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Annual Review of Marine Science

Volume 16, 2024

Welcoming More Participation in Open Data Science for the Oceans

Abstract

Open science is a global movement happening across all research fields. Enabled by technology and the open web, it builds on years of efforts by individuals, grassroots organizations, institutions, and agencies. The goal is to share knowledge and broaden participation in science, from early ideation to making research outputs openly accessible to all (open access). With an emphasis on transparency and collaboration, the open science movement dovetails with efforts to increase diversity, equity, inclusion, and belonging in science and society. The US Biden–Harris Administration and many other US government agencies have declared 2023 the Year of Open Science, providing a great opportunity to boost participation in open science for the oceans. For researchers day-to-day, open science is a critical piece of modern analytical workflows with increasing amounts of data. Therefore, we focus this article on open data science—the tooling and people enabling reproducible, transparent, inclusive practices for data-intensive research—and its intersection with the marine sciences. We discuss the state of various dimensions of open science and argue that technical advancements have outpaced our field's culture change to incorporate them. Increasing inclusivity and technical skill building are interlinked and must be prioritized within the marine science community to find collaborative solutions for responding to climate change and other threats to marine biodiversity and society.

Keyword(s): data science, inclusion, open science
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2024-01-17
2024-04-28
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Literature Cited

  1. Ancion Z, Borrell-Damián L, Mounier P, Rooryck J, Saenen B. 2022. Action plan for Diamond Open Access Rep. Sci. Eur., Brussels, Belg.; cOAlition S, Eur. Sci. Found. Strasbourg, Fr.:; Open Sch. Commun. Eur. Res. Area Soc. Sci. Humanit. (OPERAS), Brussels, Belg.; and Fr. Natl. Res. Agency Paris, Fr.:
  2. Barker M, Chue Hong NP, Katz DS, Lamprecht A-L, Martinez-Ortiz C et al. 2022. Introducing the FAIR Principles for research software. Sci. Data 9:1622
     [Google Scholar]
  3. Barone L, Williams J, Micklos D. 2017. Unmet needs for analyzing biological big data: a survey of 704 NSF principal investigators. PLOS Comput. Biol. 13:10e1005755
     [Google Scholar]
  4. Barros C, Luo Y, Chubaty AM, Eddy IMS, Micheletti T et al. 2023. Empowering ecological modellers with a PERFICT workflow: seamlessly linking data, parameterisation, prediction, validation and visualisation. Methods Ecol. Evol. 14:1173–88
     [Google Scholar]
  5. Bastille K, Hardison S, deWitt L, Brown J, Samhouri J et al. 2021. Improving the IEA approach using principles of open data science. Coast. Manag. 49:172–89
     [Google Scholar]
  6. Berberi I, Roche DG. 2022. No evidence that mandatory open data policies increase error correction. Nat. Ecol. Evol. 6:111630–33
     [Google Scholar]
  7. Binley AD, Bennett JR. 2023. The data double standard. Methods Ecol. Evol. 14:61389–97
     [Google Scholar]
  8. Binley AD, Vincent JG, Rytwinski T, Proctor CA, Urness ES et al. 2023. Patterns of community science data use in peer-reviewed research on biodiversity. Biol. Conserv. 280:109985
     [Google Scholar]
  9. Blasco GD, Ferraro DM, Cottrell RS, Halpern BS, Froehlich HE. 2020. Substantial gaps in the current fisheries data landscape. Front. Mar. Sci. 7:612831
     [Google Scholar]
  10. Bledsoe EK, Burant JB, Higino GT, Roche DG, Binning SA et al. 2022. Data rescue: saving environmental data from extinction. Proc. R. Soc. B 289:197920220938
     [Google Scholar]
  11. Braga PHP, Hébert K, Hudgins EJ, Scott ER, Edwards BPM et al. 2023. Not just for programmers: how GitHub can accelerate collaborative and reproducible research in ecology and evolution. Methods Ecol. Evol. 14:61364–80
     [Google Scholar]
  12. Burton C, Duran G, Wright V, Chmiel R. 2023. Strategies for and barriers to collaboratively developing anti-racist policies and resources as described by geoscientists of color participating in the Unlearning Racism in Geoscience (URGE) program. Earth's Future 11:2e2022EF002957
     [Google Scholar]
  13. Butler L-A, Matthias L, Simard M-A, Mongeon P, Haustein S 2023. The oligopoly's shift to open access. How for-profit publishers benefit from article processing charges. Zenodo 7806651: https://doi.org/10.5281/zenodo.7806651
    [Crossref] [Google Scholar]
  14. Callaghan CT, Mesaglio T, Ascher JS, Brooks TM, Cabras AA et al. 2022. The benefits of contributing to the citizen science platform iNaturalist as an identifier. PLOS Biol. 20:11e3001843
     [Google Scholar]
  15. Carroll SR, Garba I, Figueroa-Rodríguez OL, Holbrook J, Lovett R et al. 2020. The CARE Principles for Indigenous Data Governance. Data Sci. J. 19:143
     [Google Scholar]
  16. Champion C, Hobday AJ, Tracey SR, Pecl GT. 2018. Rapid shifts in distribution and high-latitude persistence of oceanographic habitat revealed using citizen science data from a climate change hotspot. Glob. Change Biol. 24:115440–53
     [Google Scholar]
  17. Chytrý M, Pillar VD, Price JN, Wagner V, Wiser SK, Zelený D. 2023. The benefits of publishing in society-owned scientific journals. Appl. Veg. Sci. 26:1e12705
     [Google Scholar]
  18. Cooke SJ, Nguyen VM, Young N, Reid AJ, Roche DG et al. 2021. Contemporary authorship guidelines fail to recognize diverse contributions in conservation science research. Ecol. Solut. Evid. 2:2e12060
     [Google Scholar]
  19. Culina A, Baglioni M, Crowther TW, Visser ME, Woutersen-Windhouwer S, Manghi P. 2018. Navigating the unfolding open data landscape in ecology and evolution. Nat. Ecol. Evol. 2:3420–26
     [Google Scholar]
  20. Czapanskiy MF, Ponganis PJ, Fahlbusch JA, Goldbogen JA. 2022. Compendium of R code and data for “An accelerometer-derived ballistocardiogram method for detecting heartrates in free-ranging marine mammals. .” GitHub. https://github.com/FlukeAndFeather/cetaceanbcg
    [Google Scholar]
  21. Darwin Core Task Group 2009. Darwin Core. Biodiversity Information Standards. http://www.tdwg.org/standards/450
    [Google Scholar]
  22. Emery NC, Crispo E, Supp SR, Farrell KJ, Kerkhoff AJ et al. 2021. Data science in undergraduate life science education: a need for instructor skills training. BioScience 71:121274–87
     [Google Scholar]
  23. Eur. Sci. Found 2023. What is cOAlition S?. European Science Foundation. https://www.coalition-s.org/about
    [Google Scholar]
  24. Fanelli D. 2012. Negative results are disappearing from most disciplines and countries. Scientometrics 90:3891–904
     [Google Scholar]
  25. Fenwick I, Davis A, Williams A, Butland S, Lowndes JSS. 2023. Community building for Black environmental and marine researchers: Pathways to Open Science. Openscapes Apr. 26. https://www.openscapes.org/blog/2023/04/26/pathways-report
    [Google Scholar]
  26. Filazzola A, Lortie C. 2022. A call for clean code to effectively communicate science. Methods Ecol. Evol. 13:102119–28
     [Google Scholar]
  27. Fu DY, Hughey JJ. 2019. Releasing a preprint is associated with more attention and citations for the peer-reviewed article. eLife 8:e52646
     [Google Scholar]
  28. Gaynor KM, Azevedo T, Boyajian C, Brun J, Budden AE et al. 2022. Ten simple rules to cultivate belonging in collaborative data science research teams. PLOS Comput. Biol. 18:11e1010567
     [Google Scholar]
  29. Geiger RS. 2018. Reports from the BIDS Best Practices in Data Science Series. StuartGeiger.com Nov. 11. https://newweb.stuartgeiger.com/articles/2018-11-11-BIDS-best-practices
    [Google Scholar]
  30. Genome Stand. Consort 2023. GSC Minimum Information about any Sequence (MIxS). Genome Standards Consortium. https://www.gensc.org/pages/standards-intro.html
    [Google Scholar]
  31. Gewin V. 2021. Pandemic burnout is rampant in academia. Nature 591:7850489–91
     [Google Scholar]
  32. Gil Y, David CH, Demir I, Essawy BT, Fulweiler RW et al. 2016. Toward the geoscience paper of the future: best practices for documenting and sharing research from data to software to provenance. Earth Space Sci. 3:10388–415
     [Google Scholar]
  33. Gomes DGE, Pottier P, Crystal-Ornelas R, Hudgins EJ, Foroughirad V et al. 2022. Why don't we share data and code? Perceived barriers and benefits to public archiving practices. Proc. R. Soc. B 289:198720221113
     [Google Scholar]
  34. Gownaris NJ, Vermeir K, Bittner M-I, Gunawardena L, Kaur-Ghumaan S et al. 2022. Barriers to full participation in the open science life cycle among early career researchers. Data Sci. J. 21:12
     [Google Scholar]
  35. Halpern BS, Berlow E, Williams R, Borer ET, Davis FW et al. 2020. Ecological synthesis and its role in advancing knowledge. BioScience 70:111005–14
     [Google Scholar]
  36. Hipsley CA, Sherratt E. 2019. Psychology, not technology, is our biggest challenge to open digital morphology data. Sci. Data 6:141
     [Google Scholar]
  37. Hörstmann C, Buttigieg PL, Simpson P, Pearlman J, Waite AM. 2021. Perspectives on documenting methods to create ocean best practices. Front. Mar. Sci. 7:1260
     [Google Scholar]
  38. Hostler TJ 2023. The invisible workload of open research. J. Trial Error. https://doi.org/10.36850/mr5
    [Crossref] [Google Scholar]
  39. Jenkins GB, Beckerman AP, Bellard C, Benítez-López A, Ellison AM et al. 2023. Reproducibility in ecology and evolution: minimum standards for data and code. Ecol. Evol. 13:5e9961
     [Google Scholar]
  40. Kelly R, Fleming A, Pecl GT. 2019. Citizen science and social licence: improving perceptions and connecting marine user groups. Ocean Coast. Manag. 178:104855
     [Google Scholar]
  41. Leonelli S, Spichtinger D, Prainsack B. 2015. Sticks and carrots: encouraging open science at its source. Geogr. Environ. 2:112–16
     [Google Scholar]
  42. Lowndes JSS. 2019. Open software means kinder science. Observations Dec. 10. https://blogs.scientificamerican.com/observations/open-software-means-kinder-science
    [Google Scholar]
  43. Lowndes JSS, Best BD, Scarborough C, Afflerbach JC, Frazier MR et al. 2017. Our path to better science in less time using open data science tools. Nat. Ecol. Evol. 1:60160
     [Google Scholar]
  44. Lowndes JSS, Froehlich HE, Horst A, Jayasundara N, Pinsky ML et al. 2019. Supercharge your research: a ten-week plan for open data science. Nature https://doi.org/10.1038/d41586-019-03335-4
    [Crossref] [Google Scholar]
  45. Lowndes JSS, Robinson EM. 2021. The NASA-Openscapes Framework. Zenodo 5090115. https://doi.org/10.5281/zenodo.5090115
    [Crossref]
  46. Lowndes JSS, Robinson EM. 2022. Supporting open science as a daily practice Keynote panel presented at the American Geophysical Union Fall Meeting Chicago: Dec. 12–16
  47. Marín-Spiotta E, Barnes RT, Berhe AA, Hastings MG, Mattheis A et al. 2020. Hostile climates are barriers to diversifying the geosciences. Adv. Geosci. 53:117–27
     [Google Scholar]
  48. Maureaud AA, Palacios-Abrantes J, Kitchel Z, Mannocci L, Pinsky M et al. 2023. FishGlob_data: an integrated database of fish biodiversity sampled with scientific bottom-trawl surveys. OSF Preprints 2bcjw. https://doi.org/10.31219/osf.io/2bcjw
    [Crossref]
  49. McKiernan EC, Bourne PE, Brown CT, Buck S, Kenall A et al. 2016. How open science helps researchers succeed. eLife 5:e16800
     [Google Scholar]
  50. Mekonnen A, Downs C, Effiom EO, Razafindratsima O, Stenseth NC, Chapman CA. 2021. What costs half a year's pay for African scholars? Open access. Nature 596:7871189
     [Google Scholar]
  51. Merow C, Boyle B, Enquist BJ, Feng X, Kass JM et al. 2023. Better incentives are needed to reward academic software development. Nat. Ecol. Evol. 7:5626–27
     [Google Scholar]
  52. Nakagawa S, Ivimey-Cook ER, Grainger MJ, O'Dea RE, Burke S et al. 2023. Method Reporting with Initials for Transparency (MeRIT) promotes more granularity and accountability for author contributions. Nat. Commun. 14:11788
     [Google Scholar]
  53. NASA (Natl. Aeronaut. Space Adm.) 2022. 2023: Year of Open Science. NASA Transform to Open Science (TOPS) https://nasa.github.io/Transform-to-Open-Science/year-of-open-science
    [Google Scholar]
  54. Natl. Acad. Sci. Eng. Med 2018. Open Science by Design: Realizing a Vision for 21st Century Research Washington, DC: Natl. Acad. Press
  55. Natl. Acad. Sci. Eng. Med 2023. Roundtable on Aligning Incentives for Open Scholarship. National Academies of Science, Engineering, and Medicine https://www.nationalacademies.org/our-work/roundtable-on-aligning-incentives-for-open-science
    [Google Scholar]
  56. Nosek BA, Alter G, Banks GC, Borsboom D, Bowman SD et al. 2015. Promoting an open research culture. Science 348:62421422–25
     [Google Scholar]
  57. NumFOCUS 2023. Case study: first photograph of a black hole. NumFOCUS https://numfocus.org/case-studies/first-photograph-black-hole
    [Google Scholar]
  58. O'Dea RE, Parker TH, Chee YE, Culina A, Drobniak SM et al. 2021. Towards open, reliable, and transparent ecology and evolutionary biology. BMC Biol. 19:168
     [Google Scholar]
  59. Ovando D, Caselle JE, Costello C, Deschenes O, Gaines SD et al. 2021. Assessing the population-level conservation effects of marine protected areas. Conserv. Biol. 35:61861–70
     [Google Scholar]
  60. Pecl GT, Stuart-Smith J, Walsh P, Bray DJ, Kusetic M et al. 2019. Redmap Australia: challenges and successes with a large-scale citizen science-based approach to ecological monitoring and community engagement on climate change. Front. Mar. Sci. 6:349
     [Google Scholar]
  61. Pesant S, Not F, Picheral M, Kandels-Lewis S, Le Bescot N et al. 2015. Open science resources for the discovery and analysis of Tara Oceans data. Sci. Data 2:1150023
     [Google Scholar]
  62. Poisot T, Bruneau A, Gonzalez A, Gravel D, Peres-Neto P. 2019. Ecological data should not be so hard to find and reuse. Trends Ecol. Evol. 34:6494–96
     [Google Scholar]
  63. Primack RB, Miller TK, Terry C, Marín-Spiotta E, Templer PH et al. 2023. Historically excluded groups in ecology are undervalued and poorly treated. Front. Ecol. Environ. https://doi.org/10.1002/fee.2613
    [Crossref] [Google Scholar]
  64. Ram K. 2013. Git can facilitate greater reproducibility and increased transparency in science. Source Code Biol. Med. 8:7
     [Google Scholar]
  65. Ramachandran R, Bugbee K, Murphy K. 2021. From open data to open science. Earth Space Sci. 8:5e2020EA001562
     [Google Scholar]
  66. Reichman OJ, Jones MB, Schildhauer MP. 2011. Challenges and opportunities of open data in ecology. Science 331:6018703–5
     [Google Scholar]
  67. Robinson E, Lowndes JSS. 2022. The Openscapes Flywheel: a framework for managers to facilitate and scale inclusive Open science practices. EarthArXiv X5CQ02. https://doi.org/10.31223/X5CQ02
    [Crossref]
  68. Roche DG, O'Dea RE, Kerr KA, Rytwinski T, Schuster R et al. 2022a. Closing the knowledge-action gap in conservation with open science. Conserv. Biol. 36:3e13835
     [Google Scholar]
  69. Roche DG, Raby GD, Norin T, Ern R, Scheuffele H et al. 2022b. Paths towards greater consensus building in experimental biology. J. Exp. Biol. 225:Suppl. 1jeb243559
     [Google Scholar]
  70. Secchi Disk Seafarers, Lavender S, Beaugrand G, Outram N, Barlow N et al. 2017. Seafarer citizen scientist ocean transparency data as a resource for phytoplankton and climate research. PLOS ONE 12:12e0186092
     [Google Scholar]
  71. Shea MM, Kuppermann J, Rogers MP, Smith DS, Edwards P, Boehm AB. 2023. Systematic review of marine environmental DNA metabarcoding studies: toward best practices for data usability and accessibility. PeerJ 11:e14993
     [Google Scholar]
  72. Soeharjono S, Roche DG. 2021. Reported individual costs and benefits of sharing open data among canadian academic faculty in ecology and evolution. BioScience 71:7750–56
     [Google Scholar]
  73. Stoudt S, Vásquez VN, Martinez CC. 2021. Principles for data analysis workflows. PLOS Comput. Biol. 17:3e1008770
     [Google Scholar]
  74. Sullivan BL, Phillips T, Dayer AA, Wood CL, Farnsworth A et al. 2017. Using open access observational data for conservation action: a case study for birds. Biol. Conserv. 208:5–14
     [Google Scholar]
  75. Walter P, Mullins D. 2019. From symbiont to parasite: the evolution of for-profit science publishing. Mol. Biol. Cell 30:202537–42
     [Google Scholar]
  76. Watson C. 2022. Rise of the preprint: how rapid data sharing during COVID-19 has changed science forever. Nat. Med. 28:12–5
     [Google Scholar]
  77. White House Off. Sci. Technol. Policy 2022. OSTP issues guidance to make federally funded research freely available without delay Press Release, White House Off. Sci. Technol. Policy Aug. 25. https://www.whitehouse.gov/ostp/news-updates/2022/08/25/ostp-issues-guidance-to-make-federally-funded-research-freely-available-without-delay
  78. White House Off. Sci. Technol. Policy 2023. Fact sheet: Biden-Harris Administration announces new actions to advance open and equitable research Press Release, White House Off. Sci. Technol. Policy Jan. 11. https://www.whitehouse.gov/ostp/news-updates/2023/01/11/fact-sheet-biden-harris-administration-announces-new-actions-to-advance-open-and-equitable-research
  79. Williams JJ, Drew JC, Galindo-Gonzalez S, Robic S, Dinsdale E et al. 2019. Barriers to integration of bioinformatics into undergraduate life sciences education: a national study of US life sciences faculty uncover significant barriers to integrating bioinformatics into undergraduate instruction. PLOS ONE 14:11e0224288
     [Google Scholar]
  80. Williams JJ, Tractenberg RE, Batut B, Becker E. 2023. Optimizing short-format training: an international consensus on effective, inclusive, and career-spanning professional development in the life sciences and beyond. bioRxiv 2023.03.10.531570. https://doi.org/10.1101/2023.03.10.531570
    [Crossref]
  81. Wilson G, Bryan J, Cranston K, Kitzes J, Nederbragt L, Teal TK. 2017. Good enough practices in scientific computing. PLOS Comput. Biol. 13:6e1005510
     [Google Scholar]
  82. Wolkovich EM, Regetz J, O'Connor MI 2012. Advances in global change research require open science by individual researchers. Glob. Change Biol. 18:72102–10
     [Google Scholar]
  83. Wong APS, Wijffels SE, Riser SC, Pouliquen S, Hosoda S et al. 2020. Argo data 1999–2019: two million temperature-salinity profiles and subsurface velocity observations from a global array of profiling floats. Front. Mar. Sci. 7:700
     [Google Scholar]
  84. Zastrow M. 2020. Open science takes on the coronavirus pandemic. Nature 581:7806109–10
     [Google Scholar]
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