TEPAPA: a novel in silico feature learning pipeline for mining prognostic and associative factors from text-based electronic medical records
Identifieur interne : 000D66 ( Pmc/Curation ); précédent : 000D65; suivant : 000D67TEPAPA: a novel in silico feature learning pipeline for mining prognostic and associative factors from text-based electronic medical records
Auteurs : Frank Po-Yen Lin ; Adrian Pokorny ; Christina Teng ; Richard J. EpsteinSource :
- Scientific Reports [ 2045-2322 ] ; 2017.
Abstract
Vast amounts of clinically relevant text-based variables lie undiscovered and unexploited in electronic medical records (EMR). To exploit this untapped resource, and thus facilitate the discovery of informative covariates from unstructured clinical narratives, we have built a novel computational pipeline termed
Url:
DOI: 10.1038/s41598-017-07111-0
PubMed: 28761061
PubMed Central: 5537364
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<front><div type="abstract" xml:lang="en"><p id="Par1">Vast amounts of clinically relevant text-based variables lie undiscovered and unexploited in electronic medical records (EMR). To exploit this untapped resource, and thus facilitate the discovery of informative covariates from unstructured clinical narratives, we have built a novel computational pipeline termed <italic>T</italic>
ext-based <italic>E</italic>
xploratory <italic>P</italic>
attern <italic>A</italic>
nalyser for <italic>P</italic>
rognosticator and <italic>A</italic>
ssociator discovery (TEPAPA). This pipeline combines semantic-free natural language processing (NLP), regular expression induction, and statistical association testing to identify conserved text patterns associated with outcome variables of clinical interest. When we applied TEPAPA to a cohort of head and neck squamous cell carcinoma patients, plausible concepts known to be correlated with human papilloma virus (HPV) status were identified from the EMR text, including site of primary disease, tumour stage, pathologic characteristics, and treatment modalities. Similarly, correlates of other variables (including gender, nodal status, recurrent disease, smoking and alcohol status) were also reliably recovered. Using highly-associated patterns as covariates, a patient’s HPV status was classifiable using a bootstrap analysis with a mean area under the ROC curve of 0.861, suggesting its predictive utility in supporting EMR-based phenotyping tasks. These data support using this integrative approach to efficiently identify disease-associated factors from unstructured EMR narratives, and thus to efficiently generate testable hypotheses.</p>
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<back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Frankovich, J" uniqKey="Frankovich J">J Frankovich</name>
</author>
<author><name sortKey="Longhurst, Ca" uniqKey="Longhurst C">CA Longhurst</name>
</author>
<author><name sortKey="Sutherland, Sm" uniqKey="Sutherland S">SM Sutherland</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Zheng, K" uniqKey="Zheng K">K Zheng</name>
</author>
<author><name sortKey="Mei, Q" uniqKey="Mei Q">Q Mei</name>
</author>
<author><name sortKey="Hanauer, Da" uniqKey="Hanauer D">DA Hanauer</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kahn, Mg" uniqKey="Kahn M">MG Kahn</name>
</author>
<author><name sortKey="Weng, C" uniqKey="Weng C">C Weng</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Chute, Cg" uniqKey="Chute C">CG Chute</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Sledge, Gw" uniqKey="Sledge G">GW Sledge</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Abernethy, Ap" uniqKey="Abernethy A">AP Abernethy</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Shrager, J" uniqKey="Shrager J">J Shrager</name>
</author>
<author><name sortKey="Tenenbaum, Jm" uniqKey="Tenenbaum J">JM Tenenbaum</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Jensen, Pb" uniqKey="Jensen P">PB Jensen</name>
</author>
<author><name sortKey="Jensen, Lj" uniqKey="Jensen L">LJ Jensen</name>
</author>
<author><name sortKey="Brunak, S" uniqKey="Brunak S">S Brunak</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kho, An" uniqKey="Kho A">AN Kho</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Warner, Jl" uniqKey="Warner J">JL Warner</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Denny, Jc" uniqKey="Denny J">JC Denny</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Ritchie, Md" uniqKey="Ritchie M">MD Ritchie</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Denny, Jc" uniqKey="Denny J">JC Denny</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Wei, Wq" uniqKey="Wei W">WQ Wei</name>
</author>
<author><name sortKey="Denny, Jc" uniqKey="Denny J">JC Denny</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kohane, Is" uniqKey="Kohane I">IS Kohane</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Denny, Jc" uniqKey="Denny J">JC Denny</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Uzuner, O" uniqKey="Uzuner O">O Uzuner</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Delisle, S" uniqKey="Delisle S">S DeLisle</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Roque, Fs" uniqKey="Roque F">FS Roque</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kullo, Ij" uniqKey="Kullo I">IJ Kullo</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Fernandez Breis, Jt" uniqKey="Fernandez Breis J">JT Fernández-Breis</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Richesson, Rl" uniqKey="Richesson R">RL Richesson</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Chaturvedi, Ak" uniqKey="Chaturvedi A">AK Chaturvedi</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Smith, Em" uniqKey="Smith E">EM Smith</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Gillison, Ml" uniqKey="Gillison M">ML Gillison</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Marur, S" uniqKey="Marur S">S Marur</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Anaya Saavedra, G" uniqKey="Anaya Saavedra G">G Anaya-Saavedra</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Klussmann, Jp" uniqKey="Klussmann J">JP Klussmann</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="D Ouza, G" uniqKey="D Ouza G">G D’Souza</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Begum, S" uniqKey="Begum S">S Begum</name>
</author>
<author><name sortKey="Westra, Wh" uniqKey="Westra W">WH Westra</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Mork, J" uniqKey="Mork J">J Mork</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Gillison, Ml" uniqKey="Gillison M">ML Gillison</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hafkamp, Hc" uniqKey="Hafkamp H">HC Hafkamp</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Goldenberg, D" uniqKey="Goldenberg D">D Goldenberg</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="O Ullivan, B" uniqKey="O Ullivan B">B O’Sullivan</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Toutanova, K" uniqKey="Toutanova K">K Toutanova</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Klein, D" uniqKey="Klein D">D Klein</name>
</author>
<author><name sortKey="Manning, Cd" uniqKey="Manning C">CD Manning</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Bui, Dd" uniqKey="Bui D">DD Bui</name>
</author>
<author><name sortKey="Zeng Treitler, Q" uniqKey="Zeng Treitler Q">Q Zeng-Treitler</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hall, M" uniqKey="Hall M">M Hall</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Freund, Y" uniqKey="Freund Y">Y Freund</name>
</author>
<author><name sortKey="Mason, L" uniqKey="Mason L">L Mason</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Prasse, P" uniqKey="Prasse P">P Prasse</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Savova, Gk" uniqKey="Savova G">GK Savova</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Bland, Jm" uniqKey="Bland J">JM Bland</name>
</author>
<author><name sortKey="Altman, Dg" uniqKey="Altman D">DG Altman</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Benjamini, Y" uniqKey="Benjamini Y">Y Benjamini</name>
</author>
<author><name sortKey="Hochberg, Y" uniqKey="Hochberg Y">Y Hochberg</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Hripcsak, G" uniqKey="Hripcsak G">G Hripcsak</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hripcsak, G" uniqKey="Hripcsak G">G Hripcsak</name>
</author>
<author><name sortKey="Albers, Dj" uniqKey="Albers D">DJ Albers</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hersh, Wr" uniqKey="Hersh W">WR Hersh</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
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<article-categories><subj-group subj-group-type="heading"><subject>Article</subject>
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</article-categories>
<title-group><article-title>TEPAPA: a novel in silico feature learning pipeline for mining prognostic and associative factors from text-based electronic medical records</article-title>
</title-group>
<contrib-group><contrib contrib-type="author" corresp="yes"><contrib-id contrib-id-type="orcid">http://orcid.org/0000-0001-9250-6874</contrib-id>
<name><surname>Lin</surname>
<given-names>Frank Po-Yen</given-names>
</name>
<address><email>f.lin@garvan.org.au</email>
</address>
<xref ref-type="aff" rid="Aff1">1</xref>
<xref ref-type="aff" rid="Aff2">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Pokorny</surname>
<given-names>Adrian</given-names>
</name>
<xref ref-type="aff" rid="Aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Teng</surname>
<given-names>Christina</given-names>
</name>
<xref ref-type="aff" rid="Aff3">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Epstein</surname>
<given-names>Richard J.</given-names>
</name>
<xref ref-type="aff" rid="Aff1">1</xref>
<xref ref-type="aff" rid="Aff2">2</xref>
</contrib>
<aff id="Aff1"><label>1</label>
<institution-wrap><institution-id institution-id-type="ISNI">0000 0000 9119 2677</institution-id>
<institution-id institution-id-type="GRID">grid.437825.f</institution-id>
<institution>Department of Oncology,</institution>
<institution>St Vincent’s Hospital & The Kinghorn Cancer Centre,</institution>
</institution-wrap>
Darlinghurst, NSW Australia</aff>
<aff id="Aff2"><label>2</label>
<institution-wrap><institution-id institution-id-type="ISNI">0000 0000 9983 6924</institution-id>
<institution-id institution-id-type="GRID">grid.415306.5</institution-id>
<institution>Garvan Institute of Medical Research,</institution>
</institution-wrap>
Darlinghurst, NSW Australia</aff>
<aff id="Aff3"><label>3</label>
<institution-wrap><institution-id institution-id-type="ISNI">0000 0004 0527 9653</institution-id>
<institution-id institution-id-type="GRID">grid.415994.4</institution-id>
<institution>Department of Medical Oncology,</institution>
<institution>Liverpool Hospital,</institution>
</institution-wrap>
Liverpool, Sydney, NSW Australia</aff>
</contrib-group>
<pub-date pub-type="epub"><day>31</day>
<month>7</month>
<year>2017</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>31</day>
<month>7</month>
<year>2017</year>
</pub-date>
<pub-date pub-type="collection"><year>2017</year>
</pub-date>
<volume>7</volume>
<elocation-id>6918</elocation-id>
<history><date date-type="received"><day>3</day>
<month>11</month>
<year>2016</year>
</date>
<date date-type="accepted"><day>21</day>
<month>6</month>
<year>2017</year>
</date>
</history>
<permissions><copyright-statement>© The Author(s) 2017</copyright-statement>
<license license-type="OpenAccess"><license-p><bold>Open Access</bold>
This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link>
.</license-p>
</license>
</permissions>
<abstract id="Abs1"><p id="Par1">Vast amounts of clinically relevant text-based variables lie undiscovered and unexploited in electronic medical records (EMR). To exploit this untapped resource, and thus facilitate the discovery of informative covariates from unstructured clinical narratives, we have built a novel computational pipeline termed <italic>T</italic>
ext-based <italic>E</italic>
xploratory <italic>P</italic>
attern <italic>A</italic>
nalyser for <italic>P</italic>
rognosticator and <italic>A</italic>
ssociator discovery (TEPAPA). This pipeline combines semantic-free natural language processing (NLP), regular expression induction, and statistical association testing to identify conserved text patterns associated with outcome variables of clinical interest. When we applied TEPAPA to a cohort of head and neck squamous cell carcinoma patients, plausible concepts known to be correlated with human papilloma virus (HPV) status were identified from the EMR text, including site of primary disease, tumour stage, pathologic characteristics, and treatment modalities. Similarly, correlates of other variables (including gender, nodal status, recurrent disease, smoking and alcohol status) were also reliably recovered. Using highly-associated patterns as covariates, a patient’s HPV status was classifiable using a bootstrap analysis with a mean area under the ROC curve of 0.861, suggesting its predictive utility in supporting EMR-based phenotyping tasks. These data support using this integrative approach to efficiently identify disease-associated factors from unstructured EMR narratives, and thus to efficiently generate testable hypotheses.</p>
</abstract>
<custom-meta-group><custom-meta><meta-name>issue-copyright-statement</meta-name>
<meta-value>© The Author(s) 2017</meta-value>
</custom-meta>
</custom-meta-group>
</article-meta>
</front>
</pmc>
</record>
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