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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Abstract Commonly used data citation practices rely on unverifiable retrieval methods which are susceptible to content drift, which occurs when the data associated with an identifier have been allowed to change. Based on our earlier work on reliable dataset identifiers, we propose signed citations, i.e., customary data citations extended to also include a standards-based, verifiable, unique, and fixed-length digital content signature. We show that content signatures enable independent verification of the cited content and can improve the persistence of the citation. Because content signatures are location- and storage-medium-agnostic, cited data can be copied to new locations to ensure their persistence across current and future storage media and data networks. As a result, content signatures can be leveraged to help scalably store, locate, access, and independently verify content across new and existing data infrastructures. Content signatures can also be embedded inside content to create robust, distributed knowledge graphs that can be cited using a single signed citation. We describe applications of signed citations to solve real-world data collection, identification, and citation challenges.more » « less
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Commonly used data citation practices rely on unverifiable retrieval methods which are susceptible to “content drift”, which occurs when the data associated with an identifier have been allowed to change. Based on our earlier work on reliable dataset identifiers, we propose signed citations, i.e., customary data citations extended to also include a standards-based, verifiable, unique, and fixed-length digital content signature. We show that content signatures enable independent verification of the cited content and can improve the persistence of the citation. Because content signatures are location- and storage-medium-agnostic, cited data can be copied to new locations to ensure their persistence across current and future storage media and data networks. As a result, content signatures can be leveraged to help scalably store, locate, access, and independently verify content across new and existing data infrastructures. Content signatures can also be embedded inside content to create robust, distributed knowledge graphs that can be cited using a single signed citation. We describe real-world applications of signed citations used to cite and compile distributed data collections, cite specific versions of existing data networks, and stabilize associations between URLs and content.
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A biodiversity dataset graph: GBIF, iDigBio, BioCASe
The intended use of this archive is to facilitate meta-analysis of the Global Biodiversity Information Facility, Integrated Digitized Biocollections, Biological Collection Access Service (GBIF, iDigBio, BioCASe). GBIF, iDigBio and BioCASe help provide access to biological data collections.
This dataset provides versioned provenance logs of snapshots of the GBIF, iDigBio, BioCASe network as tracked by Preston [2] between 2018-09-03 and 2020-05-02 using "preston update -u https://gbif.org,https://idigbio.org,http://biocase.org".
This publication contains two types of files: index files and provenance logs. Associated data files are hosted elsewhere for pragmatic reasons. Index files provide a way to link provenance files in time to establish a versioning mechanism. Provenance logs describe how, when, what and where the GBIF, iDigBio, BioCASe content was retrieved. For more information, please visit https://preston.guoda.bio or https://doi.org/10.5281/zenodo.1410543 .
To retrieve and verify the downloaded GBIF, iDigBio, BioCASe biodiversity dataset graph, use the preston[2] command-line tool to "clone" this dataset using:
$ java -jar preston.jar ls --remote https://zenodo.org/record/3852671/files > /dev/null
Optionally, you can retrieve all associated data (>500GB) files using:
$ java -jar preston.jar clone --remote https://zenodo.org/record/3852671/files,https://archive.org/download/biodiversity-dataset-archives/data.zip/data/,https://deeplinker.bio
Please note https://archive.org/download/biodiversity-dataset-archives/data.zip/data/ and https://deeplinker.bio are Preston remotes that provided access to GBIF, iDigBio, BioCASe data files at time of writing (25 May 2020). These remotes can replaced with any other Preston remote(s) if needed. This may take a while depending on network speed and hardware constraints. See also https://archive.org/details/biodiversity-dataset-archives .
After that, verify the index of the archive by reproducing the following provenance log history:
$ java -jar preston.jar history
<0659a54f-b713-4f86-a917-5be166a14110> <http://purl.org/pav/hasVersion> <hash://sha256/c253a5311a20c2fc082bf9bac87a1ec5eb6e4e51ff936e7be20c29c8e77dee55> .
<hash://sha256/b83cf099449dae3f633af618b19d05013953e7a1d7d97bc5ac01afd7bd9abe5d> <http://purl.org/pav/previousVersion> <hash://sha256/c253a5311a20c2fc082bf9bac87a1ec5eb6e4e51ff936e7be20c29c8e77dee55> .
<hash://sha256/7efdea9263e57605d2d2d8b79ccd26a55743123d0c974140c72c8c1cfc679b93> <http://purl.org/pav/previousVersion> <hash://sha256/b83cf099449dae3f633af618b19d05013953e7a1d7d97bc5ac01afd7bd9abe5d> .
<hash://sha256/05a877bdb8617144fe166a13bf51828d4ad1bc11631c360b9e648a9f7df2bbcd> <http://purl.org/pav/previousVersion> <hash://sha256/7efdea9263e57605d2d2d8b79ccd26a55743123d0c974140c72c8c1cfc679b93> .
<hash://sha256/b5a30bbd8d51e9faf08d4ddebbc5bda9bab1b12545172f1524ac5ebdb0038bd4> <http://purl.org/pav/previousVersion> <hash://sha256/05a877bdb8617144fe166a13bf51828d4ad1bc11631c360b9e648a9f7df2bbcd> .
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<hash://sha256/ba02b235fd445904eae45b50bc637a195f25e9ca1637bcf26b2dc7f8698aa1fe> <http://purl.org/pav/previousVersion> <hash://sha256/24b3f981c88c747f44ad3372095767cd15dcf81bd6cd2e54328a90a21409df43> .
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<hash://sha256/9a41d2583f0b8169ffdd44fb2d3a5e057eba4a10e5d9193d0c6e9dcf07c3119e> <http://purl.org/pav/previousVersion> <hash://sha256/af8f9ed321d9c403617f54a96e3217adc918970fbbfe8b8715359669f4890b63> .
<hash://sha256/b9864a749112cad2fe19e62bf5d8bad580a7036d363d16d81d5c16be325fa0fd> <http://purl.org/pav/previousVersion> <hash://sha256/9a41d2583f0b8169ffdd44fb2d3a5e057eba4a10e5d9193d0c6e9dcf07c3119e> .
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<hash://sha256/6fb7271a2da1543036e39bcdb4c415a46b5437569eaaf0ffdef3e907a2f4309f> <http://purl.org/pav/previousVersion> <hash://sha256/d79fb9207329a2813b60713cf0968fda10721d576dcb7a36038faf18027eebc1> .
<hash://sha256/ab62f4a9601f30d23353a479830f9d2dfc7898e15d2cc2d81977e898d885c908> <http://purl.org/pav/previousVersion> <hash://sha256/6fb7271a2da1543036e39bcdb4c415a46b5437569eaaf0ffdef3e907a2f4309f> .
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<hash://sha256/6c4c94cdb224d39e7c655b1a1a6afbba8daf3c9ac64c42ba72dfd346d5d3a547> <http://purl.org/pav/previousVersion> <hash://sha256/ff74959ec6e5e98e7db674afcb915f50725f049b968e9a9f10de169aa0a3dcb5> .
<hash://sha256/9c17ce013b33c3c9e6bc513cb49a14660fad9bd6f87a4f21568cc871b10ba39b> <http://purl.org/pav/previousVersion> <hash://sha256/6c4c94cdb224d39e7c655b1a1a6afbba8daf3c9ac64c42ba72dfd346d5d3a547> .
<hash://sha256/5dcf876c6cb0c5b15197acf1ea6989d41c1a1333c6a7e0437f035aa9d22a3790> <http://purl.org/pav/previousVersion> <hash://sha256/9c17ce013b33c3c9e6bc513cb49a14660fad9bd6f87a4f21568cc871b10ba39b> .
<hash://sha256/39f83f5805f32f765003c5e9ee8c69adb3889d9f26dd61bf4aa3a829ac744e2c> <http://purl.org/pav/previousVersion> <hash://sha256/5dcf876c6cb0c5b15197acf1ea6989d41c1a1333c6a7e0437f035aa9d22a3790> .
<hash://sha256/916255b2b73680595dcb22b30991a757dd223208473fb4fbe90405757bc07953> <http://purl.org/pav/previousVersion> <hash://sha256/39f83f5805f32f765003c5e9ee8c69adb3889d9f26dd61bf4aa3a829ac744e2c> .
<hash://sha256/3b39831bcc286c1db44787e21b736378f5847a16b7c39bdac3dd2011e9189dc1> <http://purl.org/pav/previousVersion> <hash://sha256/916255b2b73680595dcb22b30991a757dd223208473fb4fbe90405757bc07953> .
<hash://sha256/f13b15a20e4fe70b4a111e67ac20ef676404b8456dfc39694f2cb3a4c62a2b2d> <http://purl.org/pav/previousVersion> <hash://sha256/3b39831bcc286c1db44787e21b736378f5847a16b7c39bdac3dd2011e9189dc1> .
<hash://sha256/8aacce08462b87a345d271081783bdd999663ef90099212c8831db399fc0831b> <http://purl.org/pav/previousVersion> <hash://sha256/f13b15a20e4fe70b4a111e67ac20ef676404b8456dfc39694f2cb3a4c62a2b2d> .
If you retrieved data files, you can check the integrity of the extracted archive by confirming 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.$ java -jar preston.jar verify
hash://sha256/3eff98d4b66368fd8d1f8fa1af6a057774d8a407a4771490beeb9e7add76f362 file:/home/preston/preston-archive/data/3e/ff/3eff98d4b66368fd8d1f8fa1af6a057774d8a407a4771490beeb9e7add76f362 OK CONTENT_PRESENT_VALID_HASH 89931
hash://sha256/184886cc6ae4490a49a70b6fd9a3e1dfafce433fc8e3d022c89e0b75ea3cda0b file:/home/preston/preston-archive/data/18/48/184886cc6ae4490a49a70b6fd9a3e1dfafce433fc8e3d022c89e0b75ea3cda0b OK CONTENT_PRESENT_VALID_HASH 210344
hash://sha256/1846abf2b9623697cf9b2212e019bc1f6dc4a20da51b3b5629bfb964dc808c02 file:/home/preston/preston-archive/data/18/46/1846abf2b9623697cf9b2212e019bc1f6dc4a20da51b3b5629bfb964dc808c02 OK CONTENT_PRESENT_VALID_HASH 210344
hash://sha256/554fdab07f2372bf363a1d7ef30fcf4c32e1da98b95a6342780c5eb35e0e7b38 file:/home/preston/preston-archive/data/55/4f/554fdab07f2372bf363a1d7ef30fcf4c32e1da98b95a6342780c5eb35e0e7b38 OK CONTENT_PRESENT_VALID_HASH 202701Note 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".
Files in this data publication:
--- start of file descriptions ---
-- description of archive and its contents (this file) --
README-- executable java jar containing preston[2] v0.1.15. --
preston.jar-- individual provenance index files --
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a524b9af3f172793998e1f9c5c0e9c949cc935624a17ed3364d32bc0391c9382
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c06f4413a97a5540fbdd40bdbfb194435c154533df7fe388dfdd378084e19c3d
c585b8addfb7f7991ad74c0bae158aecefc6be5b11c28b020135e0f13040e187
c66587e9730a6f68e961240038892df656ea99a1a25f4ff8ce556c07b09a4878
ca289dce66c8b9955c223fe3e906b8f26c12cf53506cebe651b004961f7964af
cea1aab236de5de8da8954797d846c225bf2ad4f8fe3cd413e60ab029f9e1b3e
da05cc27a47e755ebe912fafae434df5bd31a5d92658fe1943acc0a2023fab32
ee473aeda889fd12ac2c76aae06314e5f279cce5f1a736d39bfc097657a82060
fcb2ee4d630a9a1440417b0c46da5bc1578a388d6aedd12189a23283b60dde7d
fef548489bd7bea43ae1c2b7755d38a87f4a8b038a466bf7e7b4ac64d665fd62
ff32a7cbc99eaf6b67695fd94284a9b1b47a76497ef4d10ffc4dae199cc0d7c3--- individual provenance logs --
05a877bdb8617144fe166a13bf51828d4ad1bc11631c360b9e648a9f7df2bbcd
09574d9c1330c2b1bec9b7bf3a55ab9273bedbfed78affd70a058a1a25e052d2
0e6b49850d96b4b58ea3759ecea45d273a48f074c4edaaec5e008791d7718781
102cbfb1e800ef795ba1e1c51a34bff9b463b34c9443435069ddc76970c1e9c9
1d3817d9cb9fc7de7a3b7a4181daba8de1e52b348280154e8a163c7dd7ee1a7e
20d36a6f879ba1dd797d4288a4f2e32719d3c674156194c2765a3ec6b43f5e17
24b3f981c88c747f44ad3372095767cd15dcf81bd6cd2e54328a90a21409df43
261177a96185166f1c301beacf7350abff03d1b5710be6bfd8c4aff9caffef12
39f83f5805f32f765003c5e9ee8c69adb3889d9f26dd61bf4aa3a829ac744e2c
3b39831bcc286c1db44787e21b736378f5847a16b7c39bdac3dd2011e9189dc1
3dd674b7ad16391629948981a9cb6f6f86937d016861c3e59cd6e6bf3589f3b7
3e7f19a8a78b51437240f49c499e6e7f89b8d58d4e3ceb9480d4356721645cee
480868b59e95f3ce2324a7308dba65795e857d34cfbdcea7440a6f2620c6fbf6
58daa9a51e5dc0911163aa1b98d68c801106734cd29eab9980814057351aeb70
5a39b7bbe9d1bc46ed2eb7bd76c490b5c85a09369a7cf7dc18fa04532679e9a7 -
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A biodiversity dataset graph: DataONE
The intended use of this archive is to facilitate (meta-)analysis of the Data Observation Network for Earth (DataONE). DataONE is a distributed infrastructure that provides information about earth observation data.
This dataset provides versioned snapshots of the DataONE network as tracked by Preston [2] between 2018-11-06 and 2020-05-07 using "preston update -u https://dataone.org".
The 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 logs and data files. In addition, index files have been individually included in this dataset publication to facilitate remote access. Index files provide a way to links provenance files in time to establish a versioning mechanism. Provenance files describe how, when, what and where the DataONE content was retrieved. For more information, please visit https://preston.guoda.bio or https://doi.org/10.5281/zenodo.1410543 .
To retrieve and verify the downloaded DataONE biodiversity dataset graph, first concatenate all the downloaded preston-*.tar.gz files (e.g., cat preston-*.tar.gz > preston.tar.gz). Then, extract the archives into a "data" folder. Alternatively, you can use the preston[2] command-line tool to "clone" this dataset using:
$ java -jar preston.jar clone --remote https://zenodo.org/record/3849494/files
After that, verify the index of the archive by reproducing the following provenance log history:
$ java -jar preston.jar history
<0659a54f-b713-4f86-a917-5be166a14110> <http://purl.org/pav/hasVersion> <hash://sha256/8c67e0741d1c90db54740e08d2e39d91dfd73566ea69c1f2da0d9ab9780a9a9f> .
<hash://sha256/3ed3acaca7ac57f546d0b8877c1927ab5e08c23eccaa8219600c59c77a72c685> <http://purl.org/pav/previousVersion> <hash://sha256/8c67e0741d1c90db54740e08d2e39d91dfd73566ea69c1f2da0d9ab9780a9a9f> .
<hash://sha256/857753997a7595a1b372b05641b58a25d9408b7ff08d557ce1fe8b73e4bd383f> <http://purl.org/pav/previousVersion> <hash://sha256/3ed3acaca7ac57f546d0b8877c1927ab5e08c23eccaa8219600c59c77a72c685> .
<hash://sha256/7ee0376f4c3f7aeeda36927a5211395e5da8201e810e8c7e638a0fe23d001e88> <http://purl.org/pav/previousVersion> <hash://sha256/857753997a7595a1b372b05641b58a25d9408b7ff08d557ce1fe8b73e4bd383f> .
<hash://sha256/68b4974d8ab7c4c7a7a4305065839b60ba460aaa862590b34c67877738feba90> <http://purl.org/pav/previousVersion> <hash://sha256/7ee0376f4c3f7aeeda36927a5211395e5da8201e810e8c7e638a0fe23d001e88> .
<hash://sha256/060a76d56255bf9482c951748c91291fddeeb20f180632132be1344e081b2372> <http://purl.org/pav/previousVersion> <hash://sha256/68b4974d8ab7c4c7a7a4305065839b60ba460aaa862590b34c67877738feba90> .
<hash://sha256/29357bdfab4548025f8a5743301f5c3c9146fa436c39e3c9e019fb9409ac9c42> <http://purl.org/pav/previousVersion> <hash://sha256/060a76d56255bf9482c951748c91291fddeeb20f180632132be1344e081b2372> .
<hash://sha256/3669cd95100d1d533eb8953ff4ec5092cbd8addb8879b3e6262191148a8a3ebb> <http://purl.org/pav/previousVersion> <hash://sha256/29357bdfab4548025f8a5743301f5c3c9146fa436c39e3c9e019fb9409ac9c42> .
<hash://sha256/8dc1663299359d271cb1b4c14ad521d0f1be67743689dd18016543dc1e097efb> <http://purl.org/pav/previousVersion> <hash://sha256/3669cd95100d1d533eb8953ff4ec5092cbd8addb8879b3e6262191148a8a3ebb> .
<hash://sha256/dc4903e8afee651db1d9bf509f20503bf9c8e89679c4bcffb46d5b97440cb6de> <http://purl.org/pav/previousVersion> <hash://sha256/8dc1663299359d271cb1b4c14ad521d0f1be67743689dd18016543dc1e097efb> .
<hash://sha256/f3bed9db3092c744604df5f50248a2ec36e564fe78a65f45c4190283bd61c807> <http://purl.org/pav/previousVersion> <hash://sha256/dc4903e8afee651db1d9bf509f20503bf9c8e89679c4bcffb46d5b97440cb6de> .
<hash://sha256/e3c7b3b14b2b792e3e2e560a1b2bef059ac93f777dee616b836317bc9cbfcbf7> <http://purl.org/pav/previousVersion> <hash://sha256/f3bed9db3092c744604df5f50248a2ec36e564fe78a65f45c4190283bd61c807> .
<hash://sha256/631a4531e7bb052816d28454bbeec3428d5e7bfd1f148c4f21ce63a6cf86c650> <http://purl.org/pav/previousVersion> <hash://sha256/e3c7b3b14b2b792e3e2e560a1b2bef059ac93f777dee616b836317bc9cbfcbf7> .
<hash://sha256/87de0898919d2212977a586965e930ae45bdd1366073591c808c208a635e2814> <http://purl.org/pav/previousVersion> <hash://sha256/631a4531e7bb052816d28454bbeec3428d5e7bfd1f148c4f21ce63a6cf86c650> .
<hash://sha256/79ec3ee370a0d38311bc352af07a36380cd3aa04dc98154cf723bbc73d12ee77> <http://purl.org/pav/previousVersion> <hash://sha256/87de0898919d2212977a586965e930ae45bdd1366073591c808c208a635e2814> .
<hash://sha256/e54b360a4ca84a4503e4c10a8a8cca062c130be7429c8fe6ea1e0e82fe113e12> <http://purl.org/pav/previousVersion> <hash://sha256/79ec3ee370a0d38311bc352af07a36380cd3aa04dc98154cf723bbc73d12ee77> .
<hash://sha256/2910f784f84e112f124a56ce54bd06b76e510f90276629d2d144ce29e326d80f> <http://purl.org/pav/previousVersion> <hash://sha256/e54b360a4ca84a4503e4c10a8a8cca062c130be7429c8fe6ea1e0e82fe113e12> .
<hash://sha256/bcb0bdff0689cfb06f586d057703e41d1c6ba409867232217081dd8cb5053c87> <http://purl.org/pav/previousVersion> <hash://sha256/2910f784f84e112f124a56ce54bd06b76e510f90276629d2d144ce29e326d80f> .
<hash://sha256/a12f8c7fbf4fbfa71536c7e1b2614a35454dac6a7fe9e1cc0b4df41ab2269bef> <http://purl.org/pav/previousVersion> <hash://sha256/bcb0bdff0689cfb06f586d057703e41d1c6ba409867232217081dd8cb5053c87> .
<hash://sha256/2b5c445f0b7b918c14a50de36e29a32854ed55f00d8639e09f58f049b85e50e3> <http://purl.org/pav/previousVersion> <hash://sha256/a12f8c7fbf4fbfa71536c7e1b2614a35454dac6a7fe9e1cc0b4df41ab2269bef> .To 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.
$ java -jar preston.jar verify
hash://sha256/e55c1034d985740926564e94decd6dc7a70f779a33e7deb931553739cda16945 file:/home/preston/preston-dataone/data/e5/5c/e55c1034d985740926564e94decd6dc7a70f779a33e7deb931553739cda16945 OK CONTENT_PRESENT_VALID_HASH 21580 hash://sha256/e55c1034d985740926564e94decd6dc7a70f779a33e7deb931553739cda16945
hash://sha256/d0ddcc2111b6134a570bcc7d89375920ef4d754130cecc0727c79d2b05a9f81f file:/home/preston/preston-dataone/data/d0/dd/d0ddcc2111b6134a570bcc7d89375920ef4d754130cecc0727c79d2b05a9f81f OK CONTENT_PRESENT_VALID_HASH 2035 hash://sha256/d0ddcc2111b6134a570bcc7d89375920ef4d754130cecc0727c79d2b05a9f81f
hash://sha256/472de9d1c9fd7e044aac409abfbfff9f12c6b69359df995d431009580ffb0f53 file:/home/preston/preston-dataone/data/47/2d/472de9d1c9fd7e044aac409abfbfff9f12c6b69359df995d431009580ffb0f53 OK CONTENT_PRESENT_VALID_HASH 1935 hash://sha256/472de9d1c9fd7e044aac409abfbfff9f12c6b69359df995d431009580ffb0f53
hash://sha256/b29879462cd43862129c5cf9b149c41ecd33ffef284a4dbea4ac1c0f90108687 file:/home/preston/preston-dataone/data/b2/98/b29879462cd43862129c5cf9b149c41ecd33ffef284a4dbea4ac1c0f90108687 OK CONTENT_PRESENT_VALID_HASH 1553 hash://sha256/b29879462cd43862129c5cf9b149c41ecd33ffef284a4dbea4ac1c0f90108687
Note 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".Files in this data publication:
--- start of file descriptions ---
-- description of archive and its contents (this file) --
README-- executable java jar containing preston[2] v0.1.15. --
preston.jar-- preston archives containing DataONE data files, associated provenance logs and a provenance index --
preston-[00-ff].tar.gz-- individual provenance index files --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--- end of file descriptions ---
References[1] Data Observation Network for Earth (DataONE, https://dataone.org) accessed from 2018-11-06 to 2020-05-07 with provenance hash://sha256/2b5c445f0b7b918c14a50de36e29a32854ed55f00d8639e09f58f049b85e50e3.
[2] https://preston.guoda.bio, https://doi.org/10.5281/zenodo.1410543 .
This work is funded in part by grant NSF OAC 1839201 from the National Science Foundation. -
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A biodiversity dataset graph: GBIF, iDigBio, BioCASe
The intended use of this archive is to facilitate meta-analysis of the Global Biodiversity Information Facility, Integrated Digitized Biocollections, Biological Collection Access Service (GBIF, iDigBio, BioCASe). GBIF, iDigBio and BioCASe help provide access to biological data collections.
This dataset provides versioned provenance logs of snapshots of the GBIF, iDigBio, BioCASe network as tracked by Preston [2] between 2018-09-03 and 2019-10-02 using "preston update -u https://gbif.org,https://idigbio.org,http://biocase.org".
This publication contains two types of files: index files and provenance logs. Associated data files are hosted elsewhere for pragmatic reasons. Index files provide a way to link provenance files in time to establish a versioning mechanism. Provenance logs describe how, when, what and where the GBIF, iDigBio, BioCASe content was retrieved. For more information, please visit https://preston.guoda.bio or https://doi.org/10.5281/zenodo.1410543 .
To retrieve and verify the downloaded GBIF, iDigBio, BioCASe biodiversity dataset graph, use the preston[2] command-line tool to "clone" this dataset using:
$ java -jar preston.jar ls --remote https://zenodo.org/record/3484205/files > /dev/null
Optionally, you can retrieve all associated data (~500GB) files using:
$ java -jar preston.jar clone --remote https://zenodo.org/record/3484205/files,https://deeplinker.bio
Please note https://deeplinker.bio is a Preston remote that provided access to GBIF, iDigBio, BioCASe data files at time of writing (13 Oct 2019). This remote can replaced with any other Preston remote(s) if needed. This may take a while depending on network speed and hardware constraints.
After that, verify the index of the archive by reproducing the following provenance log history:
$ java -jar preston.jar history
<0659a54f-b713-4f86-a917-5be166a14110> <http://purl.org/pav/hasVersion> <hash://sha256/c253a5311a20c2fc082bf9bac87a1ec5eb6e4e51ff936e7be20c29c8e77dee55> .
<hash://sha256/b83cf099449dae3f633af618b19d05013953e7a1d7d97bc5ac01afd7bd9abe5d> <http://purl.org/pav/previousVersion> <hash://sha256/c253a5311a20c2fc082bf9bac87a1ec5eb6e4e51ff936e7be20c29c8e77dee55> .
<hash://sha256/7efdea9263e57605d2d2d8b79ccd26a55743123d0c974140c72c8c1cfc679b93> <http://purl.org/pav/previousVersion> <hash://sha256/b83cf099449dae3f633af618b19d05013953e7a1d7d97bc5ac01afd7bd9abe5d> .
<hash://sha256/05a877bdb8617144fe166a13bf51828d4ad1bc11631c360b9e648a9f7df2bbcd> <http://purl.org/pav/previousVersion> <hash://sha256/7efdea9263e57605d2d2d8b79ccd26a55743123d0c974140c72c8c1cfc679b93> .
<hash://sha256/b5a30bbd8d51e9faf08d4ddebbc5bda9bab1b12545172f1524ac5ebdb0038bd4> <http://purl.org/pav/previousVersion> <hash://sha256/05a877bdb8617144fe166a13bf51828d4ad1bc11631c360b9e648a9f7df2bbcd> .
<hash://sha256/1d3817d9cb9fc7de7a3b7a4181daba8de1e52b348280154e8a163c7dd7ee1a7e> <http://purl.org/pav/previousVersion> <hash://sha256/b5a30bbd8d51e9faf08d4ddebbc5bda9bab1b12545172f1524ac5ebdb0038bd4> .
<hash://sha256/24b3f981c88c747f44ad3372095767cd15dcf81bd6cd2e54328a90a21409df43> <http://purl.org/pav/previousVersion> <hash://sha256/1d3817d9cb9fc7de7a3b7a4181daba8de1e52b348280154e8a163c7dd7ee1a7e> .
<hash://sha256/ba02b235fd445904eae45b50bc637a195f25e9ca1637bcf26b2dc7f8698aa1fe> <http://purl.org/pav/previousVersion> <hash://sha256/24b3f981c88c747f44ad3372095767cd15dcf81bd6cd2e54328a90a21409df43> .
<hash://sha256/102cbfb1e800ef795ba1e1c51a34bff9b463b34c9443435069ddc76970c1e9c9> <http://purl.org/pav/previousVersion> <hash://sha256/ba02b235fd445904eae45b50bc637a195f25e9ca1637bcf26b2dc7f8698aa1fe> .
<hash://sha256/fd27b0552c8a6800a8b3b1b822a2063a3215c1d9887badad09a62746b80846bc> <http://purl.org/pav/previousVersion> <hash://sha256/102cbfb1e800ef795ba1e1c51a34bff9b463b34c9443435069ddc76970c1e9c9> .
<hash://sha256/20d36a6f879ba1dd797d4288a4f2e32719d3c674156194c2765a3ec6b43f5e17> <http://purl.org/pav/previousVersion> <hash://sha256/fd27b0552c8a6800a8b3b1b822a2063a3215c1d9887badad09a62746b80846bc> .
<hash://sha256/7801a034fe3c7920e032d2338a690b700ca41a90a92d878fc3a67111cad16d29> <http://purl.org/pav/previousVersion> <hash://sha256/20d36a6f879ba1dd797d4288a4f2e32719d3c674156194c2765a3ec6b43f5e17> .
<hash://sha256/c1b50502b1ca87046eeb7fe4863d0cf9319b6645ff2142db69f21b4cc23332b6> <http://purl.org/pav/previousVersion> <hash://sha256/7801a034fe3c7920e032d2338a690b700ca41a90a92d878fc3a67111cad16d29> .
<hash://sha256/dc293e26154b89273791b9674d81110029f987c686b386184d0b66a5b95f9cda> <http://purl.org/pav/previousVersion> <hash://sha256/c1b50502b1ca87046eeb7fe4863d0cf9319b6645ff2142db69f21b4cc23332b6> .
<hash://sha256/f3ed6aa1bd15ee43d05e138b935040aaa745f6ca8c7e8f2dfbb0a3ae0df66f36> <http://purl.org/pav/previousVersion> <hash://sha256/dc293e26154b89273791b9674d81110029f987c686b386184d0b66a5b95f9cda> .
<hash://sha256/650a28fff3e03dadba70dc05a34c580c04203380187953fa4a2fb778353fee79> <http://purl.org/pav/previousVersion> <hash://sha256/f3ed6aa1bd15ee43d05e138b935040aaa745f6ca8c7e8f2dfbb0a3ae0df66f36> .
<hash://sha256/e4e5736e8bfec6c686eedde4c6dfa62845930d04e12dfa6f8a7d70abc3d087df> <http://purl.org/pav/previousVersion> <hash://sha256/650a28fff3e03dadba70dc05a34c580c04203380187953fa4a2fb778353fee79> .
<hash://sha256/e69d186ff3be11830c2da67d1bfeb896ec6398fc9d555fa26eaae1baa54450fb> <http://purl.org/pav/previousVersion> <hash://sha256/e4e5736e8bfec6c686eedde4c6dfa62845930d04e12dfa6f8a7d70abc3d087df> .
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<hash://sha256/58daa9a51e5dc0911163aa1b98d68c801106734cd29eab9980814057351aeb70> <http://purl.org/pav/previousVersion> <hash://sha256/480868b59e95f3ce2324a7308dba65795e857d34cfbdcea7440a6f2620c6fbf6> .
<hash://sha256/a0a18b0e32f933112084b846863438038f66f63eeeb22fa9d8d734e8a25bb208> <http://purl.org/pav/previousVersion> <hash://sha256/58daa9a51e5dc0911163aa1b98d68c801106734cd29eab9980814057351aeb70> .
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<hash://sha256/0e6b49850d96b4b58ea3759ecea45d273a48f074c4edaaec5e008791d7718781> <http://purl.org/pav/previousVersion> <hash://sha256/a7a5e7c6a4b21bdf67f48d6bea85f438b8133f674027b04625dfadec3ff985f6> .
<hash://sha256/8c0752dc6425b9c716837c9713ce284158b4cff70a1e66be2beb0677018831f4> <http://purl.org/pav/previousVersion> <hash://sha256/0e6b49850d96b4b58ea3759ecea45d273a48f074c4edaaec5e008791d7718781> .
<hash://sha256/d99fa37caa268f8061980001146ed2a566e814d0740bb1974b76847512be95d3> <http://purl.org/pav/previousVersion> <hash://sha256/8c0752dc6425b9c716837c9713ce284158b4cff70a1e66be2beb0677018831f4> .
<hash://sha256/af0bb2c89571a30815d4488e72dede84a2ffc102bb87961f06884509fd5d1dae> <http://purl.org/pav/previousVersion> <hash://sha256/d99fa37caa268f8061980001146ed2a566e814d0740bb1974b76847512be95d3> .
<hash://sha256/261177a96185166f1c301beacf7350abff03d1b5710be6bfd8c4aff9caffef12> <http://purl.org/pav/previousVersion> <hash://sha256/af0bb2c89571a30815d4488e72dede84a2ffc102bb87961f06884509fd5d1dae> .
<hash://sha256/5a39b7bbe9d1bc46ed2eb7bd76c490b5c85a09369a7cf7dc18fa04532679e9a7> <http://purl.org/pav/previousVersion> <hash://sha256/261177a96185166f1c301beacf7350abff03d1b5710be6bfd8c4aff9caffef12> .
<hash://sha256/af8f9ed321d9c403617f54a96e3217adc918970fbbfe8b8715359669f4890b63> <http://purl.org/pav/previousVersion> <hash://sha256/5a39b7bbe9d1bc46ed2eb7bd76c490b5c85a09369a7cf7dc18fa04532679e9a7> .
<hash://sha256/9a41d2583f0b8169ffdd44fb2d3a5e057eba4a10e5d9193d0c6e9dcf07c3119e> <http://purl.org/pav/previousVersion> <hash://sha256/af8f9ed321d9c403617f54a96e3217adc918970fbbfe8b8715359669f4890b63> .
<hash://sha256/b9864a749112cad2fe19e62bf5d8bad580a7036d363d16d81d5c16be325fa0fd> <http://purl.org/pav/previousVersion> <hash://sha256/9a41d2583f0b8169ffdd44fb2d3a5e057eba4a10e5d9193d0c6e9dcf07c3119e> .
<hash://sha256/09574d9c1330c2b1bec9b7bf3a55ab9273bedbfed78affd70a058a1a25e052d2> <http://purl.org/pav/previousVersion> <hash://sha256/b9864a749112cad2fe19e62bf5d8bad580a7036d363d16d81d5c16be325fa0fd> .
<hash://sha256/668d5d6e9c9e7ddb410073ff75eb7f2935c60cc62944ba1fd96ca60feec4a103> <http://purl.org/pav/previousVersion> <hash://sha256/09574d9c1330c2b1bec9b7bf3a55ab9273bedbfed78affd70a058a1a25e052d2> .
<hash://sha256/6387c9ebed9507a0fbba2d161e83c2da73e0d6fa6dd51fb19ac4a4ca75b839c7> <http://purl.org/pav/previousVersion> <hash://sha256/668d5d6e9c9e7ddb410073ff75eb7f2935c60cc62944ba1fd96ca60feec4a103> .
<hash://sha256/d79fb9207329a2813b60713cf0968fda10721d576dcb7a36038faf18027eebc1> <http://purl.org/pav/previousVersion> <hash://sha256/6387c9ebed9507a0fbba2d161e83c2da73e0d6fa6dd51fb19ac4a4ca75b839c7> .If you retrieved data files, you can check the integrity of the extracted archive by confirming 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.
$ java -jar preston.jar verify
hash://sha256/3eff98d4b66368fd8d1f8fa1af6a057774d8a407a4771490beeb9e7add76f362 file:/home/preston/preston-archive/data/3e/ff/3eff98d4b66368fd8d1f8fa1af6a057774d8a407a4771490beeb9e7add76f362 OK CONTENT_PRESENT_VALID_HASH 89931
hash://sha256/184886cc6ae4490a49a70b6fd9a3e1dfafce433fc8e3d022c89e0b75ea3cda0b file:/home/preston/preston-archive/data/18/48/184886cc6ae4490a49a70b6fd9a3e1dfafce433fc8e3d022c89e0b75ea3cda0b OK CONTENT_PRESENT_VALID_HASH 210344
hash://sha256/1846abf2b9623697cf9b2212e019bc1f6dc4a20da51b3b5629bfb964dc808c02 file:/home/preston/preston-archive/data/18/46/1846abf2b9623697cf9b2212e019bc1f6dc4a20da51b3b5629bfb964dc808c02 OK CONTENT_PRESENT_VALID_HASH 210344
hash://sha256/554fdab07f2372bf363a1d7ef30fcf4c32e1da98b95a6342780c5eb35e0e7b38 file:/home/preston/preston-archive/data/55/4f/554fdab07f2372bf363a1d7ef30fcf4c32e1da98b95a6342780c5eb35e0e7b38 OK CONTENT_PRESENT_VALID_HASH 202701Note 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".
Files in this data publication:
--- start of file descriptions ---
-- description of archive and its contents (this file) --
README-- executable java jar containing preston[2] v0.1.8. --
preston.jar-- individual provenance index files --
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ff32a7cbc99eaf6b67695fd94284a9b1b47a76497ef4d10ffc4dae199cc0d7c3--- individual provenance logs --
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References
[1] Global Biodiversity Information Facility, Integrated Digitized Biocollections, Biological Collection Access Service (GBIF, iDigBio, BioCASe, https://gbif.org,https://idigbio.org,http://biocase.org) accessed from 2018-09-03 to 2019-10-02 with provenance hash://sha256/6387c9ebed9507a0fbba2d161e83c2da73e0d6fa6dd51fb19ac4a4ca75b839c7.
[2] https://preston.guoda.bio, https://doi.org/10.5281/zenodo.1410543 .This work is funded in part by grant NSF OAC 1839201 from the National Science Foundation
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A biodiversity dataset graph: DataONE
The intended use of this archive is to facilitate meta-analysis of the Data Observation Network for Earth (DataONE). DataONE is a distributed infrastructure that provides information about earth observation data.
This dataset provides versioned snapshots of the DataONE network as tracked by Preston [2] between 2018-10-18 and 2019-10-03 using "preston update -u https://dataone.org".
The 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 logs and data files. In addition, index files have been individually included in this dataset publication to facilitate remote access. Index files provide a way to links provenance files in time to establish a versioning mechanism. Provenance files describe how, when and where the DataONE content was retrieved. For more information, please visit https://preston.guoda.bio or https://doi.org/10.5281/zenodo.1410543).
To retrieve and verify the downloaded DataONE biodiversity dataset graph, first concatenate all the downloaded preston-*.tar.gz files (e.g., cat preston-*.tar.gz > preston.tar.gz). Then, extract the archives into a "data" folder. Alternatively, you can use the preston[2] command-line tool to "clone" this dataset using:
$ java -jar preston.jar clone --remote https://zenodo.org/record/3483218/files
After that, verify the index of the archive by reproducing the following provenance log history:
$ java -jar preston.jar history
<0659a54f-b713-4f86-a917-5be166a14110> <http://purl.org/pav/hasVersion> <hash://sha256/8c67e0741d1c90db54740e08d2e39d91dfd73566ea69c1f2da0d9ab9780a9a9f> .
<hash://sha256/3ed3acaca7ac57f546d0b8877c1927ab5e08c23eccaa8219600c59c77a72c685> <http://purl.org/pav/previousVersion> <hash://sha256/8c67e0741d1c90db54740e08d2e39d91dfd73566ea69c1f2da0d9ab9780a9a9f> .
<hash://sha256/857753997a7595a1b372b05641b58a25d9408b7ff08d557ce1fe8b73e4bd383f> <http://purl.org/pav/previousVersion> <hash://sha256/3ed3acaca7ac57f546d0b8877c1927ab5e08c23eccaa8219600c59c77a72c685> .
<hash://sha256/7ee0376f4c3f7aeeda36927a5211395e5da8201e810e8c7e638a0fe23d001e88> <http://purl.org/pav/previousVersion> <hash://sha256/857753997a7595a1b372b05641b58a25d9408b7ff08d557ce1fe8b73e4bd383f> .
<hash://sha256/68b4974d8ab7c4c7a7a4305065839b60ba460aaa862590b34c67877738feba90> <http://purl.org/pav/previousVersion> <hash://sha256/7ee0376f4c3f7aeeda36927a5211395e5da8201e810e8c7e638a0fe23d001e88> .
<hash://sha256/060a76d56255bf9482c951748c91291fddeeb20f180632132be1344e081b2372> <http://purl.org/pav/previousVersion> <hash://sha256/68b4974d8ab7c4c7a7a4305065839b60ba460aaa862590b34c67877738feba90> .
<hash://sha256/29357bdfab4548025f8a5743301f5c3c9146fa436c39e3c9e019fb9409ac9c42> <http://purl.org/pav/previousVersion> <hash://sha256/060a76d56255bf9482c951748c91291fddeeb20f180632132be1344e081b2372> .
<hash://sha256/3669cd95100d1d533eb8953ff4ec5092cbd8addb8879b3e6262191148a8a3ebb> <http://purl.org/pav/previousVersion> <hash://sha256/29357bdfab4548025f8a5743301f5c3c9146fa436c39e3c9e019fb9409ac9c42> .
<hash://sha256/8dc1663299359d271cb1b4c14ad521d0f1be67743689dd18016543dc1e097efb> <http://purl.org/pav/previousVersion> <hash://sha256/3669cd95100d1d533eb8953ff4ec5092cbd8addb8879b3e6262191148a8a3ebb> .
<hash://sha256/dc4903e8afee651db1d9bf509f20503bf9c8e89679c4bcffb46d5b97440cb6de> <http://purl.org/pav/previousVersion> <hash://sha256/8dc1663299359d271cb1b4c14ad521d0f1be67743689dd18016543dc1e097efb> .
<hash://sha256/f3bed9db3092c744604df5f50248a2ec36e564fe78a65f45c4190283bd61c807> <http://purl.org/pav/previousVersion> <hash://sha256/dc4903e8afee651db1d9bf509f20503bf9c8e89679c4bcffb46d5b97440cb6de> .
<hash://sha256/e3c7b3b14b2b792e3e2e560a1b2bef059ac93f777dee616b836317bc9cbfcbf7> <http://purl.org/pav/previousVersion> <hash://sha256/f3bed9db3092c744604df5f50248a2ec36e564fe78a65f45c4190283bd61c807> .
<hash://sha256/631a4531e7bb052816d28454bbeec3428d5e7bfd1f148c4f21ce63a6cf86c650> <http://purl.org/pav/previousVersion> <hash://sha256/e3c7b3b14b2b792e3e2e560a1b2bef059ac93f777dee616b836317bc9cbfcbf7> .
<hash://sha256/87de0898919d2212977a586965e930ae45bdd1366073591c808c208a635e2814> <http://purl.org/pav/previousVersion> <hash://sha256/631a4531e7bb052816d28454bbeec3428d5e7bfd1f148c4f21ce63a6cf86c650> .To 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.
$ java -jar preston.jar verify
hash://sha256/e55c1034d985740926564e94decd6dc7a70f779a33e7deb931553739cda16945 file:/home/preston/preston-dataone/data/e5/5c/e55c1034d985740926564e94decd6dc7a70f779a33e7deb931553739cda16945 OK CONTENT_PRESENT_VALID_HASH 21580
hash://sha256/d0ddcc2111b6134a570bcc7d89375920ef4d754130cecc0727c79d2b05a9f81f file:/home/preston/preston-dataone/data/d0/dd/d0ddcc2111b6134a570bcc7d89375920ef4d754130cecc0727c79d2b05a9f81f OK CONTENT_PRESENT_VALID_HASH 2035
hash://sha256/472de9d1c9fd7e044aac409abfbfff9f12c6b69359df995d431009580ffb0f53 file:/home/preston/preston-dataone/data/47/2d/472de9d1c9fd7e044aac409abfbfff9f12c6b69359df995d431009580ffb0f53 OK CONTENT_PRESENT_VALID_HASH 1935
hash://sha256/b29879462cd43862129c5cf9b149c41ecd33ffef284a4dbea4ac1c0f90108687 file:/home/preston/preston-dataone/data/b2/98/b29879462cd43862129c5cf9b149c41ecd33ffef284a4dbea4ac1c0f90108687 OK CONTENT_PRESENT_VALID_HASH 1553Note 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".
Files in this data publication:
--- start of file descriptions ---
-- description of archive and its contents (this file) --
README-- executable java jar containing preston[2] v0.1.8. --
preston.jar-- preston archives containing DataONE data files, associated provenance logs and a provenance index --
preston-[00-ff].tar.gz-- individual provenance index files --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--- end of file descriptions ---
References[1] Data Observation Network for Earth (DataONE, https://dataone.org) accessed from 2018-10-18 to 2019-10-03 with provenance hash://sha256/631a4531e7bb052816d28454bbeec3428d5e7bfd1f148c4f21ce63a6cf86c650 .
[2] https://preston.guoda.bio, https://doi.org/10.5281/zenodo.1410543 .
This work is funded in part by grant NSF OAC 1839201 from the National Science Foundation
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A biodiversity dataset graph: DataONE
The intended use of this archive is to facilitate meta-analysis of the Data Observation Network for Earth (DataONE, [1]). DataONE is a distributed infrastructure that provides information about earth observation data.
This dataset provides versioned snapshots of the DataONE network as tracked by Preston [2] between 17 October 2018 and 7 July 2019.
The 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 eestablish a versioning mechanism. Provenance files describe how, when and where the DataONE meta-data files were retrieved. For more information, please visit https://preston.guoda.bio or https://doi.org/10.5281/zenodo.1410543).
To retrieve and verify the downloaded DataONE biodiversity dataset graph, first concatenate all the downloaded preston-*.tar.gz files (e.g., cat preston-*.tar.gz > preston.tar.gz). Then, extract the archives into a "data" folder. Alternatively, you can use the preston[2] command-line tool to "clone" this dataset using:
$ java -jar preston.jar clone --remote https://zenodo.org/record/3277312/files
After that, verify the index of the archive by reproducing the following result:
$ java -jar preston.jar history
<0659a54f-b713-4f86-a917-5be166a14110> <http://purl.org/pav/hasVersion> <hash://sha256/8c67e0741d1c90db54740e08d2e39d91dfd73566ea69c1f2da0d9ab9780a9a9f> .
<hash://sha256/3ed3acaca7ac57f546d0b8877c1927ab5e08c23eccaa8219600c59c77a72c685> <http://purl.org/pav/previousVersion> <hash://sha256/8c67e0741d1c90db54740e08d2e39d91dfd73566ea69c1f2da0d9ab9780a9a9f> .
<hash://sha256/857753997a7595a1b372b05641b58a25d9408b7ff08d557ce1fe8b73e4bd383f> <http://purl.org/pav/previousVersion> <hash://sha256/3ed3acaca7ac57f546d0b8877c1927ab5e08c23eccaa8219600c59c77a72c685> .
<hash://sha256/7ee0376f4c3f7aeeda36927a5211395e5da8201e810e8c7e638a0fe23d001e88> <http://purl.org/pav/previousVersion> <hash://sha256/857753997a7595a1b372b05641b58a25d9408b7ff08d557ce1fe8b73e4bd383f> .
<hash://sha256/68b4974d8ab7c4c7a7a4305065839b60ba460aaa862590b34c67877738feba90> <http://purl.org/pav/previousVersion> <hash://sha256/7ee0376f4c3f7aeeda36927a5211395e5da8201e810e8c7e638a0fe23d001e88> .
<hash://sha256/060a76d56255bf9482c951748c91291fddeeb20f180632132be1344e081b2372> <http://purl.org/pav/previousVersion> <hash://sha256/68b4974d8ab7c4c7a7a4305065839b60ba460aaa862590b34c67877738feba90> .
<hash://sha256/29357bdfab4548025f8a5743301f5c3c9146fa436c39e3c9e019fb9409ac9c42> <http://purl.org/pav/previousVersion> <hash://sha256/060a76d56255bf9482c951748c91291fddeeb20f180632132be1344e081b2372> .
<hash://sha256/3669cd95100d1d533eb8953ff4ec5092cbd8addb8879b3e6262191148a8a3ebb> <http://purl.org/pav/previousVersion> <hash://sha256/29357bdfab4548025f8a5743301f5c3c9146fa436c39e3c9e019fb9409ac9c42> .
<hash://sha256/8dc1663299359d271cb1b4c14ad521d0f1be67743689dd18016543dc1e097efb> <http://purl.org/pav/previousVersion> <hash://sha256/3669cd95100d1d533eb8953ff4ec5092cbd8addb8879b3e6262191148a8a3ebb> .
<hash://sha256/dc4903e8afee651db1d9bf509f20503bf9c8e89679c4bcffb46d5b97440cb6de> <http://purl.org/pav/previousVersion> <hash://sha256/8dc1663299359d271cb1b4c14ad521d0f1be67743689dd18016543dc1e097efb> .To 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.
$ java -jar preston.jar verify
hash://sha256/e55c1034d985740926564e94decd6dc7a70f779a33e7deb931553739cda16945 file:/home/preston/preston-dataone/data/e5/5c/e55c1034d985740926564e94decd6dc7a70f779a33e7deb931553739cda16945 OK CONTENT_PRESENT_VALID_HASH 21580
hash://sha256/d0ddcc2111b6134a570bcc7d89375920ef4d754130cecc0727c79d2b05a9f81f file:/home/preston/preston-dataone/data/d0/dd/d0ddcc2111b6134a570bcc7d89375920ef4d754130cecc0727c79d2b05a9f81f OK CONTENT_PRESENT_VALID_HASH 2035
hash://sha256/472de9d1c9fd7e044aac409abfbfff9f12c6b69359df995d431009580ffb0f53 file:/home/preston/preston-dataone/data/47/2d/472de9d1c9fd7e044aac409abfbfff9f12c6b69359df995d431009580ffb0f53 OK CONTENT_PRESENT_VALID_HASH 1935
hash://sha256/b29879462cd43862129c5cf9b149c41ecd33ffef284a4dbea4ac1c0f90108687 file:/home/preston/preston-dataone/data/b2/98/b29879462cd43862129c5cf9b149c41ecd33ffef284a4dbea4ac1c0f90108687 OK CONTENT_PRESENT_VALID_HASH 1553Note 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".
Files in this data publication:
README - this file
preston.jar - executable java jar containing preston[2] v0.1.1.
preston-[00-ff].tar.gz - preston archives containing DataONE meta-data files, their provenance and a provenance index.
2a5de79372318317a382ea9a2cef069780b852b01210ef59e06b640a3539cb5a - preston index file
2aecaf289def0e23a27058bf7715f226ef9189905f0be13228174825633125cf - preston index file
3d38b70198e448674be6a63d14b9817f3a956f48bba7418fa7baa086a56c05b7 - preston index file
66ad3e5e904740f1e835ac6718dda4279e0c24b204ea0d1113cda1352a5072ba - preston index file
8bf062872ce958545d361e9d53a552ffb025ac29ab875caad1157c0995d34f66 - preston index file
d9378616636be3686bbabd5bf29d50f0ef0e5ceb5ddd7dfce47f7e755b596b7d - preston index file
da26fa6e7371385ed3f61af9a766221c833060d59dfd4869bbd7110f95f288db - preston index file
e4103a75627857de3ee2e317429108611c244fc448c01d1d7bf652115c3b8a55 - preston index file
eb368fedb8f100210dd968edcf80f4d13cab3dd64135a6ab744102cf15e68c94 - preston index file
ff92b6c06ae5286bd2f1db679e0fcc4da294acb9bc01b2e9522378d99218c2e3 - preston index file[1] DataONE, https://www.dataone.org
[2] https://preston.guoda.bio, https://doi.org/10.5281/zenodo.1410543 . DataONE was crawled via Preston with "preston update -u https://dataone.org".This work is funded in part by grant NSF OAC 1839201 from the National Science Foundation
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