Planned intervention: On Wednesday April 3rd 05:30 UTC Zenodo will be unavailable for up to 2-10 minutes to perform a storage cluster upgrade.

There is a newer version of the record available.

Published November 23, 2021 | Version 0.1.0
Dataset Open

Big Bee indexed biotic interactions and review summary

  • 1. University of California, Santa Barbara
  • 2. Ronin Institute

Description

Extending Anthophila research through image and trait digitization (Big-Bee) indexed biotic interactions and review summary.

Declining populations of bees impact plant-pollinator interactions in both natural and agricultural systems. While bees and other insects pollinate most wild plants and are critical to sustaining a large proportion of global food production, they are decreasing in both numbers and diversity. Our understanding of the factors driving these declines is limited because we lack sufficient data on the distribution of bee species, and on the behavioral and anatomical traits that may make them either vulnerable or resilient to human-induced environmental changes, such as habitat loss and climate change. Fortunately, wild bees have been collected by researchers and deposited in natural history collections for over 100 years, retaining a wealth of associated attributes that can be extracted from specimen images. This project will digitally capture data and images from these historic specimens, develop tools to measure bee traits from these images and generate a comprehensive bee trait and image dataset to measure changes through time. This will increase our understanding of specific traits that put bee species at risk of decline - a critical need for both sustaining our agricultural economy and the conservation of our natural resources. In addition, the large image datasets created by this project can be used for new artificial intelligence identification tools that will help improve our future pollinator observation and monitoring efforts.

The Big-Bee project began in 2021 and is funded by the National Science Foundation to mobilize data about worldwide bee species to data aggregators (e.g., iDigBio, GBIF). The Big-Bee Thematic Collection Network (Big-Bee) will create over one million high-resolution 2D and 3D images of bee specimens, representing over 5,000 worldwide bee species, including all of the major pollinating species of the United States. The Big-Bee network includes 13 institutions and partnerships with US government agencies. Novel mechanisms for sharing image datasets will be developed and datasets of bee traits will be available through an open data portal, the Bee Library, for research and education. The Big-Bee project will engage the general public in research through community science via crowdsourcing trait measurements and data transcription from images. In addition, training and professional development for natural history collection staff, researchers, and university students in data science will be provided through the creation and implementation of workshops focusing on bee traits and species identification. All data resulting from this award will be shared with and publicly available through the national digitized biocollections resource, iDigBio.org.

This is the first archive of Big-Bee data indexed by Global Biotic Interactions (GloBI). GloBI provides open access to finding species interaction data (e.g., predator-prey, pollinator-plant, pathogen-host, parasite-host) by combining existing open datasets using open-source software. This version of the Big Bee dataset includes interactions that are not just bees. Also in this version, the datasets included in this publication are specifically those institutions in the Big Bee project network and do not represent all bee interaction data found at Global Biotic Interactions.

Bee Library Information - Statistics about Big Bee data providers

The specimens indexed by GloBI are also found on the Bee Library. To date, the number of specimens and images in the library are listed below. The Bee Library taxonomic backbone is not yet complete, so information regarding the number of species is not yet available.

1,147,415 occurrence records
936,087 (82%) georeferenced
306,242 (27%) occurrences imaged
 

 

 

 

Collection Specimens Georeferenced Imaged Interactions Indexed in GloBI (all)

Interactions Indexed in GloBI (bees)

ASU Hasbrouck Insect Collection - Bee Records 4943 4943 0 6214 604
Bee Biology and Systematics Laboratory USDA-ARS Pollinating Insect-Biology Management Systematics Research 561820 547461 0 0 0
California Academy of Sciences 805 254 0 15407 92
California Academy of Sciences - Type Collection 1838 52 77 0 0
Essig Museum of Entomology University of California Berkeley 58490 54965 0 0 0
Florida State Collection of Arthropods 1 0   0 0
Museum of Comparative Zoology Harvard University 9709 9481 495 4046 18
Natural History Museum of Los Angeles County 1 0   0 0
San Diego Natural History Museum Entomology Department 2153 1612 0 7021 8
USGS Native Bee Inventory and Monitoring Lab 98 98 0 0 0
University of California Santa Barbara Invertebrate Zoology Collection 7033 6781 1278 1663 402
University of Colorado Museum of Natural History Entomology Collection 18043 18043 0 9589 4719
University of Kansas Natural History Museum Entomology Division 464795 275004 304392 0 0
University of Michigan Museum of Zoology Division of Insects 1 0   94489 9649
University of New Hampshire Donald S. Chandler Entomological Collection 17685 17393 0 3137 3101

 

Names SpecimenCount GeorefCount

GeorefPercent

Andrenidae 192034 175698 91
Apidae 429537 311637 73
Colletidae 63652 47538 75
Halictidae 249081 216755 87
Megachilidae 199354 171859 86
Melittidae 11646 10751 92
Stenotritidae 22 22 100

 

Names SpecimenCount GeorefCount

GeorefPercent

[Higher geography: has not been verified and entered] 168 0 0
Afghanistan 1005 474 47
Albania 7 3 43
Algeria 183 86 47
Andorra 6 3 50
Angola 782 705 90
Antigua and Barbuda 3 3 100
Argentina 21973 14020 64
Arizona 1 0 0
Armenia 48 25 52
Aruba 2 2 100
Australia 11317 1961 17
Austria 4693 1214 26
Azerbaijan 34 30 88
Bahamas 125 36 29
Bangladesh 7 2 29
BAR 3 3 100
Barbados 5 4 80
Belgium 37 31 84
Belize 340 304 89
Benin 8 8 100
Bermuda 1 0 0
Bhutan 10 6 60
Bolivia 16161 7268 45
Bosnia and Herzegovina 51 2 4
Botswana 71 43 61
Brasil 3 2 67
Brazil 27652 16458 60
British Virgin Islands 3 2 67
Brunei 18 1 6
Bulgaria 803 492 61
Burkina Faso 8 0 0
Burundi 5 0 0
California 2 0 0
Cambodia 2 0 0
Cameroon 1124 65 6
Canada 14905 14077 94
Cape Verde 19 7 37
Central African Republic 116 97 84
Chad 5 0 0
CHILE 4 4 100
Chile 10950 4575 42
CHINA 34 33 97
China 692 368 53
Christmas Island 3 0 0
Colombia 5994 2563 43
Commonwealth of the Bahamas 31 5 16
Comoros 3 0 0
Congo 1 1 100
Congo the Democratic Republic of the 1 0 0
COS 2 2 100
Costa Rica 38007 30178 79
Croatia 713 462 65
Cuba 307 144 47
Cyprus 514 351 68
Czech Republic 4594 2789 61
Democratic Republic of Congo 55 41 75
Democratic Republic of the Congo 685 272 40
Denmark 27 12 44
Dominica 5 1 20
Dominican Republic 30 9 30
Ecuador 3967 2534 64
Ecuador/Peru 3 3 100
Egypt 1494 889 60
El Salvador 358 142 40
Eritrea 3 0 0
Estonia 1 0 0
Ethiopia 81 20 25
Federated States of Micronesia 3 1 33
Fiji 7 0 0
Fiji Islands 277 57 21
Finland 284 177 62
Florida 16 16 100
France 739 705 95
French Guiana 6748 2568 38
French Polynesia 35 23 66
Gabon 121 16 13
Gambia 7 3 43
Georgia 6 6 100
Germany 455 257 56
Ghana 111 40 36
Great Britain 5179 5081 98
Greece 2004 1823 91
Greenland 2 0 0
Grenada 4 2 50
Guadeloupe 35 35 100
Guatemala 1503 1085 72
Guernsey 5 0 0
Guyana 837 720 86
Haiti 22 18 82
Holland 4 0 0
Honduras 1012 658 65
Hong Kong 63 4 6
Hungary 473 443 94
Iceland 13 0 0
Idaho 1 0 0
India 6223 4297 69
Indonesia 1994 1005 50
Iran 9186 6564 71
Iran Islamic Republic of 2 2 100
Iraq 34 0 0
Ireland 7 0 0
Israel 711 100 14
Italy 1182 1117 95
Ivory Coast 6 3 50
Jamaica 296 1 0
Japan 749 159 21
Jordan 122 38 31
Kazakhstan 210 14 7
Kenya 2462 228 9
Korea 2 0 0
Kuwait 6 0 0
Kyrgyzstan 193 152 79
Lao Peoples Democratic Republic 4 4 100
Laos 7 0 0
Latvia 1 0 0
Lebanon 199 122 61
Lesotho 24 3 13
Liberia 190 12 6
Libya 90 22 24
Liechtenstein 1 0 0
Lithuania 104 6 6
Macao 2 0 0
Macedonia 150 0 0
Madagascar 3638 2078 57
Maine 22 22 100
Malawi 1202 18 1
Malaysia 3041 876 29
Maldives 32 24 75
Mali 19 2 11
Martinique 9 2 22
Massachusetts 2 2 100
Mauritius 16 5 31
Mexico 62070 37536 60
Missouri 8 0 0
Mongolia 202 115 57
Montana 1 0 0
Montenegro 2 0 0
Montserrat 25 2 8
Morocco 567 46 8
Mozambique 489 2 0
Myanmar 117 94 80
N. S. 3 3 100
N.S. 3 3 100
Namibia 375 115 31
Nepal 140 45 32
Netherlands 50 2 4
Netherlands Antilles 23 14 61
New Caledonia 21 0 0
New Hampshire 348 348 100
New Zealand 403 174 43
Nicaragua 1758 1408 80
Niger 3 2 67
Nigeria 583 87 15
Niue 1 0 0
North Carolina 13 13 100
North Korea 1 0 0
Norway 203 13 6
Ohio 3 3 100
Oman 160 135 84
Oregon 4 0 0
Pakistan 518 445 86
Palau 68 0 0
Palestine 1 0 0
Panama 10028 2190 22
PANAMA 1012 809 80
Papua New Guinea 380 79 21
Paraguay 3347 993 30
PEI 6 6 100
Pennsylvania 1 1 100
Peru 10409 9485 91
Philippines 543 34 6
Poland 370 293 79
Portugal 97 78 80
Puerto Rico 47 0 0
Qatar 40 0 0
Republic of Malta 3 0 0
Republic of the Congo 19 1 5
Romania 255 203 80
Russia 518 419 81
Russian Federation 5 5 100
Rwanda 4 0 0
Saint Barthelemy 1 1 100
Saint Kitts and Nevis 2 1 50
Saint Lucia 3 0 0
Saint Vincent 56 56 100
Saint Vincent and the Grenadines 14 0 0
Samoa 25 2 8
Saudi Arabia 336 226 67
Senegal 65 0 0
Serbia 19 14 74
Seychelles 26 0 0
Sierra Leone 27 20 74
Singapore 217 6 3
Slovakia 7120 3 0
Slovenia 46 41 89
Slovokia 5 5 100
Solomon Islands 114 2 2
Somalia 8 3 38
South Africa 12344 3004 24
South Korea 97 16 16
Spain 4638 4322 93
Sri Lanka 2640 1729 65
Sudan 114 9 8
Suriname 472 287 61
Swaziland 35 1 3
Sweden 277 195 70
Switzerland 222 188 85
Syria 45 0 0
Taiwan 219 9 4
Tajikistan 67 1 1
Tanzania 1355 396 29
TE 1 1 100
Texas 1 0 0
Thailand 2579 381 15
Togo 19 0 0
Tonga 11 0 0
Trinidad 164 153 93
Trinidad and Tobago 1132 88 8
Tunisia 197 34 17
Turkey 1018 893 88
Turkmenistan 132 11 8
Uganda 1107 9 1
Ukraine 72 64 89
United Arab Emirates 1411 380 27
United Kingdom 91 91 100
United States 776802 731500 94
Unknown 64 0 0
Uruguay 41 37 90
Uzbekistan 309 36 12
Vanuatu 63 0 0
Venezuela 3449 2175 63
Vermont 13 13 100
Viet Nam 2 2 100
Vietnam 230 225 98
VT 1 1 100
Wisconsin 3 3 100
Wyoming 2 0 0
Yemen 42 29 69
Yugoslavia 1 0 0
Zambia 205 33 16
Zimbabwe 748 718 96

GloBI Data Review Report - Datasets in Review from Global Biotic Interactions

Datasets under review:
 - California Academy of Sciences Entomology accessed via https://github.com/globalbioticinteractions/cas-ent/archive/562aea232ec74ab615f771239451e57b057dc7c0.zip on 2021-11-23T20:24:31.655Z
 - Florida State Collection of Arthropods accessed via https://github.com/globalbioticinteractions/fsca/archive/682f11686317ae81959a043bd6b493ddfc06c438.zip on 2021-11-23T20:24:54.058Z
 - Natural History Museum of Los Angeles County accessed via https://github.com/globalbioticinteractions/lacm-lacmec/archive/216b0e456b1974cdc52b455a403346db9b6fe875.zip on 2021-11-23T20:24:59.041Z
 - San Diego Natural History Museum accessed via https://github.com/globalbioticinteractions/sdnhm-sdmc/archive/7238d8b804f543250eb487b43144e1125fb3688a.zip on 2021-11-23T20:25:05.879Z
 - University of California Berkeley, Essig Museum of Entomology accessed via https://github.com/globalbioticinteractions/emec/archive/414e3efb04a566824842279a8159b942f4ce8959.zip on 2021-11-23T20:25:17.656Z
 - University of California Santa Barbara Invertebrate Zoology Collection accessed via https://github.com/globalbioticinteractions/ucsb-izc/archive/864457bf411f2b01820f9ecfb11397e453bb6572.zip on 2021-11-23T20:25:23.751Z
 - Harvard University M, Morris P J (2021). Museum of Comparative Zoology, Harvard University. Museum of Comparative Zoology, Harvard University. accessed via https://github.com/globalbioticinteractions/mcz/archive/b33635a9fc75fd7931ad968cbc11180e6467bfd7.zip on 2021-11-23T20:30:04.339Z
 - University of Kansas Natural History Museum accessed via https://github.com/globalbioticinteractions/ku-semc/archive/5180d6904c8e1e6be12897bae9c1c7c650da3ab9.zip on 2021-11-23T20:33:04.471Z
 - University of Michigan Museum of Zoology Insect Division. Full Database Export 2020-11-20 provided by Erika Tucker and Barry Oconner. accessed via https://github.com/EMTuckerLabUMMZ/ummzi/archive/6731357a377e9c2748fc931faa2ff3dc0ce3ea7a.zip on 2021-11-23T20:34:23.307Z
 - University of Colorado Museum of Natural History Entomology Collection accessed via https://github.com/globalbioticinteractions/ucm-ucmc/archive/c2a838bbf39e09b7e195b2895c107b2963167b20.zip on 2021-11-23T20:34:59.214Z
 - Arizona State University Hasbrouck Insect Collection accessed via https://github.com/globalbioticinteractions/asu-asuhic/archive/025665959d3a7a37dc9dcc532c80166359274dd7.zip on 2021-11-23T20:35:14.900Z
 - University of New Hampshire Donald S. Chandler Entomological Collection accessed via https://github.com/globalbioticinteractions/unhc-unhc/archive/d7668a6bb4545dc4da0645ecc383169ba547b0f5.zip on 2021-11-23T20:35:33.107Z

Generated on:
2021-11-23

by:
GloBI's Elton 0.10.4 
(see https://github.com/globalbioticinteractions/elton).

Note that all files ending with .tsv are files formatted 
as UTF8 encoded tab-separated values files.

https://www.iana.org/assignments/media-types/text/tab-separated-values


Included in this review archive are:

README:
  This file.

review_summary.tsv:
  Summary across all reviewed collections of total number of distinct review comments.

review_summary_by_collection.tsv:
  Summary by reviewed collection of total number of distinct review comments.

indexed_interactions_by_collection.tsv: 
  Summary of number of indexed interaction records by institutionCode and collectionCode.

review_comments.tsv.gz:
  All review comments by collection.

indexed_interactions_full.tsv.gz:
  All indexed interactions for all reviewed collections.
  
indexed_interactions_bees.tsv.zip
  All indexed interactions of bees for all reviewed collections.

indexed_interactions_simple.tsv.gz:
  All indexed interactions for all reviewed collections selecting only sourceInstitutionCode, sourceCollectionCode, sourceCatalogNumber, sourceTaxonName, interactionTypeName and targetTaxonName.

datasets_under_review.tsv:
  Details on the datasets under review.

elton.jar: 
  Program used to update datasets and generate the review reports and associated indexed interactions.

If you have questions or comments about this publication, please open an issue at https://github.com/Big-Bee-Network/issues-observations-and-questions/discussions or contact the authors by email.

Funding:
The creation of this archive was made possible by the National Science Foundation award Collaborative Research: Digitization TCN: Extending Anthophila research through image and trait digitization (Big-Bee). Award numbers: DBI:2102006, DBI:2101929, DBI:2101908, DBI:2101876, DBI:2101875, DBI:2101851, DBI:2101345, DBI:2101913, DBI:2101891 and DBI:2101850.

References:
Poelen JH, Simons JD and Mungall CH. (2014). Global Biotic Interactions: An open infrastructure to share and analyze species-interaction datasets. Ecological Informatics. https://doi.org/10.1016/j.ecoinf.2014.08.005.

Seltmann KC, Allen J, Brown BV, Carper A, Engel MS, Franz N, Gilbert E, Grinter C, Gonzalez VH, Horsley P, Lee S, Maier C, Miko I, Morris P, Oboyski P, Pierce NE, Poelen J, Scott VL, Smith M, Talamas EJ, Tsutsui ND, Tucker E (2021) Announcing Big-Bee: An initiative to promote understanding of bees through image and trait digitization. Biodiversity Information Science and Standards 5: e74037. https://doi.org/10.3897/biss.5.74037

Poelen JH, Kuhn K, & Leinweber K. (2020). globalbioticinteractions/elton 0.9.6 (0.9.6). Zenodo. https://doi.org/10.5281/zenodo.3776831

Files

indexed_interactions_bees.tsv.zip

Files (40.4 MB)

Name Size Download all
md5:f9983352bbfac49ce5b6a673cbc0d731
3.7 kB Download
md5:2c15c12bc8fe5eafddc75356b36282bd
31.1 MB Download
md5:9c28d792bb41a84091400025e00e804a
1.7 MB Preview Download
md5:38b7ebfa278afc5320211b5e941570b4
3.7 kB Download
md5:46f8eedb7c5fbda7dbf0ded3af0fdd35
6.6 MB Download
md5:c1d08dc974fb8c9353577263180de86b
724.3 kB Download
md5:2da63144edbcfbd304d2b072f7a4f90f
4.0 kB Download
md5:08149c849babb08960844d67594d80ab
113.9 kB Download
md5:43a21bf3a9e6ba71a8833faa71a5f9f5
132.8 kB Download

Additional details

Related works

Cites
Software: 10.5281/zenodo.3776831 (DOI)

References

  • Seltmann KC, Allen J, Brown BV, Carper A, Engel MS, Franz N, Gilbert E, Grinter C, Gonzalez VH, Horsley P, Lee S, Maier C, Miko I, Morris P, Oboyski P, Pierce NE, Poelen J, Scott VL, Smith M, Talamas EJ, Tsutsui ND, Tucker E (2021) Announcing Big-Bee: An initiative to promote understanding of bees through image and trait digitization. Biodiversity Information Science and Standards 5: e74037. https://doi.org/10.3897/biss.5.74037
  • Poelen JH, Simons JD and Mungall CH. (2014). Global Biotic Interactions: An open infrastructure to share and analyze species-interaction datasets. Ecological Informatics. https://doi.org/10.1016/j.ecoinf.2014.08.005.
  • Poelen JH, Kuhn T, & Leinweber K. (2020). globalbioticinteractions/elton 0.9.6 (0.9.6). Zenodo. https://doi.org/10.5281/zenodo.3776831