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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Ontological realism: A methodology for coordinated evolution of scientific ontologies</title><author><name sortKey="Smith, Barry" sort="Smith, Barry" uniqKey="Smith B" first="Barry" last="Smith">Barry Smith</name></author><author><name sortKey="Ceusters, Werner" sort="Ceusters, Werner" uniqKey="Ceusters W" first="Werner" last="Ceusters">Werner Ceusters</name></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">21637730</idno><idno type="pmc">3104413</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3104413</idno><idno type="RBID">PMC:3104413</idno><idno type="doi">10.3233/AO-2010-0079</idno><date when="2010">2010</date><idno type="wicri:Area/Pmc/Corpus">000109</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000109</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Ontological realism: A methodology for coordinated evolution of scientific ontologies</title><author><name sortKey="Smith, Barry" sort="Smith, Barry" uniqKey="Smith B" first="Barry" last="Smith">Barry Smith</name></author><author><name sortKey="Ceusters, Werner" sort="Ceusters, Werner" uniqKey="Ceusters W" first="Werner" last="Ceusters">Werner Ceusters</name></author></analytic><series><title level="j">Applied ontology</title><idno type="ISSN">1570-5838</idno><idno type="eISSN">1875-8533</idno><imprint><date when="2010">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p id="P1">Since 2002 we have been testing and refining a methodology for ontology development that is now being used by multiple groups of researchers in different life science domains. Gary Merrill, in a recent paper in this journal, describes some of the reasons why this methodology has been found attractive by researchers in the biological and biomedical sciences. At the same time he assails the methodology on philosophical grounds, focusing specifically on our recommendation that ontologies developed for scientific purposes should be constructed in such a way that their terms are seen as referring to what we call <italic>universals</italic> or <italic>types</italic> in reality. As we show, Merrill’s critique is of little relevance to the success of our realist project, since it not only reveals no actual errors in our work but also criticizes views on universals that we do not in fact hold. However, it nonetheless provides us with a valuable opportunity to clarify the realist methodology, and to show how some of its principles are being applied, especially within the framework of the OBO (Open Biomedical Ontologies) Foundry initiative.</p></div></front></TEI><pmc article-type="research-article" xml:lang="en"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<pmc-dir>properties manuscript</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-journal-id">101512824</journal-id><journal-id journal-id-type="pubmed-jr-id">36285</journal-id><journal-id journal-id-type="nlm-ta">Appl Ontol</journal-id><journal-title-group><journal-title>Applied ontology</journal-title></journal-title-group><issn pub-type="ppub">1570-5838</issn><issn pub-type="epub">1875-8533</issn></journal-meta><article-meta><article-id pub-id-type="pmid">21637730</article-id><article-id pub-id-type="pmc">3104413</article-id><article-id pub-id-type="doi">10.3233/AO-2010-0079</article-id><article-id pub-id-type="manuscript">NIHMS294028</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Ontological realism: A methodology for coordinated evolution of scientific ontologies</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Smith</surname><given-names>Barry</given-names></name><xref ref-type="corresp" rid="CR1">*</xref></contrib><contrib contrib-type="author"><name><surname>Ceusters</surname><given-names>Werner</given-names></name></contrib><aff id="A1">New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA</aff></contrib-group><author-notes><corresp id="CR1"><label>*</label>Corresponding author: Barry Smith, Department of Philosophy, University at Buffalo, 126 Park Hall, Buffalo, NY 14260, USA. Tel.: +1 716 650 0075; Fax: +1 716 645 6139; <email>phismith@buffalo.edu</email>.
</corresp></author-notes><pub-date pub-type="nihms-submitted"><day>12</day><month>5</month><year>2011</year></pub-date><pub-date pub-type="ppub"><day>15</day><month>11</month><year>2010</year></pub-date><pub-date pub-type="pmc-release"><day>31</day><month>5</month><year>2011</year></pub-date><volume>5</volume><issue>3-4</issue><fpage>139</fpage><lpage>188</lpage><permissions><copyright-statement>© 2010 – IOS Press and the authors. All rights reserved</copyright-statement><copyright-year>2010</copyright-year></permissions><abstract><p id="P1">Since 2002 we have been testing and refining a methodology for ontology development that is now being used by multiple groups of researchers in different life science domains. Gary Merrill, in a recent paper in this journal, describes some of the reasons why this methodology has been found attractive by researchers in the biological and biomedical sciences. At the same time he assails the methodology on philosophical grounds, focusing specifically on our recommendation that ontologies developed for scientific purposes should be constructed in such a way that their terms are seen as referring to what we call <italic>universals</italic> or <italic>types</italic> in reality. As we show, Merrill’s critique is of little relevance to the success of our realist project, since it not only reveals no actual errors in our work but also criticizes views on universals that we do not in fact hold. However, it nonetheless provides us with a valuable opportunity to clarify the realist methodology, and to show how some of its principles are being applied, especially within the framework of the OBO (Open Biomedical Ontologies) Foundry initiative.</p></abstract><funding-group><award-group><funding-source country="United States">National Human Genome Research Institute : NHGRI</funding-source><award-id>U54 HG004028-05 || HG</award-id></award-group></funding-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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