Dataset Open Access

Big Bee indexed biotic interactions and review summary

Seltmann, Katja C.; Poelen, Jorrit H.; Engel, Michael; Gonzalez, Victor

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

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

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

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

Bee Library Information - Statistics about Big Bee data providers

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

From Bee Library (partner indexed records)
1,172,372 occurrence records
955,937 (82%) georeferenced
315,742 (27%) occurrences imaged
615,387 (52%) identified to species
9 families
329 genera
5,871 species
6,141 total taxa (including subsp. and var.)

 

Collection Occurrences Georeferenced Imaged Total Taxa

Interactions Indexed in GloBI (bees)

ASU Hasbrouck Insect Collection - Bee
Records
11543 11542 573 213 728
Bee Biology and Systematics Laboratory,
USDA-ARS Pollinating Insect-Biology,
Management, Systematics Research
561820 547461 0 4697 N/A
California Academy of Sciences 805 254 0 5 99
California Academy of Sciences - Type
Collection
1838 52 77 1433 N/A
Essig Museum of Entomology, University
of California Berkeley
58490 54965 0 444 0
Florida State Collection of Arthropods 6959 6922 6050 238 0
Museum of Comparative Zoology, Harvard
University
10034 9806 820 570 83
Natural History Museum of Los Angeles
County
9812 4740 2546 345 0
San Diego Natural History Museum
Entomology Department
2153 1612 0 151 76
University of California Santa Barbara
Invertebrate Zoology Collection
8297 8045 1284 123 500
University of Colorado Museum of Natural
History, Entomology Collection
18043 18043 0 294 4723
University of Kansas Natural History
Museum Entomology Division
464795 275004 304392 0 112664
University of Michigan Museum of Zoology
Division of Insects
0 0 0 0 9646
University of New Hampshire, Donald S.
Chandler Entomological Collection
17685 17393 0 424 3137
USGS Native Bee Inventory and Monitoring
Lab
98 98 0 0 N/A

 

Family Distribution (from partner collections)        
Family Specimens Georeferenced Species ID Georeferenced
and
Species ID
Andrenidae 201,729 91% 61% 59%
Apidae 438,994 73% 38% 35%
Apoidea 6 17% 0% 0%
Choreutidae 92 100% 0% 0%
Colletidae 64,203 75% 46% 45%
Halictidae 251,691 87% 62% 61%
Megachilidae 201,055 86% 65% 63%
Melittidae 11,651 92% 75% 75%
Stenotritidae 22 100% 59% 59%

 

Geographic Distribution (from partner collections)

       
Country Specimens Georeferenced Species ID Georeferenced
and
Species ID
[Higher geography: has not been verified and
entered]
168 0% 76% 0%
Afghanistan 1,009 47% 3% 3%
Albania 7 43% 0% 0%
Algeria 183 47% 4% 4%
Andorra 8 63% 0% 0%
Angola 782 90% 1% 1%
Antigua and Barbuda 3 100% 0% 0%
Argentina 22,366 64% 14% 14%
Arizona 1 0% 0% 0%
Armenia 48 52% 0% 0%
Aruba 2 100% 0% 0%
Australia 11,317 17% 11% 11%
Austria 4,709 26% 2% 2%
Azerbaijan 34 88% 0% 0%
Bahamas 127 30% 73% 9%
Bangladesh 7 29% 29% 29%
BAR 3 100% 0% 0%
Barbados 5 80% 80% 80%
Belgium 37 84% 0% 0%
Belize 384 91% 50% 50%
Benin 8 100% 0% 0%
Bermuda 1 0% 0% 0%
Bhutan 10 60% 0% 0%
Bolivia 16,258 45% 16% 16%
Bosnia and Herzegovina 51 4% 0% 0%
Botswana 71 61% 18% 13%
Brasil 3 67% 100% 67%
Brazil 27,665 60% 4% 4%
British Virgin Islands 4 50% 0% 0%
Brunei 18 6% 0% 0%
Bulgaria 803 61% 0% 0%
Burkina Faso 8 0% 0% 0%
Burundi 5 0% 0% 0%
California 3 33% 0% 0%
Cambodia 2 0% 0% 0%
Cameroon 1,124 6% 3% 3%
Canada 15,116 95% 26% 25%
Cape Verde 19 37% 0% 0%
Central African Republic 116 84% 46% 30%
Chad 5 0% 0% 0%
CHILE 4 100% 100% 100%
Chile 11,065 42% 20% 19%
China 692 53% 0% 0%
CHINA 34 97% 100% 97%
Christmas Island 3 0% 0% 0%
Colombia 6,003 43% 7% 5%
Commonwealth of the Bahamas 31 16% 100% 16%
Comoros 3 0% 0% 0%
Congo 1 100% 100% 100%
Congo, the Democratic Republic of the 1 0% 0% 0%
COS 2 100% 100% 100%
Costa Rica 38,235 80% 60% 59%
Croatia 718 65% 7% 6%
Cuba 307 47% 3% 3%
Cyprus 514 68% 3% 3%
Czech Republic 4,628 61% 1% 1%
Democratic Republic of Congo 55 75% 95% 69%
Democratic Republic of the Congo 685 40% 3% 3%
Denmark 27 44% 52% 44%
Dominica 5 20% 20% 20%
Dominican Republic 34 38% 32% 32%
Ecuador 3,978 64% 14% 12%
Ecuador/Peru 3 100% 100% 100%
Egypt 1,496 60% 19% 18%
El Salvador 377 43% 9% 6%
England; United Kingdom 28 100% 0% 0%
Eritrea 3 0% 0% 0%
Estonia 9 89% 89% 89%
Ethiopia 81 25% 20% 6%
Federated States of Micronesia 3 33% 33% 33%
Fiji 7 0% 14% 0%
Fiji Islands 277 21% 0% 0%
Finland 284 62% 2% 2%
Florida 16 100% 0% 0%
France 750 95% 22% 21%
French Guiana 6,748 38% 4% 4%
French Polynesia 35 66% 49% 34%
Gabon 121 13% 60% 8%
Gambia 7 43% 71% 43%
Georgia 6 100% 0% 0%
Germany 471 58% 13% 11%
Ghana 111 36% 21% 20%
Great Britain 5,179 98% 0% 0%
Greece 2,115 91% 10% 9%
Greenland 2 0% 0% 0%
Grenada 4 50% 25% 25%
Guadeloupe 35 100% 0% 0%
Guatemala 1,546 73% 10% 10%
Guernsey 5 0% 0% 0%
Guyana 838 86% 6% 6%
Haiti 22 82% 0% 0%
Holland 4 0% 0% 0%
Honduras 1,014 65% 10% 7%
Hong Kong 63 6% 0% 0%
Hungary 473 94% 74% 73%
Iceland 13 0% 0% 0%
Idaho 1 0% 0% 0%
India 6,234 69% 7% 7%
Indonesia 1,994 50% 1% 1%
Iran 9,186 71% 38% 38%
Iran, Islamic Republic of 2 100% 0% 0%
Iraq 34 0% 0% 0%
Ireland 16 56% 6% 6%
Israel 711 14% 10% 10%
Italy 1,193 95% 12% 12%
Ivory Coast 6 50% 50% 50%
Jamaica 298 0% 2% 0%
Japan 772 23% 22% 20%
Jordan 122 31% 7% 7%
Kazakhstan 210 7% 1% 1%
Kenya 2,462 9% 4% 4%
Korea 2 0% 0% 0%
Kuwait 6 0% 0% 0%
Kyrgyzstan 193 79% 17% 17%
Lao Peoples Democratic Republic 4 100% 0% 0%
Laos 7 0% 0% 0%
Latvia 1 0% 0% 0%
Lebanon 199 61% 2% 2%
Lesotho 24 13% 13% 13%
Liberia 190 6% 6% 5%
Libya 90 24% 4% 4%
Liechtenstein 1 0% 0% 0%
Lithuania 104 6% 0% 0%
Macao 2 0% 0% 0%
Macedonia 150 0% 0% 0%
Madagascar 3,638 57% 9% 9%
Maine 22 100% 0% 0%
Malawi 1,202 1% 2% 1%
Malaysia 3,041 29% 0% 0%
Maldives 32 75% 0% 0%
Mali 19 11% 16% 11%
Martinique 9 22% 22% 22%
Massachusetts 2 100% 0% 0%
Mauritius 16 31% 31% 31%
Mexico 63,280 61% 21% 20%
Missouri 8 0% 0% 0%
Mongolia 202 57% 0% 0%
Montana 1 0% 0% 0%
Montenegro 2 0% 0% 0%
Montserrat 25 8% 0% 0%
Morocco 569 8% 9% 6%
Mozambique 489 0% 1% 0%
Myanmar 117 80% 1% 1%
N. S. 3 100% 0% 0%
N.S. 3 100% 0% 0%
Namibia 375 31% 41% 26%
Nepal 185 49% 24% 24%
Netherlands 50 4% 8% 4%
Netherlands Antilles 23 61% 0% 0%
New Caledonia 21 0% 10% 0%
New Hampshire 348 100% 0% 0%
New Zealand 406 44% 7% 6%
Nicaragua 1,764 80% 2% 1%
Niger 3 67% 67% 67%
Nigeria 583 15% 2% 2%
Niue 1 0% 0% 0%
North Carolina 13 100% 0% 0%
North Korea 1 0% 100% 0%
Norway 205 7% 2% 1%
Ohio 3 100% 0% 0%
Oman 160 84% 3% 3%
Oregon 4 0% 0% 0%
Pakistan 518 86% 6% 5%
Palau 68 0% 0% 0%
Palestine 1 0% 0% 0%
PANAMA 1,012 80% 100% 80%
Panama 10,038 22% 0% 0%
Papua New Guinea 380 21% 1% 1%
Paraguay 3,347 30% 11% 11%
PEI 6 100% 0% 0%
Pennsylvania 1 100% 0% 0%
Peru 10,452 91% 2% 2%
Philippines 558 9% 5% 4%
Poland 370 79% 9% 8%
Portugal 118 84% 4% 4%
Puerto Rico 47 0% 0% 0%
Qatar 40 0% 0% 0%
Republic of Malta 3 0% 0% 0%
Republic of the Congo 19 5% 0% 0%
Romania 260 78% 2% 0%
Russia 519 81% 3% 3%
Russian Federation 5 100% 0% 0%
Rwanda 4 0% 0% 0%
Saint Barthelemy 1 100% 0% 0%
Saint Kitts and Nevis 2 50% 0% 0%
Saint Lucia 3 0% 0% 0%
Saint Vincent 56 100% 100% 100%
Saint Vincent and the Grenadines 14 0% 0% 0%
Samoa 25 8% 8% 8%
Saudi Arabia 339 68% 0% 0%
Senegal 65 0% 0% 0%
Serbia 19 74% 0% 0%
Seychelles 26 0% 0% 0%
Sierra Leone 27 74% 78% 74%
Singapore 217 3% 0% 0%
Slovakia 7,125 0% 0% 0%
Slovenia 57 91% 0% 0%
Slovokia 5 100% 100% 100%
Solomon Islands 114 2% 2% 1%
Somalia 8 38% 75% 38%
South Africa 12,345 24% 23% 22%
South Korea 97 16% 0% 0%
Spain 4,707 93% 38% 37%
Sri Lanka 2,640 65% 1% 1%
Sudan 114 8% 5% 5%
Suriname 472 61% 1% 1%
Swaziland 35 3% 3% 3%
Sweden 278 71% 15% 13%
Switzerland 223 85% 4% 3%
Syria 45 0% 0% 0%
Taiwan 229 8% 3% 0%
Tajikistan 67 1% 0% 0%
Tanzania 1,355 29% 5% 3%
TE 1 100% 0% 0%
Texas 1 0% 0% 0%
Thailand 2,579 15% 1% 1%
Togo 19 0% 0% 0%
Tonga 11 0% 0% 0%
Trinidad 164 93% 100% 93%
Trinidad and Tobago 1,132 8% 2% 0%
Tunisia 198 18% 15% 14%
Turkey 1,023 88% 14% 11%
Turkmenistan 132 8% 5% 5%
Uganda 1,107 1% 1% 1%
Ukraine 72 89% 0% 0%
United Arab Emirates 1,411 27% 26% 26%
United Kingdom 92 100% 10% 10%
United States 794,149 94% 68% 66%
Unknown 64 0% 94% 0%
Uruguay 41 90% 0% 0%
Uzbekistan 309 12% 2% 1%
Vanuatu 63 0% 0% 0%
Venezuela 3,474 63% 22% 6%
Vermont 13 100% 0% 0%
Viet Nam 2 100% 0% 0%
Vietnam 230 98% 1% 0%
VT 1 100% 100% 100%
Wales; United Kingdom 168 100% 15% 15%
Wisconsin 3 100% 0% 0%
Wyoming 2 0% 0% 0%
Yemen 42 69% 0% 0%
Yugoslavia 1 0% 100% 0%
Zambia 205 16% 7% 5%
Zimbabwe 748 96% 2% 2%

Total Specimens with Country: 1,158,633

       

Specimens without Country or Georeferencing: 230,174

       


Generated on: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 2022-04-29T20:28:53.434Z
 - Florida State Collection of Arthropods accessed via https://github.com/globalbioticinteractions/fsca/archive/682f11686317ae81959a043bd6b493ddfc06c438.zip on 2022-04-29T20:29:19.928Z
 - Natural History Museum of Los Angeles County accessed via https://github.com/globalbioticinteractions/lacm-lacmec/archive/dafbf532c53fbadba126c81186c26d52677aa781.zip on 2022-04-29T20:29:26.571Z
 - San Diego Natural History Museum accessed via https://github.com/globalbioticinteractions/sdnhm-sdmc/archive/7238d8b804f543250eb487b43144e1125fb3688a.zip on 2022-04-29T20:30:06.240Z
 - University of California Berkeley, Essig Museum of Entomology accessed via https://github.com/globalbioticinteractions/emec/archive/93b17a3db566baa001ce9190e6fbdb60fa99dda4.zip on 2022-04-29T20:30:29.232Z
 - University of California Santa Barbara Invertebrate Zoology Collection accessed via https://github.com/globalbioticinteractions/ucsb-izc/archive/825678ad02df93f6d4469f9d8b7cc30151b9aa45.zip on 2022-04-29T20:30:54.932Z
 - 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 2022-04-29T20:39:37.991Z
 - University of Kansas Natural History Museum accessed via https://github.com/globalbioticinteractions/ku-semc/archive/d7e4bd7e9755ca86163cf90da4e7ef5eb3fb7ed0.zip on 2022-04-29T20:44:14.914Z
 - University of Michigan Museum of Zoology Insect Division. Full Database Export 2020-11-20 provided by Erika Tucker and Barry Oconner. accessed via https://github.com/EMTuckerLabUMMZ/ummzi/archive/6731357a377e9c2748fc931faa2ff3dc0ce3ea7a.zip on 2022-04-29T20:46:49.650Z
 - University of Colorado Museum of Natural History Entomology Collection accessed via https://github.com/globalbioticinteractions/ucm-ucmc/archive/c2a838bbf39e09b7e195b2895c107b2963167b20.zip on 2022-04-29T20:48:39.455Z
 - Arizona State University Hasbrouck Insect Collection accessed via https://github.com/globalbioticinteractions/asu-asuhic/archive/025665959d3a7a37dc9dcc532c80166359274dd7.zip on 2022-04-29T20:49:00.439Z
 - University of New Hampshire Donald S. Chandler Entomological Collection accessed via https://github.com/globalbioticinteractions/unhc-unhc/archive/d7668a6bb4545dc4da0645ecc383169ba547b0f5.zip on 2022-04-29T20:49:22.124Z

2022-04-29

by:
GloBI's Elton 0.12.4 
(see https://github.com/globalbioticinteractions/elton).

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

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


Included in this review archive are:

README:
  This file.

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

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

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

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

indexed_interactions_full.tsv.gz:
  All indexed interactions for all reviewed collections.

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

datasets_under_review.tsv:
  Details on the datasets under review.

elton.jar: 
  Program used to update datasets and generate the review reports and associated indexed interactions.
  
Big Bee Metrics from the Bee Library and GloBI - April 29, 2022.pdf:
 Summary statistics from the Bee Library and GloBI about data partners

indexed_interactions_bees.tsv:
 All indexed bee 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

Jorrit Poelen, Tobias Kuhn, & Katrin Leinweber. (2022). globalbioticinteractions/elton: (0.12.4). Zenodo. https://doi.org/10.5281/zenodo.6385185

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Big Bee Metrics from the Bee Library and GloBI - April 29, 2022.pdf
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datasets_under_review.tsv
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elton.jar
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indexed_interactions_bees.tsv
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indexed_interactions_by_collection.tsv
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indexed_interactions_full.tsv.gz
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README.txt
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  • Seltmann KC, Allen J, Brown BV, Carper A, Engel MS, Franz N, Gilbert E, Grinter C, Gonzalez VH, Horsley P, Lee S, Maier C, Miko I, Morris P, Oboyski P, Pierce NE, Poelen J, Scott VL, Smith M, Talamas EJ, Tsutsui ND, Tucker E (2021) Announcing Big-Bee: An initiative to promote understanding of bees through image and trait digitization. Biodiversity Information Science and Standards 5: e74037. https://doi.org/10.3897/biss.5.74037

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

  • Jorrit Poelen, Tobias Kuhn, & Katrin Leinweber. (2022). globalbioticinteractions/elton: (0.12.4). Zenodo. https://doi.org/10.5281/zenodo.6385185

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