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Perspective

eScience and the need for data standards in the life sciences: in pursuit of objectivity rather than truth

Pages 257-270 | Received 09 Jan 2013, Accepted 16 Jun 2013, Published online: 02 Sep 2013

References

  • Atran , S. 1990 . Cognitive Foundations of Natural History: Towards an Anthropology of Science , Cambridge, UK : Cambridge University Press .
  • Bonney , R. , Cooper , C. B. , Dickinson , J. , Kelling , S. , Phillips , T. , Rosenberg , K. V. and Shirk , J. 2009 . Citizen science: a developing tool for expanding science knowledge and scientific literacy . BioScience , 59 : 977 – 984 . doi: 10.1525/bio.2009.59.11.9
  • Brazma , A. 2001 . On the importance of standardisation in life sciences . Bioinformatics , 17 : 113 – 114 . doi: 10.1093/bioinformatics/17.2.113
  • Brazma , A. , Hingamp , P. , Quackenbush , J. , Sherlock , G. , Spellman , P. , Stoeckert , C. , Aach , J. , Ansorge , W. , Ball , C. A. , Causton , H. C. , Gaasterland , T. , Glenisson , P. , Holstege , F. C.P. , Kim , I. F. , Markowitz , V. , Matese , J. C. , Parkinson , H. , Robinson , A. , Sarkans , U. , Schulze-kremer , S. , Stewart , J. , Taylor , R. , Vilo , J. and Vingron , M. 2001 . Minimum information about a microarray experiment (MIAME) – towards standards for microarray data . Nature Genetics , 29 : 365 – 371 . doi: 10.1038/ng1201-365
  • Brooksbank , C. and Quackenbush , J. 2006 . Data standards: a call to action . OMICS: A Journal of Integrative Biology , 10 : 94 – 99 . doi: 10.1089/omi.2006.10.94
  • Chavan , V. and Ingwersen , P. 2009 . Towards a data publishing framework for primary biodiversity data: challenges and potentials for the biodiversity informatics community . BioMed Central Bioinformatics , 10 ( Suppl. 14 ) : S2 doi: 10.1186/1471-2105-10-S14-S2
  • Chervitz , S. A. , Deutsch , E. W. , Field , D. , Parkinson , H. , Quackenbush , J. , Rocca-Serra , P. , Sansone , S.-A. , Stoeckert , C. J. , Taylor , C. F. , Taylor , R. and Ball , C. A. 2011 . “ Bioinformatics for Omics Data ” . In Bioinformatics for Omics Data: Methods and Protocols , Edited by: Mayer , B. 31 – 69 . Totowa , NJ, USA : Springer Science+Business Media .
  • Costello , M. J. 2009 . Motivating online publication of data . BioScience , 59 : 418 – 427 . doi: 10.1525/bio.2009.59.5.9
  • Daston , L. 1992 . Objectivity and the escape from perspective . Social Studies of Science , 22 : 597 – 618 . doi: 10.1177/030631292022004002
  • Daston , L. and Galison , P. 1992 . The image of objectivity . Representations , 40 : 81 – 128 . doi: 10.1525/rep.1992.40.1.99p0137h
  • Daston , L. and Galison , P. 2007 . “ Objectivity ” . In Zone Books New York , NY, USA
  • Field , D. and Sansone , S.-A. 2006 . A Special Issue on data standards . OMICS: A Journal of Integrative Biology , 10 : 84 – 93 . doi: 10.1089/omi.2006.10.84
  • Frege , G. 1891 . Function und Begriff: Vortrag gehalten in der Sitzung vom 9. Januar 1891 der Jenaischen Gesellschaft für Medicin und Naturwissenschaft . Hermann Pohle, Jena, Germany ,
  • Frege , G. 1892 . Über Sinn und Bedeutung . Zeitschrift für Philosophie und philosophische Kritik , 100 : 25 – 50 .
  • Golde , C. M. and Gallagher , H. A. 1999 . The challenges of conducting interdisciplinary research in traditional doctoral programs . Ecosystems , 2 : 281 – 285 . doi: 10.1007/s100219900076
  • Gray , J. 2009 . “ Jim Gray on eScience: a transformed scientific method ” . In The Fourth Paradigm: Data-Intensive Scientific Discoveries , Edited by: Hey , T. , Tansley , S. and Tolle , K. xvii – xxxi . USA : Microsoft Research .
  • Greenberg , J. 2002 . Metadata and the World Wide Web . Encyclopedia of Library and Information Science , 72 : 244 – 261 .
  • Greenberg , J. 2010 . Metadata and digital information . Encyclopedia of Library and Information Science , 1 : 3610 – 3623 .
  • Hanson , B. , Sugden , A. and Alberts , B. 2011 . Making data maximally available . Science , 331 : 649 doi: 10.1126/science.1203354
  • Heintz , B. 2000 . Die Innenwelt der Mathematik: Zur Kultur und Praxis einer beweisenden Disziplin , Vienna, Austria : Springer .
  • Howe , D. , Constanzo , M. , Fey , P. , Gojobori , T. , Hannik , L. , Hide , W. , Hill , D. P. , Kania , R. , Schaeffer , M. , St pierre , S. , Twigger , S. , White , O. and Rhee , S. Y. 2008 . Big data: the future of biocuration . Nature , 455 : 47 – 50 . doi: 10.1038/455047a
  • Kukla , R. 2008 . Naturalizing objectivity . Perspectives on Science , 16 : 285 – 302 . doi: 10.1162/posc.2008.16.3.285
  • Larson , J. L. 1967 . Linnaeus and the natural method . Isis , 58 : 304 – 320 . doi: 10.1086/350265
  • Leebens-mack , J. I.M. , Vision , T. , Brenner , E. , Bowers , J. E. , Cannon , S. , Clement , M. J. , Cunningham , C. W. , Doyle , J. J. , Eisen , J. A. , Gu , X. U.N. , Harsham , J. , Jansen , R. K. , Kellogg , E. A. , Koonin , E. V. , Mishler , B. D. , Pires , C. , Qiu , Y.-L. , Rhee , S. , Sjölander , K. , Soltis , D. E. , Soltis , P. S. , Stevenson , D. W. , Wall , K. , Warnow , T. and Zmasek , C. 2006 . Taking the first steps towards a standard for reporting on phylogenies: Minimum Information about a Phylogenetic Analysis (MIAPA) . OMICS: A Journal of Integrative Biology , 10 : 231 – 237 . doi: 10.1089/omi.2006.10.231
  • Linnaeus , C. 1735 . Systema naturae sive Regna tria naturae. Systematice proposita per Classes, Ordines, Genera, & Species , Leiden , , the Netherlands : Theodor Haak .
  • Linnaeus , C. 1751 . Philosophia botanica , Stockholm , , Sweden : Kiesewetter .
  • Locke , J. 1689/1979 . An Essay Concerning Human Understanding, 1979 edition , Oxford, UK : Oxford University Press .
  • Lynch , C. 2008 . Big data: how do your data grow? . Nature , 455 : 28 – 29 . doi: 10.1038/455028a
  • Lynch , C. 2009 . “ Jim Gray's Fourth Paradigm and the Construction of the Scientific Record ” . In The Fourth Paradigm: Data-Intensive Scientific Discoveries , Edited by: Hey , T. , Tansley , S. and Tolle , K. 177 – 184 . USA : Microsoft Research .
  • Penev , L. , Mietchen , D. , Chavan , V. , Hagedorn , G. , Remsen , D. , Smith , V. and Shotton , D. 2011 . Pensoft Data Publishing Policies and Guidelines for Biodiversity Data. Pensoft Publishers . [http://www.pensoft.net/J_FILES/Pensoft_Data_Publishing_Policies_and_Guidelines.pdf, accessed 18 March 2013]
  • Piwowar , H. A. , Day , R. S. and Fridsma , D. B. 2007 . Sharing detailed research data is associated with increased citation rate . Public Library of Science One , 2 : e308
  • Redman , C. L. 1999 . Human dimensions of ecosystem studies . Ecosystems , 2 : 296 – 298 . doi: 10.1007/s100219900079
  • Sansone , S.-A. , Rocca-Serra , P. , Tong , W. , Fostel , J. , Morrison , N. , Jones , A. R. and RSBI Members . 2006 . A strategy capitalizing on synergies: The Reporting Structure for Biological Investigation (RSBI) Working Group . OMICS: A Journal of Integrative Biology , 10 : 164 – 171 . doi: 10.1089/omi.2006.10.164
  • Schulz , S. , Stenzhorn , H. , Boekers , M. and Smith , B. 2009 . Strengths and limitations of formal ontologies in the biomedical domain . Electronic Journal of Communication, Information and Innovation in Health , 3 : 31 – 45 .
  • Sidlauskas , B. , Ganapathy , G. , Hazkani-covo , E. , Jenkins , K. P. , Lapp , H. , McCall , L. W. , Price , S. , Scherle , R. , Spaeth , P. A. and Kidd , D. M. 2010 . Linking big: the continuing promise of evolutionary synthesis . Evolution , 64 : 871 – 880 . doi: 10.1111/j.1558-5646.2009.00892.x
  • Smith , B. , Kusnierczyk , W. , Schober , D. and Ceusters , W. Towards a reference terminology for ontology research and development in the biomedical domain . Proceedings of KR-MED 2006, Studies in Health Technology and Informatics , Edited by: Bodenreider , O. Vol. 124 , pp. 57 – 66 . the Netherlands : IOS Press .
  • Vogt , L. 2008 . Learning from Linnaeus: towards developing the foundation for a general structure concept for morphology . Zootaxa , 1950 : 123 – 152 .
  • Vogt , L. 2009 . The future role of bio-ontologies for developing a general data standard in biology: chance and challenge for zoo-morphology . Zoomorphology , 128 : 201 – 217 . doi: 10.1007/s00435-008-0081-5
  • Vogt , L. 2011 . Signs and terminology: science caught between language and perception . Bionomina , 4 : 1 – 41 .
  • Vogt , L. , Bartolomaeus , T. and Giribet , G. 2010 . The linguistic problem of morphology: structure versus homology and the standardization of morphological data . Cladistics , 26 : 301 – 325 . doi: 10.1111/j.1096-0031.2009.00286.x
  • Vogt , L. , Grobe , P. , Quast , B. and Bartolomaeus , T. 2012 . Fiat or bona fide boundary – a matter of granular perspective . Public Library of Science ONE , 7 : e48603
  • Wang , X. , Gorlitsky , R. and Almeida , J. S. 2005 . From XML to RDF: how semantic web technologies will change the design of ‘omic’ standards . Nature Biotechnology , 23 : 1099 – 1103 . doi: 10.1038/nbt1139
  • Wear , D. N. 1999 . Challenges to interdisciplinary discourse . Ecosystems , 2 : 299 – 301 . doi: 10.1007/s100219900080
  • Wieczorek , J. , Bloom , D. , Guralnick , R. , Blum , S. , Döring , M. , Giovanni , R. , Robertson , T. and Vieglais , D. 2012 . Darwin Core: an evolving community-developed biodiversity data standard . Public Library of Science ONE , 7 : e29715
  • Yilmaz , P. , Kottmann , R. , Field , D. , Knight , R. , Cole , J. R. , Amaral-Zettler , L. , Gilbert , J. A. , Karsch-Mizrachi , I. , Johnston , A. , Cochrane , G. , Vaughan , R. , Hunter , C. , Park , J. , Morrison , N. , Rocca-Serra , P. Sterk , P. 2011 . Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications . Nature Biotechnology , 29 : 415 – 420 . doi: 10.1038/nbt.1823

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