Identifying influenza-like illness presentation from unstructured general practice clinical narrative using a text classifier rule-based expert system versus a clinical expert
Identifieur interne : 000B58 ( Main/Exploration ); précédent : 000B57; suivant : 000B59Identifying influenza-like illness presentation from unstructured general practice clinical narrative using a text classifier rule-based expert system versus a clinical expert
Auteurs : Jayden Macrae [Nouvelle-Zélande] ; Tom Love [Nouvelle-Zélande] ; Michael G. Baker [Nouvelle-Zélande] ; Anthony Dowell [Nouvelle-Zélande] ; Matthew Carnachan [Nouvelle-Zélande] ; Maria Stubbe [Nouvelle-Zélande] ; Lynn Mcbain [Nouvelle-Zélande]Source :
- BMC Medical Informatics and Decision Making [ 1472-6947 ] ; 2015.
Descripteurs français
- KwdFr :
- MESH :
- diagnostic : Grippe humaine.
- Humains, Médecine générale, Narration, Systèmes experts, Traitement du langage naturel.
English descriptors
- KwdEn :
- MESH :
- diagnosis : Influenza, Human.
- Expert Systems, General Practice, Humans, Narration, Natural Language Processing.
Abstract
We designed and validated a rule-based expert system to identify influenza like illness (ILI) from routinely recorded general practice clinical narrative to aid a larger retrospective research study into the impact of the 2009 influenza pandemic in New Zealand.
Rules were assessed using pattern matching heuristics on routine clinical narrative. The system was trained using data from 623 clinical encounters and validated using a clinical expert as a gold standard against a mutually exclusive set of 901 records.
We calculated a 98.2 % specificity and 90.2 % sensitivity across an ILI incidence of 12.4 % measured against clinical expert classification. Peak problem list identification of ILI by clinical coding in any month was 9.2 % of all detected ILI presentations. Our system addressed an unusual problem domain for clinical narrative classification; using notational, unstructured, clinician entered information in a community care setting. It performed well compared with other approaches and domains. It has potential applications in real-time surveillance of disease, and in assisted problem list coding for clinicians.
Our system identified ILI presentation with sufficient accuracy for use at a population level in the wider research study. The peak coding of 9.2 % illustrated the need for automated coding of unstructured narrative in our study.
Url:
DOI: 10.1186/s12911-015-0201-3
PubMed: 26445235
PubMed Central: 4596422
Affiliations:
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xml:lang="fr">Nouvelle-Zélande</country><wicri:regionArea>Sapere Research Group, Wellington</wicri:regionArea><wicri:noRegion>Wellington</wicri:noRegion></affiliation></author><author><name sortKey="Baker, Michael G" sort="Baker, Michael G" uniqKey="Baker M" first="Michael G." last="Baker">Michael G. Baker</name><affiliation wicri:level="1"><nlm:aff id="Aff3">Department of Public Health, University of Otago Wellington, Wellington, New Zealand</nlm:aff><country xml:lang="fr">Nouvelle-Zélande</country><wicri:regionArea>Department of Public Health, University of Otago Wellington, Wellington</wicri:regionArea><wicri:noRegion>Wellington</wicri:noRegion></affiliation></author><author><name sortKey="Dowell, Anthony" sort="Dowell, Anthony" uniqKey="Dowell A" first="Anthony" last="Dowell">Anthony Dowell</name><affiliation wicri:level="1"><nlm:aff id="Aff4">Department of Primary Health Care & General Practice, University of Otago Wellington, Wellington, New Zealand</nlm:aff><country xml:lang="fr">Nouvelle-Zélande</country><wicri:regionArea>Department of Primary Health Care & General Practice, University of Otago Wellington, Wellington</wicri:regionArea><wicri:noRegion>Wellington</wicri:noRegion></affiliation></author><author><name sortKey="Carnachan, Matthew" sort="Carnachan, Matthew" uniqKey="Carnachan M" first="Matthew" last="Carnachan">Matthew Carnachan</name><affiliation wicri:level="1"><nlm:aff id="Aff5">Compass Health, Wellington, New Zealand</nlm:aff><country xml:lang="fr">Nouvelle-Zélande</country><wicri:regionArea>Compass Health, Wellington</wicri:regionArea><wicri:noRegion>Wellington</wicri:noRegion></affiliation></author><author><name sortKey="Stubbe, Maria" sort="Stubbe, Maria" uniqKey="Stubbe M" first="Maria" last="Stubbe">Maria Stubbe</name><affiliation wicri:level="1"><nlm:aff id="Aff4">Department of Primary Health Care & General Practice, University of Otago Wellington, Wellington, New Zealand</nlm:aff><country xml:lang="fr">Nouvelle-Zélande</country><wicri:regionArea>Department of Primary Health Care & General Practice, University of Otago Wellington, Wellington</wicri:regionArea><wicri:noRegion>Wellington</wicri:noRegion></affiliation></author><author><name sortKey="Mcbain, Lynn" sort="Mcbain, Lynn" uniqKey="Mcbain L" first="Lynn" last="Mcbain">Lynn Mcbain</name><affiliation wicri:level="1"><nlm:aff id="Aff4">Department of Primary Health Care & General Practice, University of Otago Wellington, Wellington, New Zealand</nlm:aff><country xml:lang="fr">Nouvelle-Zélande</country><wicri:regionArea>Department of Primary Health Care & General Practice, University of Otago Wellington, Wellington</wicri:regionArea><wicri:noRegion>Wellington</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Medical Informatics and Decision Making</title><idno type="eISSN">1472-6947</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Expert Systems</term><term>General Practice</term><term>Humans</term><term>Influenza, Human (diagnosis)</term><term>Narration</term><term>Natural Language Processing</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Grippe humaine (diagnostic)</term><term>Humains</term><term>Médecine générale</term><term>Narration</term><term>Systèmes experts</term><term>Traitement du langage naturel</term></keywords><keywords scheme="MESH" qualifier="diagnosis" xml:lang="en"><term>Influenza, Human</term></keywords><keywords scheme="MESH" qualifier="diagnostic" xml:lang="fr"><term>Grippe humaine</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Expert Systems</term><term>General Practice</term><term>Humans</term><term>Narration</term><term>Natural Language Processing</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Humains</term><term>Médecine générale</term><term>Narration</term><term>Systèmes experts</term><term>Traitement du langage naturel</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>We designed and validated a rule-based expert system to identify influenza like illness (ILI) from routinely recorded general practice clinical narrative to aid a larger retrospective research study into the impact of the 2009 influenza pandemic in New Zealand.</p></sec><sec><title>Methods</title><p>Rules were assessed using pattern matching heuristics on routine clinical narrative. The system was trained using data from 623 clinical encounters and validated using a clinical expert as a gold standard against a mutually exclusive set of 901 records.</p></sec><sec><title>Results</title><p>We calculated a 98.2 % specificity and 90.2 % sensitivity across an ILI incidence of 12.4 % measured against clinical expert classification. Peak problem list identification of ILI by clinical coding in any month was 9.2 % of all detected ILI presentations. Our system addressed an unusual problem domain for clinical narrative classification; using notational, unstructured, clinician entered information in a community care setting. It performed well compared with other approaches and domains. It has potential applications in real-time surveillance of disease, and in assisted problem list coding for clinicians.</p></sec><sec><title>Conclusions</title><p>Our system identified ILI presentation with sufficient accuracy for use at a population level in the wider research study. 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Collett</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Chapman, Ww" uniqKey="Chapman W">WW Chapman</name></author><author><name sortKey="Bridewell, W" uniqKey="Bridewell W">W Bridewell</name></author><author><name sortKey="Hanbury, P" uniqKey="Hanbury P">P Hanbury</name></author><author><name sortKey="Cooper, Gf" uniqKey="Cooper G">GF Cooper</name></author><author><name sortKey="Buchanan, Bg" uniqKey="Buchanan B">BG Buchanan</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Ruch, P" uniqKey="Ruch P">P Ruch</name></author><author><name sortKey="Baud, R" uniqKey="Baud R">R Baud</name></author><author><name sortKey="Geissbuhler, A" uniqKey="Geissbuhler A">A Geissbuhler</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Demner Fushman, D" uniqKey="Demner Fushman D">D Demner-Fushman</name></author><author><name 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Fridsma</name></author><author><name sortKey="Sttig, Df" uniqKey="Sttig D">DF Sttig</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hashimoto, S" uniqKey="Hashimoto S">S Hashimoto</name></author><author><name sortKey="Murakami, Y" uniqKey="Murakami Y">Y Murakami</name></author><author><name sortKey="Taniguchi, K" uniqKey="Taniguchi K">K Taniguchi</name></author><author><name sortKey="Nagai, M" uniqKey="Nagai M">M Nagai</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="De Lusignan, S" uniqKey="De Lusignan S">S De Lusignan</name></author><author><name sortKey="Van Weel, C" uniqKey="Van Weel C">C van Weel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Meystre, S" uniqKey="Meystre S">S Meystre</name></author><author><name sortKey="Haug, Pj" uniqKey="Haug P">PJ Haug</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Nouvelle-Zélande</li></country></list><tree><country name="Nouvelle-Zélande"><noRegion><name sortKey="Macrae, Jayden" sort="Macrae, Jayden" uniqKey="Macrae J" first="Jayden" last="Macrae">Jayden Macrae</name></noRegion><name sortKey="Baker, Michael G" sort="Baker, Michael G" uniqKey="Baker M" first="Michael G." last="Baker">Michael G. Baker</name><name sortKey="Carnachan, Matthew" sort="Carnachan, Matthew" uniqKey="Carnachan M" first="Matthew" last="Carnachan">Matthew Carnachan</name><name sortKey="Dowell, Anthony" sort="Dowell, Anthony" uniqKey="Dowell A" first="Anthony" last="Dowell">Anthony Dowell</name><name sortKey="Love, Tom" sort="Love, Tom" uniqKey="Love T" first="Tom" last="Love">Tom Love</name><name sortKey="Mcbain, Lynn" sort="Mcbain, Lynn" uniqKey="Mcbain L" first="Lynn" last="Mcbain">Lynn Mcbain</name><name sortKey="Stubbe, Maria" sort="Stubbe, Maria" uniqKey="Stubbe M" first="Maria" last="Stubbe">Maria Stubbe</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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