Literature DB >> 32066887

Open Science principles for accelerating trait-based science across the Tree of Life.

Rachael V Gallagher1, Daniel S Falster2, Brian S Maitner3, Roberto Salguero-Gómez4,5,6, Vigdis Vandvik7,8, William D Pearse9, Florian D Schneider, Jens Kattge10,11, Jorrit H Poelen, Joshua S Madin12, Markus J Ankenbrand13,14,15, Caterina Penone16, Xiao Feng3, Vanessa M Adams17, John Alroy18, Samuel C Andrew19, Meghan A Balk20, Lucie M Bland21, Brad L Boyle3, Catherine H Bravo-Avila22,23, Ian Brennan24, Alexandra J R Carthey18, Renee Catullo24, Brittany R Cavazos25, Dalia A Conde26,27,28, Steven L Chown29, Belen Fadrique22, Heloise Gibb30, Aud H Halbritter7,8, Jennifer Hammock31, J Aaron Hogan32, Hamish Holewa19, Michael Hope19, Colleen M Iversen33, Malte Jochum11,16,34, Michael Kearney35, Alexander Keller13,14, Paula Mabee36, Peter Manning37, Luke McCormack38, Sean T Michaletz39, Daniel S Park40, Timothy M Perez22,23, Silvia Pineda-Munoz41, Courtenay A Ray42, Maurizio Rossetto43,44, Hervé Sauquet2,43,45, Benjamin Sparrow46, Marko J Spasojevic47, Richard J Telford7,8, Joseph A Tobias48, Cyrille Violle49, Ramona Walls50, Katherine C B Weiss42, Mark Westoby18, Ian J Wright18, Brian J Enquist3,51.   

Abstract

Synthesizing trait observations and knowledge across the Tree of Life remains a grand challenge for biodiversity science. Species traits are widely used in ecological and evolutionary science, and new data and methods have proliferated rapidly. Yet accessing and integrating disparate data sources remains a considerable challenge, slowing progress toward a global synthesis to integrate trait data across organisms. Trait science needs a vision for achieving global integration across all organisms. Here, we outline how the adoption of key Open Science principles-open data, open source and open methods-is transforming trait science, increasing transparency, democratizing access and accelerating global synthesis. To enhance widespread adoption of these principles, we introduce the Open Traits Network (OTN), a global, decentralized community welcoming all researchers and institutions pursuing the collaborative goal of standardizing and integrating trait data across organisms. We demonstrate how adherence to Open Science principles is key to the OTN community and outline five activities that can accelerate the synthesis of trait data across the Tree of Life, thereby facilitating rapid advances to address scientific inquiries and environmental issues. Lessons learned along the path to a global synthesis of trait data will provide a framework for addressing similarly complex data science and informatics challenges.

Mesh:

Year:  2020        PMID: 32066887     DOI: 10.1038/s41559-020-1109-6

Source DB:  PubMed          Journal:  Nat Ecol Evol        ISSN: 2397-334X            Impact factor:   15.460


  41 in total

1.  Early bursts of body size and shape evolution are rare in comparative data.

Authors:  Luke J Harmon; Jonathan B Losos; T Jonathan Davies; Rosemary G Gillespie; John L Gittleman; W Bryan Jennings; Kenneth H Kozak; Mark A McPeek; Franck Moreno-Roark; Thomas J Near; Andy Purvis; Robert E Ricklefs; Dolph Schluter; James A Schulte Ii; Ole Seehausen; Brian L Sidlauskas; Omar Torres-Carvajal; Jason T Weir; Arne Ø Mooers
Journal:  Evolution       Date:  2010-04-29       Impact factor: 3.694

2.  Plant functional traits have globally consistent effects on competition.

Authors:  Georges Kunstler; Daniel Falster; David A Coomes; Francis Hui; Robert M Kooyman; Daniel C Laughlin; Lourens Poorter; Mark Vanderwel; Ghislain Vieilledent; S Joseph Wright; Masahiro Aiba; Christopher Baraloto; John Caspersen; J Hans C Cornelissen; Sylvie Gourlet-Fleury; Marc Hanewinkel; Bruno Herault; Jens Kattge; Hiroko Kurokawa; Yusuke Onoda; Josep Peñuelas; Hendrik Poorter; Maria Uriarte; Sarah Richardson; Paloma Ruiz-Benito; I-Fang Sun; Göran Ståhl; Nathan G Swenson; Jill Thompson; Bertil Westerlund; Christian Wirth; Miguel A Zavala; Hongcheng Zeng; Jess K Zimmerman; Niklaus E Zimmermann; Mark Westoby
Journal:  Nature       Date:  2015-12-23       Impact factor: 49.962

3.  Functional traits explain variation in plant life history strategies.

Authors:  Peter B Adler; Roberto Salguero-Gómez; Aldo Compagnoni; Joanna S Hsu; Jayanti Ray-Mukherjee; Cyril Mbeau-Ache; Miguel Franco
Journal:  Proc Natl Acad Sci U S A       Date:  2013-12-30       Impact factor: 11.205

4.  A trait database of stream invertebrates for the ecological risk assessment of single and combined effects of salinity and pesticides in South-East Australia.

Authors:  Ralf B Schäfer; Ben J Kefford; Leon Metzeling; Matthias Liess; Sinje Burgert; Richard Marchant; Vincent Pettigrove; Peter Goonan; Dayanthi Nugegoda
Journal:  Sci Total Environ       Date:  2011-03-04       Impact factor: 7.963

5.  A general model for the origin of allometric scaling laws in biology.

Authors:  G B West; J H Brown; B J Enquist
Journal:  Science       Date:  1997-04-04       Impact factor: 47.728

Review 6.  Key questions and challenges in angiosperm macroevolution.

Authors:  Hervé Sauquet; Susana Magallón
Journal:  New Phytol       Date:  2018-03-25       Impact factor: 10.151

7.  GlobTherm, a global database on thermal tolerances for aquatic and terrestrial organisms.

Authors:  Joanne M Bennett; Piero Calosi; Susana Clusella-Trullas; Brezo Martínez; Jennifer Sunday; Adam C Algar; Miguel B Araújo; Bradford A Hawkins; Sally Keith; Ingolf Kühn; Carsten Rahbek; Laura Rodríguez; Alexander Singer; Fabricio Villalobos; Miguel Ángel Olalla-Tárraga; Ignacio Morales-Castilla
Journal:  Sci Data       Date:  2018-03-13       Impact factor: 6.444

8.  The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species.

Authors:  Christopher J Mungall; Julie A McMurry; Sebastian Köhler; James P Balhoff; Charles Borromeo; Matthew Brush; Seth Carbon; Tom Conlin; Nathan Dunn; Mark Engelstad; Erin Foster; J P Gourdine; Julius O B Jacobsen; Dan Keith; Bryan Laraway; Suzanna E Lewis; Jeremy NguyenXuan; Kent Shefchek; Nicole Vasilevsky; Zhou Yuan; Nicole Washington; Harry Hochheiser; Tudor Groza; Damian Smedley; Peter N Robinson; Melissa A Haendel
Journal:  Nucleic Acids Res       Date:  2016-11-29       Impact factor: 16.971

9.  The Coral Trait Database, a curated database of trait information for coral species from the global oceans.

Authors:  Joshua S Madin; Kristen D Anderson; Magnus Heide Andreasen; Tom C L Bridge; Stephen D Cairns; Sean R Connolly; Emily S Darling; Marcela Diaz; Daniel S Falster; Erik C Franklin; Ruth D Gates; Aaron Harmer; Mia O Hoogenboom; Danwei Huang; Sally A Keith; Matthew A Kosnik; Chao-Yang Kuo; Janice M Lough; Catherine E Lovelock; Osmar Luiz; Julieta Martinelli; Toni Mizerek; John M Pandolfi; Xavier Pochon; Morgan S Pratchett; Hollie M Putnam; T Edward Roberts; Michael Stat; Carden C Wallace; Elizabeth Widman; Andrew H Baird
Journal:  Sci Data       Date:  2016-03-29       Impact factor: 6.444

10.  Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes.

Authors:  Richard C Edmunds; Baofeng Su; James P Balhoff; B Frank Eames; Wasila M Dahdul; Hilmar Lapp; John G Lundberg; Todd J Vision; Rex A Dunham; Paula M Mabee; Monte Westerfield
Journal:  Mol Biol Evol       Date:  2015-10-24       Impact factor: 16.240

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  18 in total

Review 1.  Past and future uses of text mining in ecology and evolution.

Authors:  Maxwell J Farrell; Liam Brierley; Anna Willoughby; Andrew Yates; Nicole Mideo
Journal:  Proc Biol Sci       Date:  2022-05-18       Impact factor: 5.530

2.  Linking dimensions of data on global marine animal diversity.

Authors:  Thomas J Webb; Bart Vanhoorne
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2020-11-02       Impact factor: 6.237

3.  Global abundance estimates for 9,700 bird species.

Authors:  Corey T Callaghan; Shinichi Nakagawa; William K Cornwell
Journal:  Proc Natl Acad Sci U S A       Date:  2021-05-25       Impact factor: 11.205

4.  Low availability of code in ecology: A call for urgent action.

Authors:  Antica Culina; Ilona van den Berg; Simon Evans; Alfredo Sánchez-Tójar
Journal:  PLoS Biol       Date:  2020-07-28       Impact factor: 8.029

5.  Pilot RNA-seq data from 24 species of vascular plants at Harvard Forest.

Authors:  Hannah E Marx; Stacy A Jorgensen; Eldridge Wisely; Zheng Li; Katrina M Dlugosch; Michael S Barker
Journal:  Appl Plant Sci       Date:  2021-02-14       Impact factor: 1.936

6.  Motivating data contributions via a distinct career currency.

Authors:  Mark Westoby; Daniel S Falster; Julian Schrader
Journal:  Proc Biol Sci       Date:  2021-03-03       Impact factor: 5.349

7.  Are we ready to track climate-driven shifts in marine species across international boundaries? - A global survey of scientific bottom trawl data.

Authors:  Aurore A Maureaud; Romain Frelat; Laurène Pécuchet; Nancy Shackell; Bastien Mérigot; Malin L Pinsky; Kofi Amador; Sean C Anderson; Alexander Arkhipkin; Arnaud Auber; Iça Barri; Richard J Bell; Jonathan Belmaker; Esther Beukhof; Mohamed L Camara; Renato Guevara-Carrasco; Junghwa Choi; Helle T Christensen; Jason Conner; Luis A Cubillos; Hamet D Diadhiou; Dori Edelist; Margrete Emblemsvåg; Billy Ernst; Tracey P Fairweather; Heino O Fock; Kevin D Friedland; Camilo B Garcia; Didier Gascuel; Henrik Gislason; Menachem Goren; Jérôme Guitton; Didier Jouffre; Tarek Hattab; Manuel Hidalgo; Johannes N Kathena; Ian Knuckey; Saïkou O Kidé; Mariano Koen-Alonso; Matt Koopman; Vladimir Kulik; Jacqueline Palacios León; Ya'arit Levitt-Barmats; Martin Lindegren; Marcos Llope; Félix Massiot-Granier; Hicham Masski; Matthew McLean; Beyah Meissa; Laurène Mérillet; Vesselina Mihneva; Francis K E Nunoo; Richard O'Driscoll; Cecilia A O'Leary; Elitsa Petrova; Jorge E Ramos; Wahid Refes; Esther Román-Marcote; Helle Siegstad; Ignacio Sobrino; Jón Sólmundsson; Oren Sonin; Ingrid Spies; Petur Steingrund; Fabrice Stephenson; Nir Stern; Feriha Tserkova; Georges Tserpes; Evangelos Tzanatos; Itai van Rijn; Paul A M van Zwieten; Paraskevas Vasilakopoulos; Daniela V Yepsen; Philippe Ziegler; James T Thorson
Journal:  Glob Chang Biol       Date:  2020-11-10       Impact factor: 10.863

8.  STOREFISH 2.0: a database on the reproductive strategies of teleost fishes.

Authors:  Stéphane Teletchea; Fabrice Teletchea
Journal:  Database (Oxford)       Date:  2020-11-20       Impact factor: 3.451

Review 9.  Transforming the study of organisms: Phenomic data models and knowledge bases.

Authors:  Anne E Thessen; Ramona L Walls; Lars Vogt; Jessica Singer; Robert Warren; Pier Luigi Buttigieg; James P Balhoff; Christopher J Mungall; Deborah L McGuinness; Brian J Stucky; Matthew J Yoder; Melissa A Haendel
Journal:  PLoS Comput Biol       Date:  2020-11-24       Impact factor: 4.779

10.  What is life?

Authors:  Jaime Gómez-Márquez
Journal:  Mol Biol Rep       Date:  2021-07-27       Impact factor: 2.316

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