Big Bee indexed biotic interactions and review summary

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

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

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

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

Bee Library Information - Statistics about Big Bee data providers

The specimens indexed by GloBI are also found in the Bee Library. To date, the number of specimens and images in the library are listed below. The Bee Library taxonomic backbone is not yet complete, so information regarding the number of species is not yet available. Further summary statistics are available in the Big Bee Metrics from the Bee Library and GloBI - July 27 2022.pdf file.

From Bee Library (partner indexed records)        
1,186,629 occurrence records        
969,695 (82%) georeferenced        
328,742 (28%) occurrences imaged        
628,198 (53%) identified to species        
9 families        
324 genera        
5,694 species        
5,955 total taxa (including subsp. and var.)    

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 2022-07-27T21:07:52.515Z
 - Florida State Collection of Arthropods accessed via https://github.com/globalbioticinteractions/fsca/archive/682f11686317ae81959a043bd6b493ddfc06c438.zip on 2022-07-27T21:08:22.843Z
 - Natural History Museum of Los Angeles County accessed via https://github.com/globalbioticinteractions/lacm-lacmec/archive/dafbf532c53fbadba126c81186c26d52677aa781.zip on 2022-07-27T21:08:30.461Z
 - San Diego Natural History Museum accessed via https://github.com/globalbioticinteractions/sdnhm-sdmc/archive/7238d8b804f543250eb487b43144e1125fb3688a.zip on 2022-07-27T21:08:42.352Z
 - University of California Berkeley, Essig Museum of Entomology accessed via https://github.com/globalbioticinteractions/emec/archive/93b17a3db566baa001ce9190e6fbdb60fa99dda4.zip on 2022-07-27T21:09:04.970Z
 - University of California Santa Barbara Invertebrate Zoology Collection accessed via https://github.com/globalbioticinteractions/ucsb-izc/archive/825678ad02df93f6d4469f9d8b7cc30151b9aa45.zip on 2022-07-27T21:09:31.346Z
 - 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 2022-07-27T21:22:42.893Z
 - University of Kansas Natural History Museum accessed via https://github.com/globalbioticinteractions/ku-semc/archive/d7e4bd7e9755ca86163cf90da4e7ef5eb3fb7ed0.zip on 2022-07-27T21:28:19.181Z
 - 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 2022-07-27T21:31:01.669Z
 - University of Colorado Museum of Natural History Entomology Collection accessed via https://github.com/globalbioticinteractions/ucm-ucmc/archive/c2a838bbf39e09b7e195b2895c107b2963167b20.zip on 2022-07-27T21:33:14.785Z
 - Arizona State University Hasbrouck Insect Collection accessed via https://github.com/globalbioticinteractions/asu-asuhic/archive/025665959d3a7a37dc9dcc532c80166359274dd7.zip on 2022-07-27T21:33:37.283Z
 - University of New Hampshire Donald S. Chandler Entomological Collection accessed via https://github.com/globalbioticinteractions/unhc-unhc/archive/d7668a6bb4545dc4da0645ecc383169ba547b0f5.zip on 2022-07-27T21:34:09.498Z

Generated on:
2022-07-27

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 - July 27 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