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BioTIME 2.0: Expanding and Improving a Database of Biodiversity Time Series
María Dornelas, Laura H. Antão, Amanda E. Bates, Viviana Brambilla, Jonathan M. Chase, Cher F. Y. Chow, Ada Fontrodona‐Eslava, Anne E. Magurran, Inês S. Martins, Faye Moyes, Alban Sagouis, Samuel Adu‐Acheampong, Daniel Acquah‐Lamptey, Dušan Adam, Penelope Ajani, Aitor Albaina, Pablo Almaraz, Jeong‐Seop An, Roger Sigismund Anderson, Madelaine Anderson, Alexsander Zamorano Antunes, Iván Arismendi, Linda Armbrecht, Pedro Aros‐Mardones, K. A. Sreejith, Narayanan Ayyappan, Gal Badihi, Joseph J. Bailey, Andrew H. Baird, Mark E. Baird, V. B. Sreekumar, José António Lemos Barão-Nóbrega, Adi Barash, Miguel Barbosa, Jos Barlow, Claus Bässler, Matthieu Beaumont, Natalie Beenaerts, Tiago Octavio Begot, Wallace Beiroz, Ricardo Beldade, David M. Bell, Alecia Bellgrove, Jonathan Belmaker, Lisandro Benedetti‐Cecchi, Cassandra E. Benkwitt, Pamela Medina‐van Berkum, Brandon T. Bestelmeyer, Matthew G. Betts, Maxwell Kelvin Billah, Anne D. Bjorkman, Magdalena Błażewicz, Christopher P. Bloch, Shane A. Blowes, Antonio Bode, Juliano A. Bogoni, Thomas Bolger, Timothy C. Bonebrake, Erik Bonsdorff, Roberta Bottarin, Luke N. Brokensha, Rob W. Brooker, Andrew J. Brooks, Helge Bruelheide, Thiago Almeida Bueno, Claire Laguionie, Mariana Lopes Campagnoli, James Cant, Érica Pellegrini Caramaschi, Alexandre Caron, Tadhg Carroll, Tancredi Caruso, Juan D. Carvajal‐Quintero, Giuseppe Castaldelli, Edward Castañeda‐Moya, Pedro Volkmer de Castilho, Sônia Zanini Cechin, Shahar Chaikin, U. M. Chandrashekara, Tory J. Chase, Chaolun Allen Chen, Jorge José Cherem, Sei‐Woong Choi, Erica M. Christensen, Alexander V. Christianini, Jackson W. F. Chu, Peter Coad, Carl Van Colen, Lise Comte, Elisabeth J. Cooper, Johannes H. C. Cornelissen, E. Cosson, Unai Cotano, Luc Crèvecoeur, Shannan K. Crow, Graeme S. Cumming, Vanessa S. Daga, Gabriella Damasceno, Gergana N. Daskalova, Claire H. Davies, Robert A. Davis, Frank P. Day, Sussy De‐La‐Zerda, Amy E. Deacon, Indradatta deCastro‐Arrazola, S. Degraer, Kharran Deonarinesingh, Juan C. Díaz‐Ricaurte, Chris R. Dickman, Tara Dirilgen, Ciarán J. Dolan, J. Emmett Duffy, Timothy E. Dunn, Giselda Durigan, Ciara Dwyer, Stevan Earl, Dor Edelist, Graham J. Edgar, Sally Edmondson, Ashley K. Elgin, Kari E. Ellingsen, Sarah C. Elmendorf, Ruth Eriksen, S. K. Morgan Ernest, Rubén Escribano, Paula Cabral Eterovick, Brian Evans, Jason D. Everett, Vesela Evtimova, Dan A. Exton, Andrew Fairbairn, Felipe Moreli Fantacini, Fabiano Turini Farah, Fábio Z. Farneda, Mario E. Favila, Philippe Fernandez‐Fournier, Braulio Fernández‐Zapata, Diogo F. Ferreira, Carola Ferronato, Christopher R. du Feu, Alessandra Fidélis, David A. Fifield, Vilmar Picinatto Filho, Walter Mesquita Filho, Robert N. L. Fitt, Carlos A. H. Flechtmann, William R. Fraser, Lídia Freixas, John M. Fryxell, Garrett J. Fundakowski, Scott S. Gabara, Elise Gallois, Mariana García Criado, Emili García‐Berthou, Joaquim Garrabou, Andrew R. Gates, Roberto Cazzolla Gatti, Anna Gavioli, Tal Gavriel, Benoît Gendreau-Berthiaume, Xingli Giam, Carina Gjerdrum, Michael Glemnitz, Jasmin A. Godbold, Daniel Gómez‐Gras, Rodrigo Barbosa Gonçalves, Andy Goold, Richard R. Gordon, Menachem Goren, Fernando Vilas Boas Goulart, William A. Gould, Meagan M. Grabowski, Nicholas A. J. Graham, Maurício Eduardo Graipel, Laura J. Grange, Aaron C. Greenville, Gary D. Grossman, Valeria A. Guinder, Peter Haase, Gary N. Haskins, Kris M. Havstad, Luise Hermanutz, Michael J. H. Hickford, Pamela Hidalgo, Pedro Higuchi, Andrew S. Hoey, Gert Van Hoey, Annika Hofgaard, Kristen T. Holeck, Robert D. Hollister, Richard T. Holmes, Mia O. Hoogenboom, Joaquín Hortal, Tammy Horton, Chih‐hao Hsieh, Christine L. Huffard, Ida‐Maria Huikkonen, Allen H. Hurlbert, Julian D. Hynes, Pascal Irz, Natália Macedo Ivanauskas, Akemi Iwayama, Darren K. James, Ute Jandt, Anna Jażdżewska, Merlijn Jocqué, S. Johnston, Samuel E. I. Jones, Faith A. M. Jones, Julia Jones, Edīte Juceviča, Uģis Kagainis, Maiko Kagami, Jungwon Kang, Xuejia Ke, Erin Keeley, Rebecca Kinnear, Kari Klanderud, Uwe Klinck, Roel van Klink, Stefan Klotz, C. Knockaert, Halvor Knutsen, Matti Koivula, Alessandra Kortz, Peter Kriegel, Chao‐Yang Kuo, David J. Kushner, Rosina Kyerematen, Raphaël Lagarde, Lesley T. Lancaster, Ori Frid, Wouter Van Landuyt, Eric R. Larson, Mai Lazarus, Cheol Min Lee, Jonathan S. Lefcheck, Jonas J. Lembrechts, Renato A. Ferreira de Lima, Romullo Guimarães de Sá Ferreira Lima, Nathália G. S. Lima, Cristina Linares, Sandra C. Lindstrom, Francisco Lloret, John D. Lloyd, Cleonice Maria Cardoso Lobato, David M. Lodge, Peter R. Long, Celeste López‐Abbate, Adrià López‐Baucells, Júlio Louzada, Maite Louzao, Antonella Lugliè, Micheli Ribeiro Luiz, S. Ellen Macdonald, Joshua S. Madin, André Lincoln Barroso Magalhães, Rajindra Mahabir, David Maphisa, Thomas E. Martin, Marcio Roberto Martins, Patrick T. Martone, Silvia Matesanz, Shin‐ichiro S. Matsuzaki, Thomas J. Matthews, Iain Matthews, Connie J. Maxwell, Kent P. McFarland, Brian J. McGill, Diane M. McKnight, Mike McWilliam, Jason Meador, Henning Meesenburg, Kristin Meier, Viesturs Melecis, Peter L. Meserve, Christoph F. J. Meyer, Anders Michelsen, Natali Oliva Roman Miiller, Marco Milardi, N. A. Milchakova, Robert J. Miller, Jonathan Millett, Tom Moens, Luciano Fogaça de Assis Montag, J. Moore, Jörg Müller, Akhil Murali, Shauna A. Murray, Isla H. Myers‐Smith, Randall W. Myster, Masahiro Nakamura, Sasi Nayar, Francis Neat, James A. Nelson, Michael Nelson, Boris P. Nikolov, Rym Nouioua, Collins Ayine Nsor, Michael O′Connor, Edward Adzesiwor Obodai, Amy Marie Offland, Romà Ogaya, Hisako OGURA, Thomas A. Okey, Julian D. Olden, Luiz Gustavo Rodrigues Oliveira‐Santos, Jeffrey C. Oliver, Esben Moland Olsen, V. G. Onipchenko, Daniel Oró, Dāvis Ozoliņš, Krzysztof Pabis, Bachisio Mario Padedda, Facundo X. Palacio, Alain Paquette, Sinta Trilestari Pardede, David M. Paterson, Sarah A. Pausina, Raphaël Pélissier, Steven C. Pennings, Josep Peñuelas, Felipe Walter Pereira, Nivaldo Peroni, Sergio Picó, Francesca Pilotto, Hudson T. Pinheiro, Oscar Pizarro, Roberto Pizzolotto, Francesco Pomati, Paulo dos Santos Pompeu, Dominique Ponton, Eric Post, Nicolas Poulet, Juha Pöyry, Steven J. Presley, H.H.T. Prins, Pieter Provoost, Kathleen L. Prudic, Vignesh Punjayil, Petr Pyšek, Pascal Querner, Juan P. Quimbayo, Indar W. Ramnarine, Daniel C. Reed, Peter B. Reich, Suzanne M. Remillard, Cerren Richards, Anthony J. Richardson, Itai van Rijn, Víctor H. Rivera‐Monroy, Christian Rixen, Kevin P. Robinson, Ricardo Rocha, Ricardo Ribeiro Rodrigues, Cassy Anne Rodrigues, Denise de Cerqueira Rossa‐Feres, Loreta Rosselli, Peter C. Rothlisberg, Ana Rubio, Lars G. Rudstam, Catalina S. Ruz, Nancy B. Rybicki, Gunther Van Ryckegem, Andrew L. Rypel, Jon P. Sadler, Victor S. Saito, Sofia Sal, Renato Portela Salomão, Nathan J. Sanders, Flavio Antônio Maës dos Santos, Tiágo Gomes dos Santos, Swapan Kumar Sarker, Sara E. Scanga, Marcus Schaub, Jochen Schmidt, Inger Kappel Schmidt, Robert L. Schooley, Alfred Schultz, Alberto Scotti, Amanda Serpell‐Stevens, Filipe C. Serrano, Elizabeth H. Shadwick, Matthew Shaft, Thomas W. Sherry, Erika Mayumi Shimabukuro, Jacek Siciński, Caya Sievers, Fernando Rodrigues da Silva, Ana Carolina da Silva, Juliana M. Silveira, Tadeu Siqueira, Arunkumar Kavidapadinjattathil Sivadasan, Prasad Theruvil Parambil Sivan, Agnija Skuja, Jasper A. Slingsby, Joseph R. Smith, Bruno Eleres Soares, Martin Solan, Flaviana Maluf Souza, Gabriel Barros Gonçalves de Souza, Joshua Sprague, Ulrich Stachow, J. John Stadt, Christopher D. Stallings, Radoslav Stanchev, Emily H. Stanley, Brian M. Starzomski, José Mauro Sterza, Maarten Stevens, F. Gary Stiles, Stefan Stoll, Rick D. Stuart‐Smith, Yzél Rondon Súarez, Laura Super, Sarah R. Supp, Tapio Sutela, Iain M. Suthers, Anna Suuronen, Kerrie M. Swadling, Daniel K. Szydlowski, Hisatomo Taki, Pablo A. Tedesco, Nils Teichert, Akira Terui, Gary P. Thiede, Anne Thimonier, Oliver Thomas, Peter A. Thompson, Simon Thorn, Jeremy S. Tiemann, Luı́s Felipe Toledo, Anne Tolvanen, Maria Teresa Zugliani Toniato, Ignasi Torre, Marcos Adriano Tortato, Kumiko Totsu, Andrew J. Trant, Robert R. Twilley, Hirokazu Urabe, Pierre Valade, Nelson Valdivia, Martha Isabel Vallejo, Thomas J. Valone, Jan Vanaverbeke, T. Vasconcelos, Teppo Vehanen, Fábio Venturoli, Hans M. Verheye, H.J.W. Vermeulen, Arne Verstraeten, Marcelo Vianna, Rui P. Vieira, João Paulo dos Santos Vieira‐Alencar, Marc Vilella, Jean Ricardo Simões Vitule, Vũ Văn Liên, Robert B. Waide, Paige S. Warren, Joseph P. Wayman, Sara L. Webb, Benjamin Weigel, Ellen A. R. Welti, Fritha West, Fulgor Westermann, Matthew A. Whalen, Ethan P. White, Claire E. Widdicombe, Richard Williams, Mark Williamson, Michael R. Willig, Sonja Wipf, Eric J. Woehler, Alje Woldering, Kerry D. Woods, Wubing Xu, Ruth Yahel, Z. Yang, Kyle Zawada, Camila Zornosa‐Torres, Assaf Zvuloni
Bibliographic record
VenueGlobal Ecology and Biogeography · 2025
Typearticle
Languageen
FieldEnvironmental Science
TopicSpecies Distribution and Climate Change
Canadian institutionsAlberta Ministry of Agriculture and ForestryUniversity of ReginaUniversité du Québec à MontréalUniversity of AlbertaUniversity of WaterlooMemorial University of NewfoundlandUniversity of GuelphSimon Fraser UniversityYukon Department of EnvironmentDalhousie UniversityUniversity of British ColumbiaFisheries and Oceans CanadaEnvironment and Climate Change CanadaUniversité du Québec en OutaouaisGDG EnvironnementWestern UniversityUniversité de SherbrookeUniversity of Victoria
FundersFondo de Financiamiento de Centros de Investigación en Áreas PrioritariasPacific Northwest Research StationInstituut voor Landbouw-, Visserij- en Voedingsonderzoek, Vlaamse OverheidSchool of Life and Environmental Sciences, Deakin UniversityInstituto Español de OceanografíaAgencia Estatal de InvestigaciónAustralian Antarctic DivisionFundação para a Ciência e a TecnologiaAustralian Research CouncilNatural Environment Research CouncilNatural Sciences and Engineering Research Council of CanadaCornell Atkinson Center for Sustainability, Cornell UniversityDavid R. Atkinson Center for a Sustainable Future , Cornell UniversityHorizon 2020 Framework ProgrammeU.S. Forest ServiceUniversidad de Ciencias Aplicadas y AmbientalesOffice Français de la BiodiversitéOperation WallaceaAgencia Nacional de Investigación y DesarrolloDeutsches Zentrum für integrative Biodiversitätsforschung Halle-Jena-LeipzigInstituto Milenio de OceanografíaMinisterio del Ambiente, Agua y Transición EcológicaProvincia autonoma di Bolzano - Alto AdigeUniversidad de CádizUniversidade Estadual PaulistaDeakin UniversityUniversidade Federal do ParanáHakai InstituteÅbo AkademiUniversità di PisaHelmholtz-Zentrum für UmweltforschungStiftelsen för Åbo AkademiNærings- og FiskeridepartementetDeutscher Akademischer AustauschdienstHokkaido UniversityDirectorate for Biological SciencesGöteborgs UniversitetH2020 European Research CouncilUniversidade de São PauloJapan Society for the Promotion of ScienceCoordenação de Aperfeiçoamento de Pessoal de Nível SuperiorUniversity of GhanaGeneralitat de CatalunyaMinisterio de Ciencia e InnovaciónPetrobrasHORIZON EUROPE Marie Sklodowska-Curie ActionsFlorida Fish and Wildlife Conservation CommissionUniversity of Hong KongNational Research Foundation of KoreaKerala State Council for Science, Technology and EnvironmentEuskal Herriko UnibertsitateaSuomen KulttuurirahastoPontificia Universidad Católica de ChileGovernment of the United KingdomCanada Excellence Research Chairs, Government of CanadaAustralian Marine Sciences AssociationUniversidade Federal da ParaíbaMarine National FacilityUniversidad Nacional de ColombiaFondation BertarelliAcademy of FinlandUniversiteit HasseltJames Cook UniversityCentro de Ciências do MarDeutsche ForschungsgemeinschaftAgricultural Research ServiceConselho Nacional de Desenvolvimento Científico e TecnológicoUniversidade Federal de Santa CatarinaGordon and Betty Moore FoundationMacquarie UniversityBotanical Society of Britain and IrelandCommonwealth Scientific and Industrial Research OrganisationUtah Agricultural Experiment StationUniversity of TasmaniaRoyal SocietyFundação de Amparo à Pesquisa do Estado de São PauloEuropean CommissionLeverhulme TrustFundação de Amparo à Pesquisa do Estado de Minas GeraisBridgewater State UniversityUniversity of St AndrewsEuropean Regional Development FundMinistry of EnvironmentEuropean Synchrotron Radiation FacilityAkademie Věd České RepublikyMinistry of Agriculture, Forestry and FisheriesNational Geographic SocietyFisheries Society of the British IslesUniversidade do Estado de Mato GrossoFundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de JaneiroBiodiversa+College of Science and Engineering, University of MinnesotaAgence Nationale de la RechercheNational Oceanic and Atmospheric AdministrationNorges ForskningsrådDivision of Environmental BiologyVlaamse regeringAustralian GovernmentNational Science and Technology CouncilUniwersytet ŁódzkiHelsingin YliopistoInternational Institute of Tropical ForestryNatural EnglandUniversidade de LisboaNational Institute of Food and AgricultureU.S. Fish and Wildlife ServiceLinnean Society of NSWNorthern Illinois UniversityNational Park ServiceEarthwatch InstituteJames Hutton InstituteAnglia Ruskin UniversityUniversity College DublinWildlife Conservation SocietyNational Aeronautics and Space AdministrationFonds Wetenschappelijk OnderzoekUniversité de SherbrookeOregon State UniversityFundação de Apoio ao Desenvolvimento do Ensino, Ciência e Tecnologia do Estado de Mato Grosso do SulNew Mexico State UniversityNational Research FoundationMcKnight FoundationGrantová Agentura České RepublikyUniversidade de AveiroAustralian Biological Resources StudyTel Aviv UniversityPew Charitable TrustsUniversity of Technology SydneyNational Institute of EcologyEnvironmental Studies Research FundsBelgian Federal Science Policy OfficeNational Science FoundationU.S. Department of AgricultureAcademia SinicaDivision of Graduate EducationArcticNetSmithsonian Institution
KeywordsBiodiversitySeries (stratigraphy)GeographyEcologyDatabaseEnvironmental resource managementEnvironmental scienceBiologyComputer sciencePaleontology
Abstract
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.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
metaresearch head score (Codex)0.012
metaresearch head score (Gemma)0.070
Version: metacan-v3-hybrid-931329e0061cValidation status: machine_predicted_unvalidated
Candidate categoriesnone
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Not applicable · Consensus signal: Not applicable
GenreCandidate signal: Dataset · Consensus signal: Dataset
Teacher disagreement score0.027
Threshold uncertainty score0.090
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.012 | 0.070 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.002 |
| Bibliometrics | 0.013 | 0.014 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.005 | 0.004 |
| Open science | 0.003 | 0.005 |
| Research integrity | 0.001 | 0.002 |
| Insufficient payload (model declined to judge) | 0.027 | 0.019 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
Opus teacher head0.006
GPT teacher head0.210
Teacher spread0.204 · how far apart the two teachers sit on this one work
Validation status
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
The models applied no category: nothing in the taxonomy fit this work.
Study designNot applicable
Domainnot available
GenreDataset
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".
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Citations18
Published2025
Admission routes2
Has abstractyes