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+        Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2006,7,25]],"date-time":"2006-07-25T00:00:00Z","timestamp":1153785600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC
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+        evaluation of the quality of genomic or proteomic data and computational methods
+        is vital to our ability to use them for formulating novel biological hypotheses
+        and directing further experiments. There is currently no standard approach
+        to evaluation in functional genomics. Our analysis of existing approaches
+        shows that they are inconsistent and contain substantial functional biases
+        that render the resulting evaluations misleading both quantitatively and qualitatively.
+        These problems make it essentially impossible to compare computational methods
+        or large-scale experimental datasets and also result in conclusions that generalize
+        poorly in most biological applications.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We
+        reveal issues with current evaluation methods here and suggest new approaches
+        to evaluation that facilitate accurate and representative characterization
+        of genomic methods and data. Specifically, we describe a functional genomics
+        gold standard based on curation by expert biologists and demonstrate its use
+        as an effective means of evaluation of genomic approaches. Our evaluation
+        framework and gold standard are freely available to the community through
+        our website.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>Proper
+        methods for evaluating genomic data and computational approaches will determine
+        how much we, as a community, are able to learn from the wealth of available
+        data. We propose one possible solution to this problem here but emphasize
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+        \           <journal>\r\n              <journal_metadata language=\"en\">\r\n
+        \               <full_title>BMC Genomics</full_title>\r\n                <abbrev_title>BMC
+        Genomics</abbrev_title>\r\n                <issn media_type=\"electronic\">1471-2164</issn>\r\n
+        \             </journal_metadata>\r\n              <journal_issue>\r\n                <publication_date
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+        \               <issue>1</issue>\r\n              </journal_issue>\r\n              <journal_article
+        publication_type=\"full_text\">\r\n                <titles>\r\n                  <title>Finding
+        function: evaluation methods for functional genomic data</title>\r\n                </titles>\r\n
+        \               <contributors>\r\n                  <person_name sequence=\"first\"
+        contributor_role=\"author\">\r\n                    <given_name>Chad L</given_name>\r\n
+        \                   <surname>Myers</surname>\r\n                  </person_name>\r\n
+        \                 <person_name sequence=\"additional\" contributor_role=\"author\">\r\n
+        \                   <given_name>Daniel R</given_name>\r\n                    <surname>Barrett</surname>\r\n
+        \                 </person_name>\r\n                  <person_name sequence=\"additional\"
+        contributor_role=\"author\">\r\n                    <given_name>Matthew A</given_name>\r\n
+        \                   <surname>Hibbs</surname>\r\n                  </person_name>\r\n
+        \                 <person_name sequence=\"additional\" contributor_role=\"author\">\r\n
+        \                   <given_name>Curtis</given_name>\r\n                    <surname>Huttenhower</surname>\r\n
+        \                 </person_name>\r\n                  <person_name sequence=\"additional\"
+        contributor_role=\"author\">\r\n                    <given_name>Olga G</given_name>\r\n
+        \                   <surname>Troyanskaya</surname>\r\n                  </person_name>\r\n
+        \               </contributors>\r\n                <jats:abstract xmlns:jats=\"http://www.ncbi.nlm.nih.gov/JATS1\"
+        xml:lang=\"en\">\r\n                  <jats:title>Abstract</jats:title>\r\n
+        \                 <jats:sec>\r\n                    <jats:title>Background</jats:title>\r\n
+        \                   <jats:p>Accurate evaluation of the quality of genomic
+        or proteomic data and computational methods is vital to our ability to use
+        them for formulating novel biological hypotheses and directing further experiments.
+        There is currently no standard approach to evaluation in functional genomics.
+        Our analysis of existing approaches shows that they are inconsistent and contain
+        substantial functional biases that render the resulting evaluations misleading
+        both quantitatively and qualitatively. These problems make it essentially
+        impossible to compare computational methods or large-scale experimental datasets
+        and also result in conclusions that generalize poorly in most biological applications.</jats:p>\r\n
+        \                 </jats:sec>\r\n                  <jats:sec>\r\n                    <jats:title>Results</jats:title>\r\n
+        \                   <jats:p>We reveal issues with current evaluation methods
+        here and suggest new approaches to evaluation that facilitate accurate and
+        representative characterization of genomic methods and data. Specifically,
+        we describe a functional genomics gold standard based on curation by expert
+        biologists and demonstrate its use as an effective means of evaluation of
+        genomic approaches. Our evaluation framework and gold standard are freely
+        available to the community through our website.</jats:p>\r\n                  </jats:sec>\r\n
+        \                 <jats:sec>\r\n                    <jats:title>Conclusion</jats:title>\r\n
+        \                   <jats:p>Proper methods for evaluating genomic data and
+        computational approaches will determine how much we, as a community, are able
+        to learn from the wealth of available data. We propose one possible solution
+        to this problem here but emphasize that this topic warrants broader community
+        discussion.</jats:p>\r\n                  </jats:sec>\r\n                </jats:abstract>\r\n
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