Literature DB >> 33770077

From Reductionism to Reintegration: Solving society's most pressing problems requires building bridges between data types across the life sciences.

Anne E Thessen1, Paul Bogdan2, David J Patterson3, Theresa M Casey4, César Hinojo-Hinojo5, Orlando de Lange6, Melissa A Haendel1.   

Abstract

Decades of reductionist approaches in biology have achieved spectacular progress, but the proliferation of subdisciplines, each with its own technical and social practices regarding data, impedes the growth of the multidisciplinary and interdisciplinary approaches now needed to address pressing societal challenges. Data integration is key to a reintegrated biology able to address global issues such as climate change, biodiversity loss, and sustainable ecosystem management. We identify major challenges to data integration and present a vision for a "Data as a Service"-oriented architecture to promote reuse of data for discovery. The proposed architecture includes standards development, new tools and services, and strategies for career-development and sustainability.

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Year:  2021        PMID: 33770077      PMCID: PMC7997011          DOI: 10.1371/journal.pbio.3001129

Source DB:  PubMed          Journal:  PLoS Biol        ISSN: 1544-9173            Impact factor:   8.029


  42 in total

1.  The availability of research data declines rapidly with article age.

Authors:  Timothy H Vines; Arianne Y K Albert; Rose L Andrew; Florence Débarre; Dan G Bock; Michelle T Franklin; Kimberly J Gilbert; Jean-Sébastien Moore; Sébastien Renaut; Diana J Rennison
Journal:  Curr Biol       Date:  2013-12-19       Impact factor: 10.834

2.  The case for research integration, from genomics to remote sensing, to understand biodiversity change and functional dynamics in the world's lakes.

Authors:  Stephen J Thackeray; Stephanie E Hampton
Journal:  Glob Chang Biol       Date:  2020-02-19       Impact factor: 10.863

3.  Is authorship sufficient for today's collaborative research? A call for contributor roles.

Authors:  Nicole A Vasilevsky; Mohammad Hosseini; Samantha Teplitzky; Violeta Ilik; Ehsan Mohammadi; Juliane Schneider; Barbara Kern; Julien Colomb; Scott C Edmunds; Karen Gutzman; Daniel S Himmelstein; Marijane White; Britton Smith; Lisa O'Keefe; Melissa Haendel; Kristi L Holmes
Journal:  Account Res       Date:  2020-06-30       Impact factor: 2.622

4.  The Open Knowledge Foundation: open data means better science.

Authors:  Jennifer C Molloy
Journal:  PLoS Biol       Date:  2011-12-06       Impact factor: 8.029

5.  All biology is computational biology.

Authors:  Florian Markowetz
Journal:  PLoS Biol       Date:  2017-03-09       Impact factor: 8.029

6.  Micropublication: incentivizing community curation and placing unpublished data into the public domain.

Authors:  Daniela Raciti; Karen Yook; Todd W Harris; Tim Schedl; Paul W Sternberg
Journal:  Database (Oxford)       Date:  2018-01-01       Impact factor: 3.451

7.  To increase trust, change the social design behind aggregated biodiversity data.

Authors:  Nico M Franz; Beckett W Sterner
Journal:  Database (Oxford)       Date:  2018-01-01       Impact factor: 3.451

8.  Community curation in PomBase: enabling fission yeast experts to provide detailed, standardized, sharable annotation from research publications.

Authors:  Antonia Lock; Midori A Harris; Kim Rutherford; Jacqueline Hayles; Valerie Wood
Journal:  Database (Oxford)       Date:  2020-01-01       Impact factor: 3.451

9.  Empirical study of data sharing by authors publishing in PLoS journals.

Authors:  Caroline J Savage; Andrew J Vickers
Journal:  PLoS One       Date:  2009-09-18       Impact factor: 3.240

Review 10.  Data integration in biological research: an overview.

Authors:  Vasileios Lapatas; Michalis Stefanidakis; Rafael C Jimenez; Allegra Via; Maria Victoria Schneider
Journal:  J Biol Res (Thessalon)       Date:  2015-09-02       Impact factor: 1.889

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  2 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

Review 2.  A synthetic synthesis to explore animal evolution and development.

Authors:  Mindy Liu Perkins; Lautaro Gandara; Justin Crocker
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2022-05-30       Impact factor: 6.671

  2 in total

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