Classificatory Theory in Data-intensive Science: The Case of Open Biomedical Ontologies

References

• Allen , J. F. 2001 . Bioinformatics and discovery: Induction beckons again . BioEssays , 23 : 104 – 107 .
   PubMed Web of Science ®Google Scholar
• Ashburner , M. , Ball , C. A. , Blake , J. A. , Botstein , D. , Butler , H. , Cherry , J. M. and Davis, et al , A. P. 2000 . Gene ontology: Tool for the unification of biology . Nature Genetics , 25 : 25 – 29 .
   PubMed Web of Science ®Google Scholar
• Baclawski , K. and Niu , T. 2006 . Ontologies for bioinformatics , Cambridge , MA : MIT Press .
   Google Scholar
• Bard , J. B. L. and Rhee , S. Y. 2004 . Ontologies in biology: Design, applications and future challenges . Nature Reviews Genetics , 5 : 213 – 222 .
   PubMed Web of Science ®Google Scholar
• Bernard , C. [1855] 1927 . An introduction to the study of experimental medicine , New York : Dover .
   Google Scholar
• Blake , J. A. and Bult , C. J. 2006 . Beyond the data deluge: Data integration and bio-ontologies . Journal of Biomedical Informatics , 39 : 314 – 320 .
   PubMed Web of Science ®Google Scholar
• Bogen , J. and Woodward , J. 1988 . Saving the phenomena . Philosophical Review , 97 : 303 – 352 .
   Web of Science ®Google Scholar
• Brazma , A. , Krestyaninova , M. and Sarkans , U. 2006 . Standards for systems biology . Nature Reviews Genetics , 7 : 593 – 605 .
   PubMed Web of Science ®Google Scholar
• Brigandt , I. 2009 . Natural kinds in evolution and systematics: Metaphysical and epistemological considerations . Acta Biotheoretica , 57 : 77 – 97 .
   PubMed Web of Science ®Google Scholar
• Brooksbank , C. and Quackenbush , J. 2006 . Data standards: A call to action . OMICS: A Journal of Integrative Biology , 10 : 94 – 99 .
   PubMed Web of Science ®Google Scholar
• Buetow , K. H. 2005 . Cyberinfrastructure: Empowering a ‘third way’ in biomedical research . Science , 308 : 821 – 824 .
   PubMed Web of Science ®Google Scholar
• Bult , C. J. 2006 . From information to understanding: The role of model organism databases in comparative and functional genomics . Animal Genetics , 37 ( suppl. 1 ) : 28 – 40 .
   PubMed Web of Science ®Google Scholar
• Callebaut , W. 2012 . Scientific perspectivism: A philosopher of science's response to the challenge of big data biology . Studies in History and Philosophy of Biological and Biomedical Sciences , 43 : 69 – 80 .
   PubMedGoogle Scholar
• Cartwright , N. 1983 . How the laws of physics lie , Oxford : Clarendon Press .
   Google Scholar
• Chipman , K. C. and Singh , A. K. 2009 . Predicting genetic interactions with random walks on biological networks . BMC Bioinformatics , 10 : 17
   PubMed Web of Science ®Google Scholar
• Chow-White , P. A. and García-Sancho , M. 2012 . Bidirectional shaping and spaces of convergence: Interactions between biology and computing from the first DNA sequencers to global genome databases . Science, Technology, and Human Values , 37 : 124 – 164 .
   Web of Science ®Google Scholar
• Creager , A. , H. , N. , Lunbeck , E. and Wise , M. N. 2007 . Science without laws: Model systems, cases, exemplary narratives , Chapel Hill , NC : Duke University Press .
   Google Scholar
• Darden , L. 2006 . “ Theory construction in genetics ” . In Reasoning in biological discoveries: Essays on mechanisms, interfield relations, and anomaly resolution , Edited by: Darden , L. 149 – 169 . Cambridge : Cambridge University Press .
   Google Scholar
• Dupré , J. 1993 . The disorder of things , Cambridge , MA : Harvard University Press .
   Google Scholar
• Dupré , J. 2001 . In defence of classification . Studies in History and Philosophy of Biological and Biomedical Sciences , 32 : 203 – 219 .
   Google Scholar
• Dupré , J. and O'Malley , M. A. 2007 . Metagenomics and biological ontology . Studies in History and Philosophy of Biological and Biomedical Sciences , 38 : 834 – 846 .
   PubMedGoogle Scholar
• Egaña Aranguren , M. , Bechhofer , S. , Lord , P. , Sattler , U. and Stevens , R. 2007 . Understanding and using the meaning of statements in a bio-ontology: Recasting the Gene Ontology in OWL . BMC Bioinformatics , 8 : 57
   PubMed Web of Science ®Google Scholar
• Evans , J. and Rzhesky , A. 2010 . Machine science . Science , 329 : 399 – 400 .
   PubMed Web of Science ®Google Scholar
• Gene Ontology Consortium . 2004 . Minutes of the Gene Ontology content meeting, Stanford University, 28–29 August [cited 22 November 2011]. http://www.geneontology.org/GO.meetings.shtml; INTERNET
   Google Scholar
• Gene Ontology Consortium . 2011 . Gene Ontology [cited 22 November 2011]. http://www.geneontology.org; INTERNET
   Google Scholar
• Giere , R. N. 1999 . Science without laws , Chicago , IL : University of Chicago Press .
   Google Scholar
• Griesemer , J. R. 2006 . Theoretical integration, cooperation, and theories as tracking devices . Biological Theory , 1 : 4 – 7 .
   Google Scholar
• Hacking , I. 2002 . Historical ontology , Cambridge , MA : Harvard University Press .
   Google Scholar
• Hamid Tirmizi , S. , Aitken , S. , Moreira , D. A. , Mungall , C. , Sequeda , J. , Shah , N. H. and Miranke , D. P. 2011 . Mapping between the OBO and OWL ontology languages . Journal of Biomedical Semantics , 2 ( Suppl. 1 ) : S3
   PubMedGoogle Scholar
• Hesse , M. B. 1974 . The structure of scientific inference , London : Macmillan .
   Google Scholar
• Hesse , M. B. 1980 . Revolutions and reconstructions in the philosophy of science , Brighton : Harvester Press .
   Google Scholar
• Hey , T. , Tansley , S. and Tolle , K. 2009 . The fourth paradigm: Data-intensive scientific discovery , Redmond , WA : Microsoft Research .
   Google Scholar
• Hill , D. P. , Smith , B. , McAndrews-Hill , M. S. and Blake , J. A. 2008 . Gene Ontology annotations: What they mean and where they come from . BMC Bioinformatics , 9 ( suppl. 5 ) : S2
   PubMed Web of Science ®Google Scholar
• Hoehndorf , R. , Oellrich , A. , Dumontier , M. , Kelso , J. , Rebholz-Schuhmann , D. and Herre , H. 2010 . Relations as patterns: Bridging the gap between OBO and OWL . BMC Bioinformatics , 11 : 441
   PubMed Web of Science ®Google Scholar
• Howe , D. , Costanzo , M. , Fey , P. , Gojobori , T. , Hannick , L. , Hide , W. Hill , D. P. 2008 . “ Big data: The future of biocuration ” . In Nature Vol. 455 , 47 – 50 .
   Google Scholar
• Keet , C. M. 2010 . Dependencies between ontology design parameters . International Journal of Metadata, Semantics and Ontologies , 54 : 265 – 284 .
   Google Scholar
• Kell , D. B. and Oliver , S. G. 2004 . Here is the evidence, now what is the hypothesis? The complementary roles of inductive and hypothesis-driven science in the post-genomic era . BioEssays , 26 : 99 – 105 .
   PubMed Web of Science ®Google Scholar
• Kuhn , T. S. 1962 . The structure of scientific revolutions , Chicago , IL : University of Chicago Press .
   Google Scholar
• Leonelli , S. 2009 . On the locality of data and claims about phenomena . Philosophy of Science , 76 : 737 – 749 .
   Web of Science ®Google Scholar
• Leonelli , S. 2010 . Documenting the emergence of bio-ontologies: Or, why researching bioinformatics requires HPSSB . History and Philosophy of the Life Sciences , 32 : 105 – 126 .
   PubMed Web of Science ®Google Scholar
• Leonelli , S. 2012 . Making sense of data-driven research in the biological and biomedical sciences . Studies in History and Philosophy of Biological and Biomedical Sciences , 43 : 1 – 3 .
   PubMedGoogle Scholar
• Leonelli , S. and Ankeny , R. A. 2012 . Re-thinking organisms: The impact of databases on model organism biology . Studies in History and Philosophy of Biological and Biomedical Sciences , 43 : 29 – 36 .
   PubMedGoogle Scholar
• Leonelli , S. , Diehl , A. D. , Christie , K. R. , Harris , M. A. and Lomax , J. 2011 . How the gene ontology evolves . BMC Bioinformatics , 12 : 325
   PubMed Web of Science ®Google Scholar
• Lewis , S. E. 2004 . Gene Ontology: Looking backwards and forwards . Genome Biology , 6 : 103
   PubMed Web of Science ®Google Scholar
• McAllister , J. W. 1997 . Phenomena and patterns in data sets . Erkenntnis , 47 : 217 – 228 .
   Google Scholar
• Mitchell , S. 2003 . Biological complexity and integrative pluralism , Cambridge : Cambridge University Press .
   Google Scholar
• Morgan , M. S. and Morrison , M. 1999 . Models as mediators , Edited by: Morgan , M. S. and Morrison , M. Cambridge : Cambridge University Press .
   Google Scholar
• Morrison , M. 2000 . Unifying scientific theories , Cambridge : Cambridge University Press .
   Google Scholar
• Müller-Wille , S. 2007 . Collection and collation: Theory and practice of Linnaean botany . Studies in History and Philosophy of Biological and Biomedical Sciences , 38 : 541 – 562 .
   PubMedGoogle Scholar
• Müller-Wille , S. and Charmantier , I. 2012 . Natural history and information overload: The case of Linnaeus . Studies in History and Philosophy of Biological and Biomedical Sciences , 43 : 4 – 15 .
   PubMedGoogle Scholar
• O'Malley , M. A. , Elliott , K. C. , Haufe , C. and Burian , R. M. 2009 . Philosophies of funding . Cell , 138 : 611 – 615 .
   PubMed Web of Science ®Google Scholar
• Parkhill , J. , Birney , E. and Kersey , P. 2010 . Genomic information infrastructure after the deluge . Genome Biology , 117 : 402 – 404 .
   Web of Science ®Google Scholar
• Pickstone , J. 2000 . Ways of knowing: A new history of science, technology and medicine , Chicago , IL : University of Chicago Press .
   Google Scholar
• Regt , H. W. de , Leonelli , S. and Eigner , K. 2009 . Scientific understanding: Philosophical perspectives , Edited by: de Regt , H. W. , Leonelli , S. and Eigner , K. Pittsburgh , PA : Pittsburgh University Press .
   Google Scholar
• Renear , A. H. and Palmer , C. L. 2009 . Strategic reading, ontologies, and the future of scientific publishing . Science , 325 : 828 – 832 .
   PubMed Web of Science ®Google Scholar
• Reydon , T. A. C. 2010 . “ Natural kind theory as a tool for philosophy of science ” . In EPSA epistemology and methodology of science: Launch of the European Philosophy of Science Association , Edited by: Suárez , M. , Dorato , M. and Rédei , M. 245 – 254 . Dordrecht : Springer .
   Google Scholar
• Rhee , S. Y. and Crosby , B. 2005 . Biological databases for plant research . Plant Physiology , 138 : 1 – 3 .
   PubMed Web of Science ®Google Scholar
• Schaffner , K. F. 1993 . Discovery and explanation in biology and medicine , Chicago , IL : University of Chicago Press .
   Google Scholar
• Smith , B. , Ashburner , M. , Rosse , C. , Bard , J. , Bug , W. , Ceusters , W. and Goldberg, et al , L. J. 2007 . The OBO Foundry: Coordinated evolution of ontologies to support biomedical data integration . Nature Biotechnology , 25 : 1251 – 1255 .
   PubMed Web of Science ®Google Scholar
• Smith , B. and Ceusters , W. 2010 . Ontological realism: A methodology for coordinated evolution of scientific ontologies . Applied Ontology , 5 : 79 – 108 .
   Web of Science ®Google Scholar
• Smith , B. , Ceusters , W. , Klagges , B. , Köhler , J. , Kumar , A. , Lomax , J. , Mungall , C. , Neuhaus , F. , Rector , A. L. and Rosse , C. 2005 . Relations in biomedical ontologies . Genome Biology , 6 : R46
   PubMed Web of Science ®Google Scholar
• Strasser , B. J. 2011 . The experimenter's museum: GenBank, natural history, and the moral economies of biomedicine . Isis , 102 : 60 – 96 .
   PubMed Web of Science ®Google Scholar
• Vernon , A. and Paracer , S. S. 2000 . Symbiosis: An introduction to biological associations , Oxford : Oxford University Press .
   Google Scholar
• Wylie , A. 2002 . Thinking from things: Essays in the philosophy of archaeology , Berkeley : University of California Press .
   Google Scholar