA-ARS Pollinating Insect-Biology, Management, Systematics Research 561820 547461 0 0 0 California Academy of Sciences 873 286 3 16957 117 California Academy of Sciences - Type Collection 1838 59 83 0 0 Essig Museum of Entomology, University of California Berkeley 58548 55022 0 0 0 Florida State Collection of Arthropods 12290 12246 8979 0 0 Museum of Comparative Zoology, Harvard University 22020 21099 11595 6476 1535 Natural History Museum of Los Angeles County 16442 7420 3372 0 0 San Diego Natural History Museum Entomology Department 4065 1690 1980 8678 90 University of California Santa Barbara Invertebrate Zoology Collection 8678 8416 2646 1940 659 University of Colorado Museum of Natural History, Entomology Collection 18043 18043 0 9589 4723 University of Kansas Natural History Museum Entomology Division 464896 275180 304405 119947 112674 University of Michigan Museum of Zoology Division of Insects 17738 15143 14995 53602 4120 University of New Hampshire, Donald S. Chandler Entomological Collection 17685 17393 0 3137 3137 USGS Native Bee Inventory and Monitoring Lab 101 101 0 0 0 Generated on: GloBI Data Review Report - Datasets in Review from Global Biotic Interactions GloBI Data Review Report Datasets under review: - University of Michigan Museum of Zoology, Division of Insects accessed via https://github.com/globalbioticinteractions/ummz-ummzi/archive/d9282e51f29f3157af2e5869a09ea8a111ddea34.zip on 2023-04-25T19:48:17.288Z - Arizona State University Hasbrouck Insect Collection accessed via https://github.com/globalbioticinteractions/asu-asuhic/archive/4ed77cb9ca8e526269d4678692e2844c950022f8.zip on 2023-04-25T19:49:18.649Z - California Academy of Sciences Entomology and Entomology Type Collection accessed via https://github.com/globalbioticinteractions/cas-ent/archive/47d385b73a63aa379cd5e6d3615005ba78b0ffc1.zip on 2023-04-25T19:50:01.820Z - University of California Berkeley, Essig Museum of Entomology accessed via https://github.com/globalbioticinteractions/emec/archive/93b17a3db566baa001ce9190e6fbdb60fa99dda4.zip on 2023-04-25T19:50:38.682Z - Florida State Collection of Arthropods accessed via https://github.com/globalbioticinteractions/fsca/archive/682f11686317ae81959a043bd6b493ddfc06c438.zip on 2023-04-25T19:51:09.435Z - University of Kansas Natural History Museum accessed via https://github.com/globalbioticinteractions/ku-semc/archive/a9c7cb81050eef68b4428667206a219da458f517.zip on 2023-04-25T19:51:51.861Z - Natural History Museum of Los Angeles County accessed via https://github.com/globalbioticinteractions/lacm-lacmec/archive/dafbf532c53fbadba126c81186c26d52677aa781.zip on 2023-04-25T19:53:50.488Z - 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 2023-04-25T20:05:19.619Z - San Diego Natural History Museum accessed via https://github.com/globalbioticinteractions/sdnhm-sdmc/archive/7238d8b804f543250eb487b43144e1125fb3688a.zip on 2023-04-25T20:11:18.816Z - University of Colorado Museum of Natural History Entomology Collection accessed via https://github.com/globalbioticinteractions/ucm-ucmc/archive/60530dcc82d33c9675a4026ad60dc40bea8f2a91.zip on 2023-04-25T20:11:45.143Z - University of California Santa Barbara Invertebrate Zoology Collection accessed via https://github.com/globalbioticinteractions/ucsb-izc/archive/66a4e39589d1dfa299d07985546c4be522ff60d8.zip on 2023-04-25T20:12:06.236Z - University of New Hampshire Donald S. Chandler Entomological Collection accessed via https://github.com/globalbioticinteractions/unhc-unhc/archive/d7668a6bb4545dc4da0645ecc383169ba547b0f5.zip on 2023-04-25T20:12:21.404Z Generated on: 2023-04-25 by: GloBI's Elton 0.12.6 (see https://github.com/globalbioticinteractions/elton). Note that all files ending with .tsv are files formatted as UTF8 encoded tab-separated values files. https://www.iana.org/assignments/media-types/text/tab-separated-values indexed_interactions_bees.tsv: All indexed bee interactions datasets.zip: All datasets reviewed for this publication Big Bee Metrics from the Bee Library and GloBI - Apr 25, 2023.pdf: Summary statistics from the Bee Library and GloBI about data partners 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. Funding: 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: DBI:2102006, DBI:2101929, DBI:2101908, DBI:2101876, DBI:2101875, DBI:2101851, DBI:2101345, DBI:2101913, DBI:2101891 and DBI:2101850. References: Poelen JH, Simons JD and Mungall CH. (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. 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. https://doi.org/10.3897/biss.5.74037 Jorrit Poelen, Tobias Kuhn, & Katrin Leinweber. (2022). globalbioticinteractions/elton: 0.12.5 (0.12.5). Zenodo. https://doi.org/10.5281/zenodo.7267926"],"Other":["{"references": ["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. https://doi.org/10.3897/biss.5.74037", "Poelen JH, Simons JD and Mungall CH. (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.", "Jorrit Poelen, Tobias Kuhn, & Katrin Leinweber. (2022). globalbioticinteractions/elton: (0.12.4). Zenodo. https://doi.org/10.5281/zenodo.6385185"]}"]} 

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4. Global Bee Interaction Data

   https://doi.org/10.5281/zenodo.12639658  

   Seltmann, Katja C; Poelen, Jorrit H; Global_Biotic_Interaction_Community (January 2024, Zenodo)

   Last modified: July 3, 2024 IntroductionThis dataset comprises all bee interactions indexed by Global Biotic Interactions (GloBI; Poelen et al. 2014). It is published quarterly by the Big Bee Project (Seltmann et al. 2021) to summarize all available knowledge about bee interactions from natural history collections, community science observations (i.e., iNaturalist), and the literature. Interactions include flower visitation, parasitic interactions (mite, viral), lecty, and many others. Data DescriptionPlease see the [integration process page](https://www.globalbioticinteractions.org/process) to better understand how Global Biotic Interactions combines datasets from various sources. The complete interaction dataset for all species can be accessed via https://www.globalbioticinteractions.org/data. Data is filtered for unique records based on the interaction description and source citation. Archives contain full data records and unique filtered records in tab-delimited format. Dataset column name definitions https://api.globalbioticinteractions.org/interactionFields or https://api.globalbioticinteractions.org/interactionFields Duplicate records occur in the database because more than one provider shares information. This is most frequently occuring in museum specimen data and duplicates can be identified evaluating the institutionCode, collectionCode and catalogNumber fields. The file catalogNumber_counts.tsv groups records by these three fields for this dataset, but does not filter out duplicate records. Additionally, this dataset includes the citation information provided by the data publisher. The provided sourceCitation may not include information about the primary provider (often the natural history collection) the specimen data originates and the catalogNumber should be referenced to understand the original source of the data. Summary statistics about the dataset can be found in the bees-only-review.pdf file. This review of all bee data indexed by Global Biotic Interactions was created using GloBI’s Interaction Data Review Report Framework via repository https://github.com/Big-Bee-Network/select-bee-interactions.sh. Metrics Date Total bee records 07-17-2020 232,906 01-24-2021 257,738 11-17-2021 226,160 06-01-2022 286,818 11-07-2022 429,308 01-18-2024 842,819 07-03-2024 1,109,057   Date Andrenidae Apidae Colletidae Halictidae 07-17-2020 73,463 106,222 20,821 58,880 01-24-2021 77,824 120,919 21,376 63,945 11-17-2021 25,535 134,517 10,568 43,070 06-01-2022 78,016 144,827 20,409 64,054 11-07-2022 84,172 171,378 30,792 79,155 01-18-2024 166,473 334,224 63,847 171,931 07-03-2024 289,400 371,953 83,337 190,562   Date Megachilidae Melittidae Stenotritidae 07-17-2020 44,449 2,511 23 01-24-2021 48,856 2,624 18 11-17-2021 37,001 995 9 06-01-2022 54,516 2,994 18 11-07-2022 61,391 2,396 24 01-18-2024 100,814 5,088 442 07-03-2024 162,587 4,964 438   Included Resources count sourceCitation 219440 Symbiota Collections of Arthropods Network (SCAN) 156437 University of Kansas Natural History Museum 150780 Digital Bee Collections Network, 2014 (and updates). Version: 2015-03-18. National Science Foundation grant DBI#0956388 134657 USGS Biodiversity Information Serving Our Nation (BISON) IPT 126820 http://iNaturalist.org is a place where you can record what you see in nature, meet other nature lovers, and learn about the natural world. 44522 PaDIL Bee records from the Pests and Diseases Image Library, http://www.padil.gov.au. 38658 University of Michigan Museum of Zoology Insect Division. Full Database Export 2020-11-20 provided by Erika Tucker and Barry Oconner. 27711 Carril OM, Griswold T, Haefner J, Wilson JS. (2018) Wild bees of Grand Staircase-Escalante National Monument: richness, abundance, and spatio-temporal beta-diversity. PeerJ 6:e5867 https://doi.org/10.7717/peerj.5867 15506 Seltmann, K., Van Wagner, J., Behm, R., Brown, Z., Tan, E., & Liu, K. (2020). BID: A project to share biotic interaction and ecological trait data about bees (Hymenoptera: Anthophila). UC Santa Barbara: Cheadle Center for Biodiversity and Ecological Restoration. Retrieved from https://escholarship.org/uc/item/1g21k7bf 14666 Web of Life. http://www.web-of-life.es . 14577 Pensoft Darwin Core Archives available via Integrated Publication Toolkit 13447 University of Colorado Museum of Natural History Entomology Collection 13296 https://mangal.io - the ecological interaction database. 10705 National Database Plant Pollinators. Center for Plant Conservation at San Diego Zoo Global. Accessed via https://saveplants.org/national-collection/pollinator-search/ on 2020-06-05. 8529 Ollerton, J., Trunschke, J. ., Havens, K. ., Landaverde-González, P. ., Keller, A. ., Gilpin, A.-M. ., Rodrigo Rech, A. ., Baronio, G. J. ., Phillips, B. J., Mackin, C. ., Stanley, D. A., Treanore, E. ., Baker, E. ., Rotheray, E. L., Erickson, E. ., Fornoff, F. ., Brearley, F. Q. ., Ballantyne, G. ., Iossa, G. ., Stone, G. N., Bartomeus, I. ., Stockan, J. A., Leguizamón, J., Prendergast, K. ., Rowley, L., Giovanetti, M., de Oliveira Bueno, R., Wesselingh, R. A., Mallinger, R., Edmondson, S., Howard, S. R., Leonhardt, S. D., Rojas-Nossa, S. V., Brett, M., Joaqui, T., Antoniazzi, R., Burton, V. J., Feng, H.-H., Tian, Z.-X., Xu, Q., Zhang, C., Shi, C.-L., Huang, S.-Q., Cole, L. J., Bendifallah, L., Ellis, E. E., Hegland, S. J., Straffon Díaz, S., Lander, T. A. ., Mayr, A. V., Dawson, R. ., Eeraerts, M. ., Armbruster, W. S. ., Walton, B. ., Adjlane, N. ., Falk, S. ., Mata, L. ., Goncalves Geiger, A. ., Carvell, C. ., Wallace, C. ., Ratto, F. ., Barberis, M. ., Kahane, F. ., Connop, S. ., Stip, A. ., Sigrist, M. R. ., Vereecken, N. J. ., Klein, A.-M., Baldock, K. ., & Arnold, S. E. J. . (2022). Pollinator-flower interactions in gardens during the COVID-19 pandemic lockdown of 2020. Journal of Pollination Ecology, 31, 87–96. https://doi.org/10.26786/1920-7603(2022)695 8014 Redhead, J.W.; Coombes, C.F.; Dean, H.J.; Dyer, R.; Oliver, T.H.; Pocock, M.J.O.; Rorke, S.L.; Vanbergen, A.J.; Woodcock, B.A.; Pywell, R.F. (2018). Plant-pollinator interactions database for construction of potential networks. NERC Environmental Information Data Centre. https://doi.org/10.5285/6d8d5cb5-bd54-4da7-903a-15bd4bbd531b 7630 CaraDonna, P.J. 2020. Temporal variation in plant-pollinator interactions, Rocky Mountain Biological Laboratory, CO, USA, 2013 - 2015 ver 1. Environmental Data Initiative. https://doi.org/10.6073/pasta/27dc02fe1655e3896f20326fed5cb95f (Accessed 2021-04-16). 6921 Purdue Entomological Research Collection 6911 Arizona State University Hasbrouck Insect Collection 6430 LaManna, JA, Burkle, LA, Belote, RT, Myers, JA. Biotic and abiotic drivers of plant–pollinator community assembly across wildfire gradients. J Ecol. 2020; 00: 1– 14. https://doi.org/10.1111/1365-2745.13530 . 6288 Pensoft Darwin Core Archives with associateTaxa columns 6269 Eardley C, Coetzer W. 2016. Catalogue of Afrotropical Bees. 6114 University of Michigan Museum of Zoology, Division of Insects 5089 Magrach, Ainhoa et al. (2017), Data from: Plant-pollinator networks in semi-natural grasslands are resistant to the loss of pollinators during blooming of mass-flowering crops, Dryad, Dataset, https://doi.org/10.5061/dryad.k0q1n 3860 Giselle Muschett & Francisco E. Fontúrbel. 2021. A comprehensive catalogue of plant – pollinator interactions for Chile 3720 Frost Entomological Museum, Pennsylvania State University 3670 Natural History Collections managed by Arctos (https://arctosdb.org) accessed via https://vertnet.org . 3620 Sarah E Miller. 6/19/2015. Species associations manually extracted from datasets https://www.nceas.ucsb.edu/interactionweb/resources.html. 3581 Robert L. Minckley San Bernardino Valley from the year 2000 to 2011. 3581 University of New Hampshire Collection of Insects and other Arthropods UNHC-UNHC 3581 University of New Hampshire Donald S. Chandler Entomological Collection 2242 Sarah E. Miller. 07/06/2017. Information extracted from dataset https://www.idigbio.org/portal/recordsets/db4bb0df-8539-4617-ab5f-eb118aa3126b. 2223 Bartomeus, Ignasi (2013): Plant-Pollinator Network Data. figshare. Dataset. https://doi.org/10.6084/m9.figshare.154863.v1 2110 Illinois Natural History Survey Insect Collection 2074 Florida State Collection of Arthropods 2035 Ed Baker; Ian J. Kitching; George W. Beccaloni; Amoret Whitaker et al. (2016). Dataset: NHM Interactions Bank. Natural History Museum Data Portal (data.nhm.ac.uk). https://doi.org/10.5519/0060767 1762 Poelen, Jorrit H. (2023). A biodiversity dataset graph: Biological Associations in TaxonWorks hash://sha256/a4d651aac5220487835e6178511886e98b845b2d98cb7c5447fb2b042e0654d2 hash://md5/849edbe55e31e54ea5cdaba0188c5655 (0.2) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.8253729 1681 Harvard University M, Morris P J (2021). Museum of Comparative Zoology, Harvard University. Museum of Comparative Zoology, Harvard University. 1563 Ballantyne, Gavin; Baldock, Katherine C. R.; Willmer, Pat G. (2015), Data from: Constructing more informative plant-pollinator networks: visitation and pollen deposition networks in a heathland plant community, Dryad, Dataset, https://doi.org/10.5061/dryad.17pp3 1365 Sarah E Miller. 5/30/2016. Interations from various papers. 1281 Sarah E Miller. 4/18/2016. Species associations from Wardeh, M. et al. Database of host-pathogen and related species interactions, and their global distribution. Sci. Data 2:150049 doi: 10.1038/sdata.2015.49 (2015) 1102 University of California Santa Barbara Invertebrate Zoology Collection 1086 Cohen JM, Sauer EL, Santiago O, Spencer S, Rohr JR. 2020. Divergent impacts of warming weather on wildlife disease risk across climates. Science. doi:10.1126/science.abb1702 939 Allen Hurlbert. 2017. Avian Diet Database. 918 Texas A&M University Insect Collection 906 Del Risco, A.A., Montoya, Á.M., García, V. et al. Data synthesis and dynamic visualization converge into a comprehensive biotic interaction network: a case study of the urban and rural areas of Bogotá D.C.. Urban Ecosyst (2021). https://doi.org/10.1007/s11252-021-01133-3 872 Cristina Preda and Quentin Groom. 2014. Species associations manually extracted from literature. 754 United States Geological Survey (USGS) Pollinator Library. https://www.npwrc.usgs.gov/pollinator. 752 Sarah E Miller. 6/22/2015. Species associations manually extracted from datasets https://www.nceas.ucsb.edu/interactionweb/resources.html. 750 RCPol: Online Pollen Catalogs Network. 2016. https://rcpol.org.br/ 744 Classen, Alice; Steffan-Dewenter, Ingolf (2020): Plant-pollinator interactions along an elevational gradient on Mt. Kilimanjaro. PANGAEA, https://doi.org/10.1594/PANGAEA.911390 704 Yale University Peabody Museum Collections Data Portal 677 The Albert J. Cook Arthropod Research Collection 541 Udy, Kristy; Reininghaus, Hannah; Scherber, Christoph; Tscharntke, Teja (2020), Data from: Plant-pollinator interactions along an urbanization gradient from cities and villages to farmland landscapes, Dryad, Dataset, https://doi.org/10.5061/dryad.4mw6m906s 524 Pardee, G.L., Ballare, K.M., Neff, J.L., Do, L.Q., Ojeda, D., Bienenstock, E.J., Brosi, B.J., Grubesic, T.H., Miller, J.A., Tong, D. and Jha, S., 2023. Local and Landscape Factors Influence Plant-Pollinator Networks and Bee Foraging Behavior across an Urban Corridor. Land, 12(2), p.362. https://www.mdpi.com/2073-445X/12/2/362 511 Sarah E Miller. 6/25/2015. Species associations manually extracted from Robertson, C. 1929. Flowers and insects: lists of visitors to four hundred and fifty-three flowers. Carlinville, IL, USA, C. Robertson. 511 The International Barcode of Life Consortium (2016). International Barcode of Life project (iBOL). Occurrence dataset https://doi.org/10.15468/inygc6 454 Seltzer, Carrie; Wysocki, William; Palacios, Melissa; Eickhoff, Anna; Pilla, Hannah; Aungst, Jordan; Mercer, Aaron; Quicho, Jamie; Voss, Neil; Xu, Man; J. Ndangalasi, Henry; C. Lovett, Jon; J. Cordeiro, Norbert (2015): Plant-animal interactions from Africa. figshare. https://dx.doi.org/10.6084/m9.figshare.1526128 342 Mycology Collections Data Portal (MyCoPortal). 2020. https://mycoportal.org 292 Global Web Database (http://globalwebdb.com): an online collection of food webs. Accessed via https://www.globalwebdb.com/Service/DownloadArchive on 2017-10-12. 268 University of Wisconsin Stevens Point, Stephen J. Taft Parasitological Collection 241 University of Hawaii Insect Museum 168 Sarah E Miller. 12/13/2016. Species associations manually extracted from Onstad, D.W. EDWIP: Ecological Database of the World's Insect Pathogens. Champaign, Illinois: Illinois Natural History Survey, [23/11/2016]. http://insectweb.inhs.uiuc.edu/Pathogens/EDWIP. 153 California Academy of Sciences Entomology and Entomology Type Collection 127 Olito, Colin; Fox, Jeremy W. (2015), Data from: Species traits and abundances predict metrics of plant–pollinator network structure, but not pairwise interactions, Dryad, Dataset, https://doi.org/10.5061/dryad.7st32 114 Kari Lintulaakso. 2023. MammalBase Diet Database. 106 Brose, U. (2018). GlobAL daTabasE of traits and food Web Architecture (GATEWAy) version 1.0 [Data set]. German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig. https://doi.org/10.25829/IDIV.283-3-756 104 Groom, Q.J., Maarten De Groot, M. & Marčiulynienė, D. (2020) Species interation data manually extracted from literature for species . 96 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 . 93 Jakovos Demetriou and Quentin Groom 2014. Species associations of Sceliphron manually extracted from literature. 92 San Diego Natural History Museum 80 Price Institute of Parasite Research, School of Biological Sciences, University of Utah 59 National Museum of Natural History, Smithsonian Institution IPT RSS Feed 56 Poelen, JH (2016). Plant pathogen-host interactions scraped from Common Names of Plant Diseases published by the American Phytopathological Society at http://www.apsnet.org/publications/commonnames/Pages/default.aspx using Samara, a Planteome (http://planteome.org) plant-trait scraper. 50 Florez-Montero, G.L., Muylaert, R.L., Nogueira, M.R., Geiselman, C., Santana, S.E., Stevens, R.D., Tschapka, M., Rodrigues, F.A. and Mello, M.A.R. (2022), NeoBat Interactions: A data set of bat–plant interactions in the Neotropics. Ecology. Accepted Author Manuscript e3640. https://doi.org/10.1002/ecy.3640 50 Ferrer-Paris, José R.; Sánchez-Mercado, Ada Y.; Lozano, Cecilia; Zambrano, Liset; Soto, José; Baettig, Jessica; Leal, María (2014): A compilation of larval host-plant records for six families of butterflies (Lepidoptera: Papilionoidea) from available electronic resources. figshare. http://dx.doi.org/10.6084/m9.figshare.1168861 39 Pocock, Michael J. O.; Evans, Darren M.; Memmott, Jane (2012), Data from: The robustness and restoration of a network of ecological networks, Dryad, Dataset, https://doi.org/10.5061/dryad.3s36r118 37 Sarah E Miller. 9/19/2016. Species associations extracted from Graystock, P., Blane, E.J., McFrederick, Q.S., Goulson, D. and Hughes, W.O., 2016. Do managed bees drive parasite spread and emergence in wild bees?. International Journal for Parasitology: Parasites and Wildlife, 5(1), pp.64-75. 36 Mihara, T., Nishimura, Y., Shimizu, Y., Nishiyama, H., Yoshikawa, G., Uehara, H., Hingamp, P., Goto, S., and Ogata, H.; Linking virus genomes with host taxonomy. Viruses 8, 66 doi:10.3390/v8030066 (2016). 36 Quentin J. Groom. 2020. Species interactions of species on the List of invasive alien species of Union concern 33 IPBES. (2016). The assessment report of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services on pollinators, pollination and food production. Table 2.4.3 p88 Zenodo. https://doi.org/10.5281/zenodo.3402857 30 Brigham Young University Arthropod Museum 24 Geiselman, Cullen K. & Sarah Younger. 2020. Bat Eco-Interactions Database. www.batbase.org 24 Geiselman, Cullen K. and Tuli I. Defex. 2015. Bat Eco-Interactions Database. www.batplant.org 23 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 . 21 Species Connect. https://speciesconnect.com 17 http://invertebrates.si.edu/parasites.htm 14 Gandhi, K. J. K., & Herms, D. A. (2009). North American arthropods at risk due to widespread Fraxinus mortality caused by the Alien Emerald ash borer. Biological Invasions, 12(6), 1839–1846. doi:10.1007/s10530-009-9594-1. 12 Food Webs and Species Interactions in the Biodiversity of UK and Ireland (Online). 2017. Data provided by Malcolm Storey. Also available from http://bioinfo.org.uk. 12 Sarah E Miller. 5/28/2015. Arnaud, Paul Henri. A Host-parasite Catalog of North American Tachinidae (Diptera). Washington, D.C.: U.S. Dept. of Agriculture, Science and Education Administration, 1978. 10 University of California Santa Barbara Herbarium 9 Field Museum of Natural History IPT 8 Brose, U. et al., 2005. Body sizes of consumers and their resources. Ecology, 86(9), pp.2545–2545. Available at: http://dx.doi.org/10.1890/05-0379. 8 Strong, Justin S., and Shawn J. Leroux. 2014. "Impact of Non-Native Terrestrial Mammals on the Structure of the Terrestrial Mammal Food Web of Newfoundland, Canada." PLOS ONE 9 (8): e106264. https://doi.org/10.1371/journal.pone.0106264 7 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. 5 Froese, R. and D. Pauly. Editors. 2018. FishBase. World Wide Web electronic publication. www.fishbase.org, version (10/2018). 5 Pinnegar, J.K. (2014). DAPSTOM - An Integrated Database & Portal for Fish Stomach Records. Version 4.7. Centre for Environment, Fisheries & Aquaculture Science, Lowestoft, UK. February 2014, 39pp. 4 Aja Sherman, Cullen Geiselman. 2021. Bat Co-Roosting Database 4 Bernice Pauahi Bishop Museum, J. Linsley Gressitt Center for Research in Entomology 4 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 4 Sarah E Miller. 7/7/2016. Text gathered from Wirta, H.K., Vesterinen, E.J., Hambäck, P.A., Weingartner, E., Rasmussen, C., Reneerkens, J., Schmidt, N.M., Gilg, O. and Roslin, T., 2015. Exposing the structure of an Arctic food web. Ecology and evolution, 5(17), pp.3842-3856. 4 Sarah E Miller. 9/15/2016. Species associations extracted from http://parasiticplants.siu.edu/index.html. 4 Sarah E. Miller. 04/14/2015. Extracted from literature Scott, J.A. 1986.  The Butterflies of North America.  Stanford University Press, Stanford, CA 4 Scott L. Gardner and Gabor R. Racz (2021). University of Nebraska State Museum - Parasitology. Harold W. Manter Laboratory of Parasitology. University of Nebraska State Museum. 2 Deans, Andrew (2021). Catalog of Rose Gall, Herb Gall, and Inquiline Gall Wasps (Hymenoptera: Cynipidae) of the United States, Canada, and Mexico 2 Jorrit H. Poelen. 2017. Species interactions associated with known species interaction datasets. 2 Museum for Southwestern Biology (MSB) Parasite Collection 2 Sarah E Miller. 4/20/2015. Species associations manually extracted from various papers and articles from site https://repository.si.edu 2 Seltmann, Katja C. 2020. Biotic species interactions about ticks manually extracted from literature. 2 Species Interactions of Australia Database (SIAD): Helping us to understand species interactions in Australia and beyond. http://www.discoverlife.org/siad/ . 1 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 1 Grundler MC (2020) SquamataBase: a natural history database and R package for comparative biology of snake feeding habits. Biodiversity Data Journal 8: e49943. https://doi.org/10.3897/BDJ.8.e49943 1 Gunther KA et al. 2014 Dietary breadth of grizzly bears in the Greater Yellowstone Ecosystem. Ursus 25(1):60-72 1 Sarah E Miller. 7/6/2016. Arctos collection. Included files bee_data_BID.sh - script for separating bee records into family uniq_citations.tsv - list of unique citations indicating bee interactions Andrenidae_data_unique.tsv - Andrenidae records     Apidae_data_unique.tsv - Apidae records         Colletidae_data_unique.tsv - Colletidae records Halictidae_data_unique.tsv - Halictidae records     Megachilidae_data_unique.tsv - Megachilidae records     Melittidae_data_unique.tsv - Melittidae records Stenotritidae_data_unique.tsv - Stenotritidae records bees-only-interactions.tsv.zip - list of all bee interaction data indexed on Global Biotic Interactions from GloBI version 2024-06-07 produced by https://github.com/Big-Bee-Network/select-bee-interactions.sh bees-only-review.pdf - Review of all bee data indexed by Global Biotic Interactions using GloBI’s Interaction Data Review Report Framework via repository https://github.com/Big-Bee-Network/select-bee-interactions.sh catalogNumber_counts.tsv - counts by catalogNumber in dataset. Duplicate catalog numbers indicate duplicated data shared by multiple data providers. ReferencesGloBI 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. Poelen JH, Simons JD, Mungall CJ (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 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. https://doi.org/10.3897/biss.5.74037 Poelen, JS & Seltmann, KS (2024) Bees Only Please: Bees Only Please: Selecting Hundreds of Thousands of Possible Bee Interactions Using a Laptop, Open Datasets, and Small (but Mighty) Commandline Tools. https://www.globalbioticinteractions.org/2024/06/07/bees-only-please Ascher, J. S. and J. Pickering (2020) Discover Life bee species guide and world checklist (Hymenoptera: Apoidea: Anthophila). http://www.discoverlife.org/mp/20q?guide=Apoidea_species. Acknowledgements This project is supported by the National Science Foundation. Award numbers: DBI:2102006, DBI:2101929, DBI:2101908, DBI:2101876, DBI:2101875, DBI:2101851, DBI:2101345, DBI:2101913, DBI:2101891 and DBI:2101850 

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5. UC Santa Barbara Invertebrate Zoology Collection (UCSB-IZC) Data Archive and Biodiversity Dataset Graph

   https://doi.org/10.5281/zenodo.5557670  

   Cheadle Center for Biodiversity and Ecological Restoration, University of (January 2021, Zenodo)

   {"Abstract":["A biodiversity dataset graph: UCSB-IZC<\/p>\n\nThe intended use of this archive is to facilitate (meta-)analysis of the UC Santa Barbara Invertebrate Zoology Collection (UCSB-IZC). UCSB-IZC is a natural history collection of invertebrate zoology at Cheadle Center of Biodiversity and Ecological Restoration, University of California Santa Barbara.<\/p>\n\nThis dataset provides versioned snapshots of the UCSB-IZC network as tracked by Preston [2,3] on 2021-10-08 using [preston track "https://api.gbif.org/v1/occurrence/search/?datasetKey=d6097f75-f99e-4c2a-b8a5-b0fc213ecbd0"].<\/p>\n\nThis archive contains 14137 images related to 33730 occurrence/specimen records. See included sample-image.jpg and their associated meta-data sample-image.json [4].<\/p>\n\nThe archive consists of 256 individual parts (e.g., preston-00.tar.gz, preston-01.tar.gz, ...) to allow for parallel file downloads. The archive contains three types of files: index files, provenance files and data files. Only two index and provenance files are included and have been individually included in this dataset publication. Index files provide a way to links provenance files in time to establish a versioning mechanism.<\/p>\n\nTo retrieve and verify the downloaded UCSB-IZC biodiversity dataset graph, first download preston-*.tar.gz. Then, extract the archives into a "data" folder. Alternatively, you can use the Preston [2,3] command-line tool to "clone" this dataset using:<\/p>\n\n$$ java -jar preston.jar clone --remote https://archive.org/download/preston-ucsb-izc/data.zip/,https://zenodo.org/record/5557670/files<\/p>\n\nAfter that, verify the index of the archive by reproducing the following provenance log history:<\/p>\n\n$$ java -jar preston.jar history\n<urn:uuid:0659a54f-b713-4f86-a917-5be166a14110> <http://purl.org/pav/hasVersion> <hash://sha256/d5eb492d3e0304afadcc85f968de1e23042479ad670a5819cee00f2c2c277f36> .<\/p>\n\nTo check the integrity of the extracted archive, confirm that each line produce by the command "preston verify" produces lines as shown below, with each line including "CONTENT_PRESENT_VALID_HASH". Depending on hardware capacity, this may take a while.<\/p>\n\n$ java -jar preston.jar verify\nhash://sha256/ce1dc2468dfb1706a6f972f11b5489dc635bdcf9c9fd62a942af14898c488b2c    file:/home/jhpoelen/ucsb-izc/data/ce/1d/ce1dc2468dfb1706a6f972f11b5489dc635bdcf9c9fd62a942af14898c488b2c    OK    CONTENT_PRESENT_VALID_HASH    66438    hash://sha256/ce1dc2468dfb1706a6f972f11b5489dc635bdcf9c9fd62a942af14898c488b2c\nhash://sha256/f68d489a9275cb9d1249767244b594c09ab23fd00b82374cb5877cabaa4d0844    file:/home/jhpoelen/ucsb-izc/data/f6/8d/f68d489a9275cb9d1249767244b594c09ab23fd00b82374cb5877cabaa4d0844    OK    CONTENT_PRESENT_VALID_HASH    4093    hash://sha256/f68d489a9275cb9d1249767244b594c09ab23fd00b82374cb5877cabaa4d0844\nhash://sha256/3e70b7adc1a342e5551b598d732c20b96a0102bb1e7f42cfc2ae8a2c4227edef    file:/home/jhpoelen/ucsb-izc/data/3e/70/3e70b7adc1a342e5551b598d732c20b96a0102bb1e7f42cfc2ae8a2c4227edef    OK    CONTENT_PRESENT_VALID_HASH    5746    hash://sha256/3e70b7adc1a342e5551b598d732c20b96a0102bb1e7f42cfc2ae8a2c4227edef\nhash://sha256/995806159ae2fdffdc35eef2a7eccf362cb663522c308aa6aa52e2faca8bb25b    file:/home/jhpoelen/ucsb-izc/data/99/58/995806159ae2fdffdc35eef2a7eccf362cb663522c308aa6aa52e2faca8bb25b    OK    CONTENT_PRESENT_VALID_HASH    6147    hash://sha256/995806159ae2fdffdc35eef2a7eccf362cb663522c308aa6aa52e2faca8bb25b<\/p>\n\nNote that a copy of the java program "preston", preston.jar, is included in this publication. The program runs on java 8+ virtual machine using "java -jar preston.jar", or in short "preston".<\/p>\n\nFiles in this data publication:<\/p>\n\n--- start of file descriptions ---<\/p>\n\n-- description of archive and its contents (this file) --\nREADME<\/p>\n\n-- executable java jar containing preston [2,3] v0.3.1. --\npreston.jar<\/p>\n\n-- preston archive containing UCSB-IZC (meta-)data/image files, associated provenance logs and a provenance index --\npreston-[00-ff].tar.gz<\/p>\n\n-- individual provenance index files --\n2a5de79372318317a382ea9a2cef069780b852b01210ef59e06b640a3539cb5a<\/p>\n\n-- example image and meta-data --\nsample-image.jpg (with hash://sha256/916ba5dc6ad37a3c16634e1a0e3d2a09969f2527bb207220e3dbdbcf4d6b810c)\nsample-image.json (with hash://sha256/f68d489a9275cb9d1249767244b594c09ab23fd00b82374cb5877cabaa4d0844)<\/p>\n\n--- end of file descriptions ---<\/p>\n\n\nReferences<\/p>\n\n[1] Cheadle Center for Biodiversity and Ecological Restoration (2021). University of California Santa Barbara Invertebrate Zoology Collection. Occurrence dataset https://doi.org/10.15468/w6hvhv accessed via GBIF.org on 2021-10-08 as indexed by the Global Biodiversity Informatics Facility (GBIF) with provenance hash://sha256/d5eb492d3e0304afadcc85f968de1e23042479ad670a5819cee00f2c2c277f36.\n[2] https://preston.guoda.bio, https://doi.org/10.5281/zenodo.1410543 .\n[3] MJ Elliott, JH Poelen, JAB Fortes (2020). Toward Reliable Biodiversity Dataset References. Ecological Informatics. https://doi.org/10.1016/j.ecoinf.2020.101132\n[4] Cheadle Center for Biodiversity and Ecological Restoration (2021). University of California Santa Barbara Invertebrate Zoology Collection. Occurrence dataset https://doi.org/10.15468/w6hvhv accessed via GBIF.org on 2021-10-08. https://www.gbif.org/occurrence/3323647301 . hash://sha256/f68d489a9275cb9d1249767244b594c09ab23fd00b82374cb5877cabaa4d0844 hash://sha256/916ba5dc6ad37a3c16634e1a0e3d2a09969f2527bb207220e3dbdbcf4d6b810c<\/p>"],"Other":["This work is funded in part by grant NSF OAC 1839201 and NSF DBI 2102006 from the National Science Foundation."]} 

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