Literature DB >> 26167542

Achieving human and machine accessibility of cited data in scholarly publications.

Joan Starr1, Eleni Castro2, Mercè Crosas2, Michel Dumontier3, Robert R Downs4, Ruth Duerr5, Laurel L Haak6, Melissa Haendel7, Ivan Herman8, Simon Hodson9, Joe Hourclé10, John Ernest Kratz1, Jennifer Lin11, Lars Holm Nielsen12, Amy Nurnberger13, Stefan Proell14, Andreas Rauber15, Simone Sacchi13, Arthur Smith16, Mike Taylor17, Tim Clark18.   

Abstract

Reproducibility and reusability of research results is an important concern in scientific communication and science policy. A foundational element of reproducibility and reusability is the open and persistently available presentation of research data. However, many common approaches for primary data publication in use today do not achieve sufficient long-term robustness, openness, accessibility or uniformity. Nor do they permit comprehensive exploitation by modern Web technologies. This has led to several authoritative studies recommending uniform direct citation of data archived in persistent repositories. Data are to be considered as first-class scholarly objects, and treated similarly in many ways to cited and archived scientific and scholarly literature. Here we briefly review the most current and widely agreed set of principle-based recommendations for scholarly data citation, the Joint Declaration of Data Citation Principles (JDDCP). We then present a framework for operationalizing the JDDCP; and a set of initial recommendations on identifier schemes, identifier resolution behavior, required metadata elements, and best practices for realizing programmatic machine actionability of cited data. The main target audience for the common implementation guidelines in this article consists of publishers, scholarly organizations, and persistent data repositories, including technical staff members in these organizations. But ordinary researchers can also benefit from these recommendations. The guidance provided here is intended to help achieve widespread, uniform human and machine accessibility of deposited data, in support of significantly improved verification, validation, reproducibility and re-use of scholarly/scientific data.

Entities:  

Keywords:  Data Science; Data accessibility; Data archiving; Data citation; Digital Libraries; Human–Computer Interaction; Machine accessibility; World Wide Web and Web Science

Year:  2015        PMID: 26167542      PMCID: PMC4498574          DOI: 10.7717/peerj-cs.1

Source DB:  PubMed          Journal:  PeerJ Comput Sci        ISSN: 2376-5992


  16 in total

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Authors:  C Glenn Begley; Lee M Ellis
Journal:  Nature       Date:  2012-03-28       Impact factor: 49.962

2.  Collecting, comparing, and computing sequences: the making of Margaret O. Dayhoff's Atlas of Protein Sequence and Structure, 1954-1965.

Authors:  Bruno J Strasser
Journal:  J Hist Biol       Date:  2010       Impact factor: 1.326

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Authors: 
Journal:  Nature       Date:  2009-12-17       Impact factor: 49.962

4.  The case for cloud computing in genome informatics.

Authors:  Lincoln D Stein
Journal:  Genome Biol       Date:  2010-05-05       Impact factor: 13.583

5.  Unique identifiers for authors.

Authors:  John H R Maunsell
Journal:  J Neurosci       Date:  2014-05-21       Impact factor: 6.167

6.  Public availability of published research data in high-impact journals.

Authors:  Alawi A Alsheikh-Ali; Waqas Qureshi; Mouaz H Al-Mallah; John P A Ioannidis
Journal:  PLoS One       Date:  2011-09-07       Impact factor: 3.240

7.  Identifiers.org and MIRIAM Registry: community resources to provide persistent identification.

Authors:  Nick Juty; Nicolas Le Novère; Camille Laibe
Journal:  Nucleic Acids Res       Date:  2011-12-02       Impact factor: 16.971

8.  Ten simple rules for the care and feeding of scientific data.

Authors:  Alyssa Goodman; Alberto Pepe; Alexander W Blocker; Christine L Borgman; Kyle Cranmer; Merce Crosas; Rosanne Di Stefano; Yolanda Gil; Paul Groth; Margaret Hedstrom; David W Hogg; Vinay Kashyap; Ashish Mahabal; Aneta Siemiginowska; Aleksandra Slavkovic
Journal:  PLoS Comput Biol       Date:  2014-04-24       Impact factor: 4.475

9.  Why most published research findings are false.

Authors:  John P A Ioannidis
Journal:  PLoS Med       Date:  2005-08-30       Impact factor: 11.613

10.  On the reproducibility of science: unique identification of research resources in the biomedical literature.

Authors:  Nicole A Vasilevsky; Matthew H Brush; Holly Paddock; Laura Ponting; Shreejoy J Tripathy; Gregory M Larocca; Melissa A Haendel
Journal:  PeerJ       Date:  2013-09-05       Impact factor: 2.984

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  29 in total

1.  FAIRness and Usability for Open-access Omics Data Systems.

Authors:  Daniel C Berrios; Afshin Beheshti; Sylvain V Costes
Journal:  AMIA Annu Symp Proc       Date:  2018-12-05

2.  The Information Sharing Statement Grows Some Teeth.

Authors:  David N Kennedy
Journal:  Neuroinformatics       Date:  2017-04

3.  A very simple, re-executable neuroimaging publication.

Authors:  Satrajit S Ghosh; Jean-Baptiste Poline; David B Keator; Yaroslav O Halchenko; Adam G Thomas; Daniel A Kessler; David N Kennedy
Journal:  F1000Res       Date:  2017-02-10

4.  Everything Matters: The ReproNim Perspective on Reproducible Neuroimaging.

Authors:  David N Kennedy; Sanu A Abraham; Julianna F Bates; Albert Crowley; Satrajit Ghosh; Tom Gillespie; Mathias Goncalves; Jeffrey S Grethe; Yaroslav O Halchenko; Michael Hanke; Christian Haselgrove; Steven M Hodge; Dorota Jarecka; Jakub Kaczmarzyk; David B Keator; Kyle Meyer; Maryann E Martone; Smruti Padhy; Jean-Baptiste Poline; Nina Preuss; Troy Sincomb; Matt Travers
Journal:  Front Neuroinform       Date:  2019-02-07       Impact factor: 4.081

5.  Perspectives and expectations in structural bioinformatics of metalloproteins.

Authors:  Sen Yao; Robert M Flight; Eric C Rouchka; Hunter N B Moseley
Journal:  Proteins       Date:  2017-03-15

Review 6.  Data sharing in psychology.

Authors:  Maryann E Martone; Alexander Garcia-Castro; Gary R VandenBos
Journal:  Am Psychol       Date:  2018 Feb-Mar

7.  Let's be pragmatic about clinical data.

Authors: 
Journal:  Sci Data       Date:  2015-07-07       Impact factor: 6.444

8.  Community next steps for making globally unique identifiers work for biocollections data.

Authors:  Robert P Guralnick; Nico Cellinese; John Deck; Richard L Pyle; John Kunze; Lyubomir Penev; Ramona Walls; Gregor Hagedorn; Donat Agosti; John Wieczorek; Terry Catapano; Roderic D M Page
Journal:  Zookeys       Date:  2015-04-06       Impact factor: 1.546

9.  The FAIR Guiding Principles for scientific data management and stewardship.

Authors:  Mark D Wilkinson; Michel Dumontier; I Jsbrand Jan Aalbersberg; Gabrielle Appleton; Myles Axton; Arie Baak; Niklas Blomberg; Jan-Willem Boiten; Luiz Bonino da Silva Santos; Philip E Bourne; Jildau Bouwman; Anthony J Brookes; Tim Clark; Mercè Crosas; Ingrid Dillo; Olivier Dumon; Scott Edmunds; Chris T Evelo; Richard Finkers; Alejandra Gonzalez-Beltran; Alasdair J G Gray; Paul Groth; Carole Goble; Jeffrey S Grethe; Jaap Heringa; Peter A C 't Hoen; Rob Hooft; Tobias Kuhn; Ruben Kok; Joost Kok; Scott J Lusher; Maryann E Martone; Albert Mons; Abel L Packer; Bengt Persson; Philippe Rocca-Serra; Marco Roos; Rene van Schaik; Susanna-Assunta Sansone; Erik Schultes; Thierry Sengstag; Ted Slater; George Strawn; Morris A Swertz; Mark Thompson; Johan van der Lei; Erik van Mulligen; Jan Velterop; Andra Waagmeester; Peter Wittenburg; Katherine Wolstencroft; Jun Zhao; Barend Mons
Journal:  Sci Data       Date:  2016-03-15       Impact factor: 6.444

10.  Data publication with the structural biology data grid supports live analysis.

Authors:  Peter A Meyer; Stephanie Socias; Jason Key; Elizabeth Ransey; Emily C Tjon; Alejandro Buschiazzo; Ming Lei; Chris Botka; James Withrow; David Neau; Kanagalaghatta Rajashankar; Karen S Anderson; Richard H Baxter; Stephen C Blacklow; Titus J Boggon; Alexandre M J J Bonvin; Dominika Borek; Tom J Brett; Amedeo Caflisch; Chung-I Chang; Walter J Chazin; Kevin D Corbett; Michael S Cosgrove; Sean Crosson; Sirano Dhe-Paganon; Enrico Di Cera; Catherine L Drennan; Michael J Eck; Brandt F Eichman; Qing R Fan; Adrian R Ferré-D'Amaré; J Christopher Fromme; K Christopher Garcia; Rachelle Gaudet; Peng Gong; Stephen C Harrison; Ekaterina E Heldwein; Zongchao Jia; Robert J Keenan; Andrew C Kruse; Marc Kvansakul; Jason S McLellan; Yorgo Modis; Yunsun Nam; Zbyszek Otwinowski; Emil F Pai; Pedro José Barbosa Pereira; Carlo Petosa; C S Raman; Tom A Rapoport; Antonina Roll-Mecak; Michael K Rosen; Gabby Rudenko; Joseph Schlessinger; Thomas U Schwartz; Yousif Shamoo; Holger Sondermann; Yizhi J Tao; Niraj H Tolia; Oleg V Tsodikov; Kenneth D Westover; Hao Wu; Ian Foster; James S Fraser; Filipe R N C Maia; Tamir Gonen; Tom Kirchhausen; Kay Diederichs; Mercè Crosas; Piotr Sliz
Journal:  Nat Commun       Date:  2016-03-07       Impact factor: 14.919

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