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1. Global Bee Interaction Data

   https://doi.org/10.5281/zenodo.17715382  

   Seltmann, Katja C; Poelen, Jorrit H; Global_Biotic_Interaction_Community (January 2025, Zenodo)

   {"Abstract":["Last modified: January 09, 2025\n\nIntroductionThis 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.\n\nData DescriptionPlease see the integration process page 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.\n\nData 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.\n\nDataset column name definitions https://api.globalbioticinteractions.org/interactionFields or https://api.globalbioticinteractions.org/interactionFields\n\nDuplicate 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.\n\nIf you know of a missing dataset, or wish to share your dataset, please contact us!\n\n \n\nMetrics\n\n\n\n\nDate\n\n\nTotal bee records\n\n\n\n07-17-2020\n232,906\n\n\n01-24-2021\n257,738\n\n\n11-17-2021\n226,160\n\n\n06-01-2022\n286,818\n\n\n11-07-2022\n429,308\n\n\n01-18-2024\n842,819\n\n\n07-03-2024\n1,109,057\n\n\n01-09-2025\n1,223,768\n\n\n11-25-2025\n2,480,473\n\n\n\n\n \n\n\n\n\nDate\nAndrenidae\nApidae\nColletidae\nHalictidae\n\n\n07-17-2020\n73,463\n106,222\n20,821\n58,880\n\n\n01-24-2021\n77,824\n120,919\n21,376\n63,945\n\n\n11-17-2021\n25,535\n134,517\n10,568\n43,070\n\n\n06-01-2022\n78,016\n144,827\n20,409\n64,054\n\n\n11-07-2022\n84,172\n171,378\n30,792\n79,155\n\n\n01-18-2024\n166,473\n334,224\n63,847\n171,931\n\n\n07-03-2024\n\n\n289,400\n\n\n\n371,953\n\n\n\n83,337\n\n\n\n190,562\n\n\n\n01-09-2025\n\n\n204,565\n\n\n\n686,195\n\n\n\n70,724\n\n\n\n241,856\n\n\n\n11-25-2025\n\n\n269,191\n\n\n\n1,509,768\n\n\n\n129,763\n\n\n\n386,203\n\n\n\n\n\n \n\n\n\n\nDate\nMegachilidae\nMelittidae\nStenotritidae\n\n\n07-17-2020\n44,449\n2,511\n23\n\n\n01-24-2021\n48,856\n2,624\n18\n\n\n11-17-2021\n37,001\n995\n9\n\n\n06-01-2022\n54,516\n2,994\n18\n\n\n11-07-2022\n61,391\n2,396\n24\n\n\n01-18-2024\n100,814\n5,088\n442\n\n\n07-03-2024\n\n\n162,587\n\n\n\n4,964\n\n438\n\n\n01-09-2025\n\n\n126,113\n\n\n\n5,928\n\n441\n\n\n11-25-2025\n\n\n174,935\n\n\n\n9,764\n\n849\n\n\n\n\n \n\nIncluded files\n\n\n\nfilter_and_count_bee_families.sh - script for separating bee records into family and counting number of records for each family\n\ncitation-count.sh - script for counting citations\n\nfamily_counts.tsv - counts by family\n\nglobi-bees-filtered_file.tsv.gz - list of all bee interaction data indexed on Global Biotic Interactions from GloBI version 2025-Nov-25 produced by [filter_and_count_bee_families.sh].\n\ninteractions.tsv.gz - archive of the full Global Biotic Interaction dataset on November 25, 2025. Downloaded from https://www.globalbioticinteractions.org\n\n\n \n\nInteraction Sources\n\nBelow is a list of sources that contributed to this dataset, along with raw counts of unique interactions and links to the corresponding digital archives and reviews. These datasets are indexed and reviewed by Global Biotic Interactions (GloBI) using automated, reproducible workflows that extract species-interaction records, reconcile taxonomic names against authoritative catalogs, and summarize the findings. Each review produces a versioned digital archive to ensure long-term preservation and to document data provenance. For details, see the Methods section within each linked archive.\n\n\n\n\ncount\nsource\n\n\n276746\n\n\n\n\nhttp://iNaturalist.org is a place where you can record what you see in nature, meet other nature lovers, and learn about the natural world.\n\n\n\n\n266822\n\n\n\n\nReji Chacko, M., Albouy, C., Altermatt, F., Brändle, M., Casanelles Abella, J., Boussange, V., Campell, F., Ellis, W. N., Fopp, F., Gossner, M. M., Ho., H., Joss, A., Kipf, P., Neff, F., Petrović, A., Prié, V., Tomanović, Ž., Zimmerli, N., Pellissier, L. (2024). trophiCH v1 - a food web for Switzerland. EnviDat. https://www.doi.org/10.16904/envidat.467.\n\n\n\n\n258683\n\n\n\n\nUSGS Biodiversity Information Serving Our Nation (BISON) IPT\n\n\n\n\n180849\n\n\n\n\necdysis - a portal for live-managing arthropod occurrence data\n\n\n\n\n113301\n\n\n\n\nDigital Bee Collections Network, 2014 (and updates). Version: 2015-03-18. National Science Foundation grant DBI 0956388; PBI: Phytophagous Insects as a Model Group for Documenting Planetary Biodiversity (Insecta: Heteroptera: Miridae: Orthotylinae, Phylinae). Version: 08 Mar 2016. National Science Foundation grant DBI#0316495; Tri-Trophic Thematic Collection Network, 2014 (and updates). Version: 08 Mar 2016. http://tcn.amnh.org/. National Science Foundation grant(s) EF#1115081, EF#1115103, EF#1115080, EF#1115144, EF#1115191, EF#1115104, EF#1115115\n\n\n\n\n112006\n\n\n\n\nUniversity of Kansas Natural History Museum - Snow Entomological Museum Collection\n\n\n\n\n79134\n\n\n\n\nSymbiota Collections of Arthropods Network (SCAN)\n\n\n\n\n62736\n\n\n\n\nFrost Entomological Museum, Pennsylvania State University\n\n\n\n\n49513\n\n\n\n\nLanuza et al. (2025), EuPPollNet: A European Database of Plant-Pollinator Networks. Global Ecol Biogeogr, 34: e70000. https://doi.org/10.1111/geb.70000\n\n\n\n\n41298\n\n\n\n\nBalfour, N.J., Castellanos, M.C., Goulson, D., Philippides, A. and Johnson, C., 2022. DoPI: The Database of Pollinator Interactions. Ecology, 103, e3801.\n\n\n\n\n28517\n\n\n\n\nPaDIL Bee records from the Pests and Diseases Image Library, http://www.padil.gov.au.\n\n\n\n\n27114\n\n\n\n\nGuzman, Laura Melissa; Kelly, Tyler; Elle, Elizabeth, 2022, "A dataset for pollinator diversity and their interactions with plants in the Pacific NorthWest", https://doi.org/10.5683/SP3/WTEZNH, Borealis, V1\n\n\n\n\n24564\n\n\n\n\nUniversity of Michigan Museum of Zoology Insect Division. Full Database Export 2020-11-20 provided by Erika Tucker and Barry Oconner.\n\n\n\n\n23727\n\n\n\n\nCarril 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\n\n\n\n\n18757\n\n\n\n\nA. Thessen. 2014. Species associations extracted from EOL text data objects via text mining.\n\n\n\n\n18003\n\n\n\n\nPensoft Darwin Core Archives available via Integrated Publication Toolkit\n\n\n\n\n17603\n\n\n\n\nDorey, J.B., Fischer, E.E., Chesshire, P.R. et al. A globally synthesised and flagged bee occurrence dataset and cleaning workflow. Sci Data 10, 747 (2023). https://doi.org/10.1038/s41597-023-02626-w\n\n\n\n\n17088\n\n\n\n\nVandame R, Mérida J, Sagot P, Madrigal González D, Bedolla García B Y, González-Vanegas P A, Cultid-Medina C A, Barrios J M (2023). Potential host plant records recovered from ECOAB wild bee collection, Mexico. Version 1.10. Comisión nacional para el conocimiento y uso de la biodiversidad.\n\n\n\n\n15763\n\n\n\n\nSchwarz, Benjamin et al. (2021). Data from: Temporal scale-dependence of plant-pollinator networks [Dataset]. Dryad. https://doi.org/10.5061/dryad.qz612jmbp\n\n\n\n\n10211\n\n\n\n\nPensoft Darwin Core Archives with associateTaxa columns\n\n\n\n\n9104\n\n\n\n\nAmerican Museum of Natural History Hymenoptera\n\n\n\n\n8678\n\n\n\n\nAubouin, L., Genoud, D., Givord-Coupeau, B. et al. BeeFunc, a comprehensive trait database for French bees. Sci Data 12, 1302 (2025). https://doi.org/10.1038/s41597-025-05626-0\n\n\n\n\n8657\n\n\n\n\nWeb of Life. http://www.web-of-life.es .\n\n\n\n\n6600\n\n\n\n\nUniversity of Michigan Museum of Zoology, Division of Insects\n\n\n\n\n6331\n\n\n\n\nAllen-Perkins, Alfonso, Magrach, Ainhoa, Dainese, Matteo, Garibaldi, Lucas A., Kleijn, David, Rader, Romina, Reilly, James R., et al. 2022. "CropPol: A Dynamic, Open and Global Database on Crop Pollination." 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K. and Jones, Lance E. and Mills, Kirby L. and Scholtens, Brian G. and Simons, Meagan and Thompson, Cody and Tourville, Jordon and Valdovinos, Fernanda S.}, year={2024}, month=jul }\n\n\n\n\n5531\n\n\n\n\nhttps://mangal.io - the ecological interaction database.\n\n\n\n\n5316\n\n\n\n\nClint Otto, Russ Bryant, and Ned H. Euliss Jr., 2020, The U.S. Geological Survey Pollinator Library Dataset: U.S. Geological Survey. https://doi.org/10.5066/P9DSS3VL\n\n\n\n\n4688\n\n\n\n\nUniversity of Colorado Museum of Natural History Entomology Collection\n\n\n\n\n4680\n\n\n\n\nNational 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.\n\n\n\n\n4284\n\n\n\n\nSeltmann, 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). 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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\n\n\n\n\n2831\n\n\n\n\nRobert L. Minckley San Bernardino Valley from the year 2000 to 2011.\n\n\n\n\n2778\n\n\n\n\nHarvard University M, Morris P J (2021). Museum of Comparative Zoology, Harvard University. Museum of Comparative Zoology, Harvard University.\n\n\n\n\n2252\n\n\n\n\nGiselle Muschett & Francisco E. Fontúrbel. 2021. A comprehensive catalogue of plant – pollinator interactions for Chile\n\n\n\n\n2068\n\n\n\n\nCohen 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\n\n\n\n\n2038\n\n\n\n\nSarah E. Miller. 07/06/2017. Information extracted from dataset https://www.idigbio.org/portal/recordsets/db4bb0df-8539-4617-ab5f-eb118aa3126b.\n\n\n\n\n1884\n\n\n\n\nInternational Council for the Exploration of the Sea (ICES). Year of The Stomach Datasets.\n\n\n\n\n1815\n\n\n\n\nhttp://gomexsi.tamucc.edu\n\n\n\n\n1812\n\n\n\n\n@article {Keck2025.01.24.634685, author = {Keck, Fran{\\c c}ois and Broadbent, Henry and Altermatt, Florian},title = {Extracting massive ecological data on state and interactions of species using large language models},year = {2025},doi = {10.1101/2025.01.24.634685},journal = {bioRxiv}}\n\n\n\n\n1766\n\n\n\n\nFricke, E.C., Svenning, J. 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The diversity and evolution of pollination systems in large plant clades: Apocynaceae as a case study. Ann Bot. 2019 Jan 23;123(2):311-325. doi: 10.1093/aob/mcy127. PMID: 30099492; PMCID: PMC6344220.\n\n\n\n\n760\n\n\n\n\nIllinois Natural History Survey Insect Collection\n\n\n\n\n721\n\n\n\n\nPoelen, J. H. (2024). A biodiversity dataset graph: Biological Associations in TaxonWorks hash://sha256/e4a47c067d6c125da60c9a1b92b5eecdea539cb8666cd3aed99db347ae5b8ed0 hash://md5/686007de79cc2a49ab23fd3debe56e3f [Data set]. Zenodo. https://doi.org/10.5281/zenodo.11151783\n\n\n\n\n711\n\n\n\n\nTexas A&M University Insect Collection\n\n\n\n\n703\n\n\n\n\nNatural History Collections managed by Arctos (https://arctosdb.org) accessed via https://vertnet.org .\n\n\n\n\n688\n\n\n\n\nRusso, Laura; Fitzpatrick, Una; Larkin, Michelle et al. (2022). Database of plant-flower visitor interactions from Ireland [Dataset]. Dryad. https://doi.org/10.5061/dryad.kwh70rz47\n\n\n\n\n634\n\n\n\n\nClassen, Alice; Steffan-Dewenter, Ingolf (2020): Plant-pollinator interactions along an elevational gradient on Mt. Kilimanjaro. PANGAEA, https://doi.org/10.1594/PANGAEA.911390\n\n\n\n\n627\n\n\n\n\nA review of the status of web-based African Plant-Pollinator Interaction data.\n\n\n\n\n607\n\n\n\n\nScott L. Gardner and Gabor R. Racz (2021). University of Nebraska State Museum - Parasitology. Harold W. Manter Laboratory of Parasitology. University of Nebraska State Museum.\n\n\n\n\n590\n\n\n\n\nNational Museum of Natural History, Smithsonian Institution IPT RSS Feed\n\n\n\n\n563\n\n\n\n\nRaymond, B., Marshall, M., Nevitt, G., Gillies, C., van den Hoff, J., Stark, J.S., Losekoot, M., Woehler, E.J., and Constable, A.J. (2011) A Southern Ocean dietary database. Ecology 92(5):1188. Available from http://dx.doi.org/10.1890/10-1907.1 . Data set supplied by Ben Raymond.\n\n\n\n\n555\n\n\n\n\nSarah E Miller. 6/22/2015. Species associations manually extracted from datasets https://www.nceas.ucsb.edu/interactionweb/resources.html.\n\n\n\n\n492\n\n\n\n\nRCPol: Online Pollen Catalogs Network. 2016. https://rcpol.org.br/\n\n\n\n\n480\n\n\n\n\nPinnegar, 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.\n\n\n\n\n459\n\n\n\n\nPardee, 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\n\n\n\n\n437\n\n\n\n\nThe Albert J. Cook Arthropod Research Collection\n\n\n\n\n409\n\n\n\n\nSarah 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.\n\n\n\n\n384\n\n\n\n\nBoreux, Virginie; Klein, Alexandra-Maria (2019). Global pollinator database. figshare. Dataset. https://doi.org/10.6084/m9.figshare.9980471.v1\n\n\n\n\n334\n\n\n\n\nFroese, R. and D. Pauly. Editors. 2018. FishBase. World Wide Web electronic publication. www.fishbase.org, version (10/2018).\n\n\n\n\n320\n\n\n\n\nHurlbert, A. H., Olsen, A. M., Sawyer, M. M., and Winner, P. M. 2021. Avian Diet Database. https://doi.org/10.5281/zenodo.5151056\n\n\n\n\n296\n\n\n\n\nGlobal Web Database (http://globalwebdb.com): an online collection of food webs. Accessed via https://www.globalwebdb.com/Service/DownloadArchive on 2017-10-12.\n\n\n\n\n290\n\n\n\n\nCalifornia Academy of Sciences Entomology and Entomology Type Collection\n\n\n\n\n290\n\n\n\n\nSarah E Miller. 06/10/2015. Species associations manually extracted from Chamberlin, W. J. The Buprestidae of North America, Exclusive of Mexico, a Catalogue including Synonomy, Bibliography, Distribution, Type Locality and Hosts of Each Species,. 1926.\n\n\n\n\n274\n\n\n\n\nBENSCH, S., HELLGREN, O. and PÉREZ‐TRIS, J. (2009), MalAvi: a public database of malaria parasites and related haemosporidians in avian hosts based on mitochondrial cytochrome b lineages. Molecular Ecology Resources, 9: 1353-1358. https://doi.org/10.1111/j.1755-0998.2009.02692.x\n\n\n\n\n263\n\n\n\n\nCanterbury Museum. (2025). Canterbury Museum (CMNZ) collection insect specimen-plant flower interactions (0.4) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.15429172\n\n\n\n\n263\n\n\n\n\nFood 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.\n\n\n\n\n259\n\n\n\n\nhttp://invertebrates.si.edu/parasites.htm\n\n\n\n\n248\n\n\n\n\nWorldFAIR pilot data from: VisitationData_Luisa_Carvalheiro.\n\n\n\n\n246\n\n\n\n\nEneida 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 .\n\n\n\n\n230\n\n\n\n\nUniversity of Hawaii Insect Museum\n\n\n\n\n211\n\n\n\n\nPalomares, M.L.D. and D. Pauly. Editors. 2018. SeaLifeBase. World Wide Web electronic publication. www.sealifebase.org, version (10/2018).\n\n\n\n\n204\n\n\n\n\n@article{Sabino_2022, doi = {10.1016/j.agee.2022.108012}, url = {https://doi.org/10.1016%2Fj.agee.2022.108012}, year = 2022, month = {sep}, publisher = {Elsevier {BV}}, volume = {335}, pages = {108012}, author = {William Sabino and Luciano Costa and Tamires Andrade and Juliana Teixeira and Gustavo Araújo and André Luís Acosta and Luísa Carvalheiro and Tereza Cristina Giannini}, title = {Status and trends of pollination services in Amazon agroforestry systems}, journal = {Agriculture, Ecosystems & Environment}}\n\n\n\n\n181\n\n\n\n\nBrigham Young University Arthropod Museum\n\n\n\n\n179\n\n\n\n\nStokland, J.; Dahlberg, A.; Meyke, E.; Schigel, D.; Siitonen, J. (2006) The Nordic saproxylic database - a comprehensive overview of the biological diversity in dead wood. 1st European Congress of Conservation Biology - "Diversity for Europe". August 2006, Hungary. Book of Abstracts. Society of Conservation Biology (USA) & Blackwell Publishing (UK) p. 159 .\n\n\n\n\n169\n\n\n\n\nUniversity of Wisconsin Stevens Point, Stephen J. Taft Parasitological Collection\n\n\n\n\n164\n\n\n\n\nStephens, P. R., Pappalardo, P. , Huang, S. , Byers, J. E., Farrell, M. J., Gehman, A. , Ghai, R. R., Haas, S. E., Han, B. , Park, A. W., Schmidt, J. P., Altizer, S. , Ezenwa, V. O. and Nunn, C. L. (2017), Global Mammal Parasite Database version 2.0. Ecology, 98: 1476-1476. doi:10.1002/ecy.1799\n\n\n\n\n162\n\n\n\n\nBrose, U. et al., 2005. Body sizes of consumers and their resources. Ecology, 86(9), pp.2545–2545. Available at: https://doi.org/10.1890/05-0379.\n\n\n\n\n159\n\n\n\n\nCruz, G.L.T., Winck, G.R., D’Andrea, P.S. et al. Integrating databases for spatial analysis of parasite-host associations and the novel Brazilian dataset. Sci Data 10, 757 (2023). https://doi.org/10.1038/s41597-023-02636-8\n\n\n\n\n143\n\n\n\n\nYale University Peabody Museum Collections Data Portal\n\n\n\n\n141\n\n\n\n\nWIRC / University of Wisconsin Madison WIS-IH / Wisconsin Insect Research Collection\n\n\n\n\n134\n\n\n\n\nBartomeus, Ignasi (2013): Plant-Pollinator Network Data. figshare. Dataset. https://doi.org/10.6084/m9.figshare.154863.v1\n\n\n\n\n133\n\n\n\n\nSarah 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.\n\n\n\n\n128\n\n\n\n\nLlewelyn, J., Strona, G., Dickman, C.R., Greenville, A.C., Wardle, G.M., Lee, M.S.Y., Doherty, S., Shabani, F., Saltré, F. and Bradshaw, C.J.A. (2023), Predicting predator–prey interactions in terrestrial endotherms using random forest. Ecography e06619. https://doi.org/10.1111/ecog.06619\n\n\n\n\n119\n\n\n\n\nSpecies Interactions of Australia Database (SIAD): Helping us to understand species interactions in Australia and beyond. http://www.discoverlife.org/siad/ .\n\n\n\n\n116\n\n\n\n\nField Museum of Natural History IPT\n\n\n\n\n106\n\n\n\n\nGroom, Q.J., Maarten De Groot, M. & Marčiulynienė, D. (2020) Species interation data manually extracted from literature for species .\n\n\n\n\n106\n\n\n\n\nLintulaakso, K., Tatti, N. and Žliobaitė, I., 2023. Quantifying mammalian diets. Mammalian Biology, 103(1), pp.53-67. https://doi.org/10.1007/s42991-022-00323-6\n\n\n\n\n99\n\n\n\n\nMihara, 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).\n\n\n\n\n92\n\n\n\n\nSan Diego Natural History Museum\n\n\n\n\n79\n\n\n\n\nCarlson, C.J. et al., 2021. The Global Virome in One Network (VIRION): an atlas of vertebrate-virus associations. Available at: http://dx.doi.org/10.1101/2021.08.06.455442\n\n\n\n\n79\n\n\n\n\nCristina Preda and Quentin Groom. 2014. Species associations manually extracted from literature.\n\n\n\n\n72\n\n\n\n\nFaulwetter S, Markantonatou V, Pavloudi C, Papageorgiou N, Keklikoglou K, Chatzinikolaou E, Pafilis E, Chatzigeorgiou G, Vasileiadou K, Dailianis T, Fanini L, Koulouri P, Arvanitidis C (2014) Polytraits: A database on biological traits of marine polychaetes. Biodiversity Data Journal 2: e1024. doi:10.3897/BDJ.2.e1024 . Available at http://polytraits.lifewatchgreece.eu.\n\n\n\n\n62\n\n\n\n\nUS National Museum of Natural History Ixodes Records\n\n\n\n\n60\n\n\n\n\nAlmeida, F. (2005) Trophic Ecology of Atlantic Cod, off Cape Cod, MA, from F/V Riena Marie NEC-FA2001-1 in the Gulf of Maine from 2001-2004 (NEC-CoopRes project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version final) Version Date 2005-10-01 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/3087\n\n\n\n\n54\n\n\n\n\nFarr, David F.; Rossman, Amy Y.; Castlebury, Lisa A. (2021). United States National Fungus Collections Fungus-Host Dataset. Ag Data Commons. https://doi.org/10.15482/USDA.ADC/1524414.\n\n\n\n\n53\n\n\n\n\nSoleto-Casas RC and Simões N (2020). Parasitic and commensal invertebrates of echinoderms from American Tropical And Subtropical Atlantic manually extracted from literature.\n\n\n\n\n48\n\n\n\n\nSemantic Prototypes in Research Ecoinformatics (SPIRE). Data provided by Joel Sachs. See also http://ebiquity.umbc.edu/get/a/publication/297.pdf .\n\n\n\n\n45\n\n\n\n\nOlito, 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\n\n\n\n\n43\n\n\n\n\nPrice Institute of Parasite Research, School of Biological Sciences, University of Utah\n\n\n\n\n40\n\n\n\n\nSarah E Miller. 9/19/2017. Species associations manually extracted from Benesh, D. P., Lafferty, K. D. and Kuris, A. (2017), A life cycle database for parasitic acanthocephalans, cestodes, and nematodes. Ecology, 98: 882. doi:10.1002/ecy.1680\n\n\n\n\n37\n\n\n\n\nPocock, 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\n\n\n\n\n36\n\n\n\n\nQuentin J. Groom. 2020. Species interactions of species on the List of invasive alien species of Union concern\n\n\n\n\n34\n\n\n\n\nSarah E Miller. 6/20/2015. Species associations manually extracted from datasets https://www.nceas.ucsb.edu/interactionweb/resources.html.\n\n\n\n\n32\n\n\n\n\nBallantyne, 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\n\n\n\n\n31\n\n\n\n\nShaw, 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\n\n\n\n\n27\n\n\n\n\nMuseum for Southwestern Biology (MSB) Parasite Collection\n\n\n\n\n27\n\n\n\n\nSarah E Miller. 5/17/2016. Wenzel, Rupert L., and Vernon J. Tipton. Appendix: Classified List of Hosts and Parasites. Chicago, Ill.: Field Museum of Natural History, 1966.\n\n\n\n\n26\n\n\n\n\nSarah 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.\n\n\n\n\n23\n\n\n\n\nAgosti, 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 .\n\n\n\n\n23\n\n\n\n\nUdy, 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\n\n\n\n\n20\n\n\n\n\nIPBES. (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\n\n\n\n\n20\n\n\n\n\nSherman, Aja C.; Geiselman, Cullen; Simons, Nancy B.; Upham, Nathan S.; Poelen, Jorrit H.; Reeder, DeeAnn M.; Bertolino, Sandro; Groom, Quentin; Phelps, Kendra; Agosti, Donat; Willoughby, Anna R. In Preparation. Bat-Co-Roosting Database develop by the Biodiversity-related knowledge hub on COVID-19.\n\n\n\n\n19\n\n\n\n\nSeltzer, 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\n\n\n\n\n18\n\n\n\n\nJakovos Demetriou and Quentin Groom 2014. Species associations of Sceliphron manually extracted from literature.\n\n\n\n\n17\n\n\n\n\nSpecies Connect. https://speciesconnect.com\n\n\n\n\n16\n\n\n\n\nGeiselman, Cullen K. & Sarah Younger. 2020. Bat Eco-Interactions Database. www.batbase.org\n\n\n\n\n14\n\n\n\n\nFabricia Sousa Paz, Carlos Eduardo Pinto, Rafael Melo de Brito, Vera Lucia Imperatriz-Fonseca, Tereza Cristina Giannini, Edible Fruit Plant Species in the Amazon Forest Rely Mostly on Bees and Beetles as Pollinators, Journal of Economic Entomology, Volume 114, Issue 2, April 2021, Pages 710–722, https://doi.org/10.1093/jee/toaa284\n\n\n\n\n14\n\n\n\n\nScientific Committee on Antarctic Research. (2023). SCAR Southern Ocean Diet and Energetics Database (2023-04-04) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.7796465 hash://md5/e41e29d8fb3c2d731f292ec08798cf6b hash://md5/05abf23c0b9e5f4bc721ff407455af0a hash://sha256/7a344b858ab8d1daeca1da49843e8bf957f1116ff9e10a29176ab5c02cb49bef\n\n\n\n\n12\n\n\n\n\nBernice Pauahi Bishop Museum, J. Linsley Gressitt Center for Research in Entomology\n\n\n\n\n12\n\n\n\n\nGaden S. Robinson; Phillip R. Ackery; Ian Kitching; George W Beccaloni; Luis M. Hernández (2023). HOSTS (from HOSTS - a Database of the World's Lepidopteran Hostplants) [Data set resource]. Natural History Museum. https://data.nhm.ac.uk/dataset/hosts/resource/877f387a-36a3-486c-a0c1-b8d5fb69f85a via Natural History Museum (2023). Data Portal query on 1 resources created at 2023-05-24 11:19:42.032183 PID https://doi.org/10.5519/qd.bsucrxdz\n\n\n\n\n12\n\n\n\n\nGandhi, 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.\n\n\n\n\n12\n\n\n\n\nMeyer R.S., et al., Beach environmental DNA fills gaps in photographic biomonitoring to track spatiotemporal community turnover across 82 phyla. Environmental DNA, submitted June 3, 2019.\n\n\n\n\n10\n\n\n\n\nConsortium of Small Vertebrate Collections\n\n\n\n\n10\n\n\n\n\nLee, Leshon; Tan, David J. X.; Oboňa, Jozef; Gustafsson, Daniel R.; Ang, Yuchen; Meier, Rudolf (2021). Phoresy Records Appendix.xlsx. figshare. Dataset. https://doi.org/10.6084/m9.figshare.12671711.v1\n\n\n\n\n9\n\n\n\n\nC. Anela Choy, Steven H. D. Haddock, Bruce H. Robison. 2017. Deep pelagic food web structure as revealed by in situ feeding observations. Proc. R. Soc. B 2017 284 20172116; DOI:10.1098/rspb.2017.2116.\n\n\n\n\n8\n\n\n\n\nSarah E Miller. 7/6/2016. Arctos collection.\n\n\n\n\n6\n\n\n\n\nGeiselman, Cullen K. and Tuli I. Defex. 2015. Bat Eco-Interactions Database. www.batplant.org\n\n\n\n\n5\n\n\n\n\nNEON Biorepository Portal at Arizona State University (ASU)\n\n\n\n\n4\n\n\n\n\nSarah E Miller. 4/20/2015. Species associations manually extracted from various papers and articles from site https://repository.si.edu\n\n\n\n\n4\n\n\n\n\nSarah 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.\n\n\n\n\n4\n\n\n\n\nSarah 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.\n\n\n\n\n4\n\n\n\n\nUniversity of California Santa Barbara Herbarium\n\n\n\n\n3\n\n\n\n\nGippet, J.M.W., Bates, O.K., Moulin, J. et al. The global risk of infectious disease emergence from giant land snail invasion and pet trade. Parasites Vectors 16, 363 (2023). https://doi.org/10.1186/s13071-023-06000-y\n\n\n\n\n3\n\n\n\n\nJorrit H. Poelen. 2017. Species interactions associated with known species interaction datasets.\n\n\n\n\n3\n\n\n\n\nMinisterio del Ambiente, Agua y Transición Ecológica de Ecuador - MAATE.\n\n\n\n\n3\n\n\n\n\nSarah E Miller. 9/15/2016. Species associations extracted from http://parasiticplants.siu.edu/index.html.\n\n\n\n\n3\n\n\n\n\nSarah E Miller. 9/3/2015. Species associations manually extracted from JSTOR.\n\n\n\n\n3\n\n\n\n\nSchriml, L. M., Arze, C., Nadendla, S., Ganapathy, A., Felix, V., Mahurkar, A., … Hall, N. (2009). GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database. Nucleic Acids Research, 38(Database), D754–D764. doi:10.1093/nar/gkp832\n\n\n\n\n2\n\n\n\n\nCarnegie Invertebrate Zoology Collection\n\n\n\n\n2\n\n\n\n\nF. Gabriel. Muñoz. 2017. Palm-Animal frugivore associations extracted from literature with Biodiversity Observations Miner for SouthEast Asia.\n\n\n\n\n2\n\n\n\n\nFerrer-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\n\n\n\n\n2\n\n\n\n\nInouye, David (2017). An Access database of records collated from the literature about flies pollinating or at least visiting flowers, updated 2017. https://doi.org/10.13016/M2SZ73 http://hdl.handle.net/1903/19193 hash://sha256/a9ab0a6173d34695c85f5fb8947e196478d1253d9d79b0662921ef4e36639c05\n\n\n\n\n2\n\n\n\n\nPaleo Digitization Working Group. Biological associations extracted from fossil specimens.\n\n\n\n\n2\n\n\n\n\nQuentin J. Groom. 2020. Bat interation data manually extracted from literature.\n\n\n\n\n2\n\n\n\n\nSarah E. Miller. 04/14/2015. Extracted from literature Scott, J.A. 1986.  The Butterflies of North America.  Stanford University Press, Stanford, CA\n\n\n\n\n2\n\n\n\n\nStrona, G., Palomares, M. L. D., Bailly, N., Galli, P., & Lafferty, K. D. (2013). Host range, host ecology, and distribution of more than 11 800 fish parasite species. Ecology, 94(2), 544–544. doi:10.1890/12-1419.1\n\n\n\n\n2\n\n\n\n\nStrong, 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\n\n\n\n\n2\n\n\n\n\nThessen AE. 2017. Biotic Interactions in Greenland. GloBI. 10.5281/zenodo.266824\n\n\n\n\n1\n\n\n\n\nBourlat SJ, Koch M, Kirse A, Langen K, Espeland M, Giebner H, Decher J, Ssymank A, Fonseca VG (2023) Metabarcoding dietary analysis in the insectivorous bat Nyctalus leisleri and implications for conservation. Biodiversity Data Journal 11: e111146. https://doi.org/10.3897/BDJ.11.e111146\n\n\n\n\n1\n\n\n\n\nCamargo-Sanabria, A.A., Fernández, J.A., Hernández-Quiroz, N.S., Buitrago-Torres, D.L. and Álvarez-Córdova, F. (2025), Ecological Interactions of Terrestrial Mammals in the Chihuahuan Desert: A Systematic Map. Mam Rev e70001. https://doi.org/10.1111/mam.70001\n\n\n\n\n1\n\n\n\n\nDe 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\n\n\n\n\n1\n\n\n\n\nDeans, Andrew (2021). Catalog of Rose Gall, Herb Gall, and Inquiline Gall Wasps (Hymenoptera: Cynipidae) of the United States, Canada, and Mexico\n\n\n\n\n1\n\n\n\n\nGunther KA et al. 2014 Dietary breadth of grizzly bears in the Greater Yellowstone Ecosystem. Ursus 25(1):60-72\n\n\n\n\n1\n\n\n\n\nHiveTracks WorldFAIR Test Data.\n\n\n\n\n1\n\n\n\n\nSarah E Miller. 3/4/2015. Species associations manually extracted from http://onlinelibrary.wiley.com/doi/10.1111/j.1474-919X.2009.00907.x/suppinfo.\n\n\n\n\n1\n\n\n\n\nSarah E Miller. 5/21/2015. Text gathered from http://www.biodiversitylibrary.org/\n\n\n\n\n1\n\n\n\n\nVanderweyen A, Fraiture A, Groom Q, Desmet P, Reyserhove L (2019). Catalogue of the Rust Fungi of Belgium. Botanic Garden Meise.\n\n\n\n\n1\n\n\n\n\nVanderweyen, A., & Fraiture, A. (2009). Catalogue des Uredinales de Belgique, 1re partie, Chaconiaceae, Coleosporiaceae, Cronartiaceae, Melampsoraceae, Phragmidiaceae, Pucciniastraceae, Raveneliaceae et Uropyxidaceae. Lejeunia, Revue de Botanique|Vanderweyen, A., & Fraiture, A. (2009). Catalogue des Uredinales de Belgique, 2ème partie, Pucciniaceae (sauf Puccinia)(suite 2). Lejeunia, Revue de Botanique.|Vanderweyen, A., & Fraiture, A. (2012). CATALOGUE DES UREDINALES DE Belgique 3ème partie Pucciniaceae (genre Puccinia). Lejeunia, Revue de Botanique.\n\n\n\n\n1\n\n\n\n\nZeke Marshall. 2021. Species interactions manually extracted from literature.\n\n\n\n\n\n\n \n\nReferences\n\nPoelen 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\n\nSeltmann 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\n\nPoelen, 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\n\nAscher, 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.\n\nAcknowledgements\n\nThis 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 "],"Other":["Please cite the resources, natural history collections and publications where the data originated as found in uniq_citations.tsv file above. Also, please cite Poelen et. al (above in References) to cite Global Biotic Interactions."]} 

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2. Litter chemistry and masses for the MELNHE NxP fertilization experiment

   https://doi.org/10.6073/pasta/8b2975a3a02cbcfb1b0a12ac954576d4  

   Fisk, Melany C; Yanai, Ruth D; Hong, Sunghoon D; See, Craig R; Goswami, Shinjini (January 2022, Environmental Data Initiative)

   The Multiple Element Limitation in Northern Hardwood Ecosystems (MELNHE) project studies N, P, and Ca acquisition and limitation of forest productivity through a series of nutrient manipulations in northern hardwood forests. This data set includes litterfall chemistry and mass for litter collected approximately weekly through the fall litterfall season, either composited over the entire fall season or selected from individual collection times, pre-treatment (2009), and post-treatment (2012, 2014, 2016, 2018). Additional detail on the MELNHE project, including a datatable of site descriptions and a pdf file with the project description and diagram of plot configuration can be found in this data package: https://portal.edirepository.org/nis/mapbrowse?scope=knb-lter-hbr&identifier=344 These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station. 

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3. Tab and comma delimited versions of Discover Life bee species guide and world checklist (Hymenoptera: Apoidea: Anthophila)

   https://doi.org/10.5281/zenodo.10019874  

   Seltmann, Katja; Poelen, Jorrit (January 2024, Zenodo)

   Introduction This archive includes a tab-delimited (tsv) and comma-delimited (csv) version of the Discover Life bee species guide and world checklist (Hymenoptera: Apoidea: Anthophila). Discover Life is an important resource for bee species names and this update is from Draft-55, November 2020. Data were accessed and transformed into a tsv file in August 2023 using Global Biotic Interactions (GloBI) nomer software. GloBI now incorporates the Discover Life bee species guide and world checklist in its functionality for searching for bee interactions. Update! New Dataset also includes Subgenera Names A new, tab-delimited version of the Discover Life taxonomy as derived from Dorey et. al, 2023 can be found via Zenodo at https://doi.org/10.5281/zenodo.10463762. This version of the Discover Life world species guide and checklist includes subgeneric names. Citation Please cite the original source for this data as: Ascher, J. S. and J. Pickering. 2022.Discover Life bee species guide and world checklist (Hymenoptera: Apoidea: Anthophila).http://www.discoverlife.org/mp/20q?guide=Apoidea_species Draft-56, 21 August, 2022 nomer nomer is a command-line application for working with taxonomic resources offline. nomer incorporates many of the present taxonomic catalogs (e.g., catalog of life, ITIS, EOL, NCBI) and provides simple tools for comparing between resources or resolving taxonomic names based on one or more taxonomic name catalogs. Discover Life is in nomer version 0.5.1 and this full dataset can be recreated by installing nomer from https://github.com/globalbioticinteractions/nomer and running $ nomer list discoverlife > discoverlife.tsv Data Columns Discover Life provides a world name checklist and includes other names (synonyms and homonyms) that refer to the same species. In the tsv file, the provided name is both the accepted, or checklist name, or "other name." All names will be listed as a providedName. Below is an example subset of the transformed version of the data. providedExternalId= link to name on Discover Life providedName=an accepted or "other name" in the Discover Life bee checklist. "Other names" can be synonyms or homonyms. providedAuthorship=authorship for the providedName providedRank=rank of the providedName providedPath=higher taxonomy of the providedName. This will be the same as the accepted name or resolvedName relationName=relationship between the "other name" and the bee name in the Discover Life checklist. It may include itself resolvedExternalID=an accepted name in the Discover Life bee checklist resolvedExternalId=link to name on Discover Life resolvedAuthorship=authorship of the accepted, or checklist name resolvedRank=rank of the accepted, or checklist name resolvedPath=higher taxonomy of the accepted, or checklist name Changes No major changes to format in this version. References Jorrit Poelen, & José Augusto Salim. (2022). globalbioticinteractions/nomer: (0.2.11). Zenodo. https://doi.org/10.5281/zenodo.6128011 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 Dorey, J.B., Fischer, E.E., Chesshire, P.R. et al. A globally synthesised and flagged bee occurrence dataset and cleaning workflow. Sci Data 10, 747 (2023). https://doi.org/10.1038/s41597-023-02626-w 

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4. Enzyme Substrate Classification Dataset for SDRs and SAM-MTases

   https://doi.org/10.5281/zenodo.7141435  

   Jinich, Adrian; Rappoport, Dmitrij (January 2022, Zenodo)

   This dataset contains sequence information, three-dimensional structures (from AlphaFold2 model), and substrate classification labels for 358 short-chain dehydrogenase/reductases (SDRs) and 953 S-adenosylmethionine dependent methyltransferases (SAM-MTases).</p> The aminoacid sequences of these enzymes were obtained from the UniProt Knowledgebase (https://www.uniprot.org). The sets of proteins were obtained by querying using InterPro protein family/domain identifiers corresponding to each family: IPR002347 (SDRs) and IPR029063 (SAM-MTases). The query results were filtered by UniProt annotation score, keeping only those with score above 4-out-of-5, and deduplicated by exact sequence matches.</p> The structures were submitted to the publicly available AlphaFold2 protein structure predictor (J. Jumper et al., Nature, 2021, 596, 583) using the ColabFold notebook (https://colab.research.google.com/github/sokrypton/ColabFold/blob/v1.1-premultimer/batch/AlphaFold2_batch.ipynb, M. Mirdita, S. Ovchinnikov, M. Steinegger, Nature Meth., 2022, 19, 679, https://github.com/sokrypton/ColabFold). The model settings used were  msa_model = MMSeq2(Uniref+Environmental), num_models = 1, use_amber = False, use_templates = True, do_not_overwrite_results = True. The resulting PDB structures are included as ZIP archives</p> The classification labels were obtained from the substrate and product annotations of the enzyme UniProtKB records. Two approaches were used: substrate clustering based on molecular fingerprints and manual substrate type classification. For the substate clustering, Morgan fingerprints were generated for all enzymatic substrates and products with known structures (excluding cofactors) with radius = 3 using RDKit (https://rdkit.org). The fingerprints were projected onto two-dimensional space using the UMAP algorithm (L. McInnes, J. Healy, 2018, arXiv 1802.03426) and Jaccard metric and clustered using k-means. This procedure generated 9 clusters for SDR substrates and 13 clusters for SAM-MTases. The SMILES representations of the substrates are listed in the SDR_substrates_to_cluster_map_2DIMUMAP.csv and SAM_substrates_to_13clusters_map_2DIMUMAP.csv files.</p> The following manually defined classification tasks are included for SDRs: NADP/NAD cofactor classification; phenol substrate, sterol substrate, coenzyme A (CoA) substrate. For SAM-MTases, the manually defined classification tasks are: biopolymer (protein/RNA/DNA) vs. small molecule substrate, phenol subsrates, sterol substrates, nitrogen heterocycle substrates. The SMARTS strings used to define the substrate classes are listed in substructure_search_SMARTS.docx.  </p> 

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5. Tree DBH response to nitrogen and phosphorus fertilization in the MELNHE study, Hubbard Brook Experimental Forest, Bartlett Experimental Forest, and Jeffers Brook

   https://doi.org/10.6073/pasta/377b1fd44bd88a58e9654ab207e50706  

   Fisk, Melany C; Yanai, Ruth D; Fahey, Timothy J (January 2022, Environmental Data Initiative)

   The Multiple Element Limitation in Northern Hardwood Ecosystems (MELNHE) project studies N and P acquisition and limitation of forest productivity through a series of nutrient manipulations in northern hardwood forests. This data set includes tree diameters at breast height (DBH) collected pre-treatment (2008, 2009, and 2010), and post-treatment (2011, 2015, and 2019). Additional detail on the MELNHE project, including a datatable of site descriptions and a pdf file with the project description and diagram of plot configuration can be found in this data package: https://portal.edirepository.org/nis/mapbrowse?scope=knb-lter-hbr&identifier=344 These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station. 

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