Document Type
Article
Publication Date
2025
DOI
10.1111/geb.70003
Publication Title
Global Ecology and Biogeography
Volume
34
Issue
5
Pages
e70003
Abstract
Motivation: Here, we make available a second version of the BioTIME database, which compiles records of abundance estimates for species in sample events of ecological assemblages through time. The updated version expands version 1.0 of the database by doubling the number of studies and includes substantial additional curation to the taxonomic accuracy of the records, as well as the metadata. Moreover, we now provide an R package (BioTIMEr) to facilitate use of the database.
Main Types of Variables Included: The database is composed of one main data table containing the abundance records and 11 metadata tables. The data are organised in a hierarchy of scales where 11,989,233 records are nested in 1,603,067 sample events, from 553,253 sampling locations, which are nested in 708 studies. A study is defined as a sampling methodology applied to an assemblage for a minimum of 2 years.
Spatial Location and Grain: Sampling locations in BioTIME are distributed across the planet, including marine, terrestrial and freshwater realms. Spatial grain size and extent vary across studies depending on sampling methodology. We recommend gridding of sampling locations into areas of consistent size.
Time Period and Grain: The earliest time series in BioTIME start in 1874, and the most recent records are from 2023. Temporal grain and duration vary across studies. We recommend doing sample-level rarefaction to ensure consistent sampling effort through time before calculating any diversity metric.
Major Taxa and Level of Measurement: The database includes any eukaryotic taxa, with a combined total of 56,400 taxa.
Software Format: csv and. SQL.
Rights
© 2025 The Authors.
This is an open access article under the terms of the Creative Commons Attribution 4.0 International (CC BY 4.0) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
Data Availability
Article states: "A static stable release of BioTIME version 2.0 can be found in Zenodo (https://doi.org/10.5281/zenodo.10932823). Code used in data curation and standardisation can be found at github.com/bioTIMEHub/BioTIME. The R package BioTIMEr is available in CRAN and can be found at github.com/bioTIMEHub/BioTIMEr."
Original Publication Citation
Dornelas, M., Antao, L. H., Bates, A. E., Brambilla, V., Chase, J. M., Chow, C. F. Y., Fontrodona-Eslava, A., Magurran, A. E., Martins, I. S., Moyes, F., Sagouis, A., Adu-Acheampong, S., Acquah-Lamptey, D., Adam, D., Ajani, P. A., Albaina, A., Almaraz, P., An, J. S., Anderson, R. S.,…Zvuloni, A. (2025). BioTIME 2.0: Expanding and improving a database of biodiversity time series. Global Ecology and Biogeography, 34(5), 1-18, Article e70003. https://doi.org/10.1111/geb.70003
Repository Citation
Dornelas, Maria; Antão, Laura H.; Bates, Amanda E.; Brambilla, Viviana; Chase, Jonathan M.; Chow, Cher F. Y.; Fontrodona-Eslava, Ada; Magurran, Anne E.; Martins, Inês S.; Moyes, Faye; Sagouis, Alban; Adu-Acheampong, Samuel; Acquah-Lamptey, Daniel; Adam, Dušan; Ajani, Penelope A.; Albaina, Aitor; Almaraz, Pablo; An, Jeongseop; Anderson, Roger Sigismund; Anderson, Madelaine Jean Robertson; Antunes, Alexsander Z.; Arismendi, Ivan; Armbrecht, Linda; Aros-Mardones, Pedro; Ashtamoorthy, Sreejith Kalpuzha; Ayyappan, Narayanan; Badihi, Gal; Bailey, Joseph J.; Baird, Andrew H.; Baird, Mark Edward; Balakrishnan, Sreekumar Vadakkethil; Barão-Nóbrega, José António L.; Barash, Adi; Barbosa, Miguel; Barlow, Jos; Bässler, Claus; Beaumont, Matthieu; Beenaerts, Natalie; Begot, Tiago Octavio; Beiroz, Wallace; Beldade, Ricardo; Bell, David M.; Bellgrove, Alecia; Belmaker, Jonathan; Benedetti-Cecchi, Lisandro; Benkwitt, Cassandra E.; Medina-van Berkum, Pamela; Bestelmeyer, Brandon T.; Betts, Matthew C.; Billah, Maxwell Kelvin; Bjorkman, Anne D.; Błażewicz, Magdalena; Bloch, Christopher P.; Blowes, Shane A.; Bode, Antonio; Bogoni, Juliano A.; Bolger, Thomas; Bonebrake, Timothy C.; Bonsdorff, Erik; Bottarin, Roberta; Brokensha, Luke N.; Brooker, Rob W.; Brooks, Andrew J.; Bruelheide, Helge; Bueno, Thiago Almeida; Laguionie, Claire; Campagnoli, Mariana Lopes; Cant, James; Caramaschi, Erica Pellegrini; Caron, Alexandre; Carroll, Tadhg; Caruso, Tancredi; Carvajal-Quintero, Juan; Castaldelli, Giuseppe; Castañeda-Moya, Edward; Castilho, Pedro V.; Cechin, Sonia Zanini; Chaikin, Shahar; Manjunatha Chandrashekara, Uchangi; Chase, Tory J.; Chen, Chaolun Allen; Cherem, Jorge José; Choi, Sei-Woong; Christensen, Erica M.; Christianini, Alexander V.; Chu, Jackson Wing Four; Coad, Peter; Colen, Carl Van; Comte, Lise; Cooper, Elisabeth J.; Cornelissen, J. Hans C.; Cosson, Eddy; Cotano, Unai; Crevecoeur, Luc; Crow, Shannan Kyle; Cumming, Graeme S.; Daga, Vanessa S.; Damasceno, Gabriella; Daskalova, Gergana N.; Davies, Claire H.; Davis, Robert A.; Day, Frank P.; De-La-Zerda, Sussy; Elizabeth Deacon, Amy; Castro-Arrazola, Indradatta de; Degraer, Steven; Deonarinesingh, Kharran; Diaz-Ricaurte, Juan C.; Dickman, Christopher R.; Dirilgen, Tara; Dolan, Ciaran John; Duffy, J. Emmett; Dunn, Timothy E.; Durigan, Giselda; Dwyer, Ciara; Earl, Steven; Edelist, Dor; Edgar, Graham John; Edmonson, Sally; Elgin, Ashley K.; Ellingsen, Kari Elsa; Elmendorf, Sarah C.; Eriksen, Ruth S.; Morgan Ernest, S. K.; Escribano, Ruben; Eterovick, Paula Cabral; Evans, Brian S.; Everett, Jason D.; Evtimova, Vesela; Exton, Dan A.; Fairbairn, Andrew J.; Fantacini, Filipe Moreli; Farah, Fabiano Turini; Zanella Farneda, Fábio; Favila, Mario E.; Fernandez-Fournier, Philippe; Fernández-Zapata, Braulio; Ferreira, Diogo F.; Ferronato, Carola; Feu, Christopher R. du; Fidelis, Alessandra; Fifield, David A.; Filho, Vilmar Picinatto; Filho, Walter Mesquita; Fitt, Robert N. L.; Flechtmann, Carlos A. H.; Fraser, William R.; Fraser, Donna L.; Freixas, Lídia; Fryxell, John; Fundakowski, Garrett J.; Gabara, Scott Stanley; Gallois, Elise; Criado, Mariana Garcia; García-Berthou, Emili; Garrabou, Joaquim; Gates, Andrew R.; Gatti, Roberto Cazzola; Gavioli, Anna; Gavriel, Tal; Gendreau-Berthiaume, Benoit; Giam, Xingli; Gjerdrum, Carina; Glemnitz, Michael; Godbold, Jasmin Annica; Gómez-Gras, Daniel; Gonçalves, Rodrigo Barbosa; Goold, Andy; Gordon, Richard R.; Goren, Menachem; Boas Goulart, Fernando Vilas; Gould, William G.; Graboski, Meagan M.; Graham, Nicholas A. J.; Eduardo Graipel, Maurício; Grange, Laura J.; Greenville, Aaron C.; Grossman, Gary D.; Guinder, Valeria A.; Haase, Peter; Haskins, Gary N.; Havstad, Kris; Hermanutz, Luise; Hickford, Michael Julian Hames; Hidalgo, Pamela; Higuchi, Pedro; Hoey, Andrew S.; Hoey, Gert Van; Hofgaard, Annika; Holeck, Kristen T.; Hollister, Robert D.; Holmes, Richard T.; Hoogenboom, Mia Odell; Hortal, Joaquín; Horton, Tammy; Hsieh, Chih-Hao; Huffard, Christine L.; Huikkonen, Ida-Maria; Hurlbert, Allen H.; Hynes, Julian; Irz, Pascal; Ivanauskas, Natalia Macedo; Iwayama, Akemi; James, Darren K.; Jandt, Ute; Jażdżewska, Anna M.; Jocque, Merlijn; Johnston, Sophie T.; Jones, Samuel E. I.; Jones, Faith A. M.; Jones, Julia A.; Jucevica, Edite; Kagainis, Ugis; Kagami, Maiko; Kang, Jungwon; Ke, Xuejia; Keeley, Erin Colleen; Kinnear, Rebecca; Klanderud, Kari; Klinck, Uwe; Klink, Roel van; Klotz, Stefan; Kockaert, Carolien; Knutsen, Halvor; Koivula, Matti; Kortz, Alessandra; Kriegel, Peter; Kuo, Chao-Yang; Kushner, David J.; Kyerematen, Rosina; Lagarde, Raphaël; Lancaster, Lesley T.; Landau, Ori Frid; Landuyt, Wouter Van; Larson, Eric R.; Lazarus, Mai; Lee, Cheol Min; Lefcheck, Jonathan S.; Lembrechts, Jonas J.; Ferreira de Lima, Renato A.; Guimarães Lima, Romullo; Lima, Nathália G. S.; Linares, Cristina; Lindstrom, Sandra C.; Lloret, Francisco; Lloyd, John David; Lobato, Cleonice Maria Cardoso; Lodge, David M.; Long, Peter Richard; López-Abbate, Celeste; López-Baucells, Adrià; Louzada, Julio; Louzao, Maite; Lugliè, Antonella; Luiz, Micheli Ribeiro; Macdonald, S. Ellen; Madin, Joshua S.; Magalhães, André Lincoln Barroso; Mahabir, Rajindra; Maphisa, David; Martin, Thomas Edward; Martins, Marcio; Martone, Patrick T.; Matesanz, Silvia; Matsuzaki, Shin-ichiro S.; Matthews, Thomas J.; Matthews, Iain McCombe; Maxwell, Connie J.; McFarland, Kent P.; McGill, Brian J.; McKnight, Diane Marie; McWilliam, Michael J.; Meador, Jason; Meesenburg, Henning; Meier, Kristin; Melecis, Viesturs; Meserve, Peter L.; Meyer, Christoph F. J.; Michelsen, Anders; Miiller, Natali Olivia Roman; Milardi, Marco; Milchakova, Nataliya; Miller, Robert J.; Millett, Jonathan; Moens, Tom; Montag, Luciano F. A.; Moore, Jon; Müller, Jörg; Murali, Akhil; Murray, Shauna Ann; Myers-Smith, Isla H.; Myster, Randall W.; Nakamura, Masahiro; Nayar, Sasi; Neat, Francis; Nelson, James A.; Nelson, Michael Paul; Nikolov, Boris P.; Nouioua, Rym; Nsor, Collins Ayine; Connor, Michael O'; Obodai, Edward Adzesiwor; Offland, Amy Marie; Ogaya, Romà; Ogura, Hisako; Okey, Thomas A.; Olden, Julian D.; Oliveira-Santos, Luiz Gustavo Rodrigues; Oliver, Jeffrey C.; Olsen, Esben Moland; Onipchenko, Vladimir G.; Oro, Daniel; Ozolins, Dais; Pabis, Krzysztof; Padedda, Bachisio Mario; Palacio, Facundo X.; Paquette, Alain; Pardede, Sinta Trilestari; Patersib, David M.; Pausina, Sarah; Pélissier, Raphaël; Pennings, Steven C.; Penuelas, Josep; Pereira, Felipe Walter; Peroni, Nivaldo; Picó, Sergio; Pilotto, Francesca; Pinheiro, Hudson Tercio; Pizarro, Oscar; Pizzolotto, Roberto; Pomati, Francesco; Pompeu, Paulo Santos; Ponton, Dominique; Post, Eric; Poulet, Nicolas; Pöyry, Juha; Presley, Steven J.; Prins, Herbert H. T.; Provoost, Pieter; Prudic, Kathleen L.; Punjayil, Vignesh; Pyšek, Petr; Querner, Pascal; Quimbayo, Juan Pablo; Ramnarine, Indar W.; Reed, Daniel C.; Reich, Peter Bernard; Remillard, Suzanne M.; Richards, Cerren; Richardson, Anthony James; Rijin, Itai van; Rivera-Monroy, Victor H.; Rixen, Christian; Robinson, Kevin Peter; Rocha, Ricardo; Rodrigues, Ricardo R.; Rodrigues, Cassy; Roos, Bjørn de; C. de Rossa-Feres, Denise de; Rosselli, Loreta; Rothlisberg, Peter Charles; Rubio, Ana; Rudstam, Lars G.; Ruz, Catalina S.; Rybicki, Nancy B.; Ryckegem, Gunther Van; Rypel, Andrew L.; Sadler, Jon P.; Saito, Victor Satoru; Sal, Sofia; Salomão, Renato Portela; Sanders, Nathan J.; Santos, Flavio A. M.; Santos, Tiago Gomes dos; Sarker, Swapan Kumar; Scanga, Sara E.; Schaub, Marcus; Schmidt, Jochen; Schmidt, Inger Kappel; Schooley, Robert L.; Schultz, Alfred; Scotti, Alberto; Serpell-Stevens, Amanda; Serrano, Filipe C.; Shadwick, Elizabeth H.; Shaft, Matthew; Sherry, Thomas W.; Shimabukuro, Erika Mayumi; Siciński, Jacek; Sievers, Caya; Silva, Fernando Rodrigues da; Silva, Ana Carolina da; Silveira, Juliana M.; Siqueira, Tadeu; Sivadasan, Arunkumar Kavidapadinjattathil; Sivan, Prasad Theruvil Parambil; Skuja, Agnija; Slaughter, Amalia L.; Slingsby, Jasper A.; Smith, Joseph R.; Soares, Bruno Eleres; Solan, Martin; Souza, Flaviana Maluf; Souza, Gabriel B. G.; Sprague, Joshua L.; Stachow, Ulrich; Stadt, J. John; Stallings, Christopher D.; Stanchev, Radoslav Hristov; Stanley, Emily H.; Starzomski, Brian M.; Sterza, Jose Mauro; Stevens, Maarten; Stiles, F. Gary; Stoll, Stefan; Stuart-Smith, Rick D.; Súarez, Yzel Rondon; Super, Laura; Supp, Sarah R.; Sutela, Tapio; Suthers, Iain M.; Suuronen, Anna; Swadling, Kerrie M.; Szydlowski, Daniel K.; Taki, Hisatomo; Taylor, Sara Jeanne Snell; Tedesco, Pablo A.; Teichert, Nils; Terui, Akira; Thiede, Gary P.; Thimonier, Anne; Thomas, Oliver; Thompson, Peter Allan; Thorn, Simon; Tiemann, Jeremy S.; Toledo, Luís Felipe; Tolvanen, Anne; Toniato, Maria Teresa Zugliani; Torre, Ignasi; Tortato, Marcos Adriano; Totsu, Kumiko; Trant, Andrew; Twilley, Robert R.; Urabe, Hirokazu; Valade, Pierre; Valdivia, Nelson; Vallejo, Martha Isabel; Valone, Thomas J.; Vanaverbeke, Jan; Vasconcelos, Tiago Silveira; Vehanen, Teppo; Venturoli, Fábio; Verheye, Hans M.; Wietse Vermeulen, Hendrik Jannes; Verstraeten, Arne; Vianna, Marcelo; Vieira, Rui; Vieira-Alencar, João Paulo Santos; Vilella, Marc; Vitule, Jean Ricardo Simões; Vu, Lien Van; Waide, Robert B.; Warren, Paige S.; Wayman, Joseph Paul; Webb, Sara L.; Weigel, Benjamin; Welti, Ellen A. R.; West, Fritha; Westermann, Fulgor; Whalen, Matthew A.; White, Ethan P.; Widdicombe, Claire E.; Williams, Richard; Williamson, Mark; Willig, Michael R.; Wipf, Sonja; Woehler, Eric J.; Woldering, Alje; Woods, Kerry D.; Xu, Wu-Bing; Yahel, Ruthy; Yang, Zeren; Zawada, Kyle J. A.; Zornosa-Torres, Camila; and Zvuloni, Assaf, "BioTIME 2.0: Expanding and Improving a Database of Biodiversity Time Series" (2025). Biological Sciences Faculty Publications. 647.
https://digitalcommons.odu.edu/biology_fac_pubs/647
List of database tables with field descriptions and explanations, and table of classifications of abundance and biomass within BioTIME.
geb70003-sup-0002-files2.pdf (289 kB)
Tutorial for data curation.
geb70003-sup-0003-files3.docx (215 kB)
List of data sources.
geb70003-sup-0004-files4.docx (38 kB)
Change Log for Updates compared with BioTIME 1.0
geb70003-sup-0005-files5.csv (1 kB)
Proportional representation of Animalia phyla and Chromista, Fungi, Plantae and Protozoa Kingdoms in BioTIME 2.0.
Included in
Biodiversity Commons, Biology Commons, Cataloging and Metadata Commons, Data Science Commons, Ecology and Evolutionary Biology Commons, Other Animal Sciences Commons