FCAView Tab: Tab: FCAView A Concept- -Oriented View Generation Tool for Oriented View Generation Tool for A Concept Clinical Data Using Formal Concept Analysis Clinical Data Using Formal Concept Analysis Guoqian Jiang Jiang, Katsuhiko Ogasawara, Naoki , Katsuhiko Ogasawara, Naoki Nishimoto Nishimoto, , Guoqian Akira Endoh Endoh, , Tsunetaro Tsunetaro Sakurai Sakurai Akira Department of Medical Informatics, Hokkaido University Department of Medical Informatics, Hokkaido University Graduate School of Medicine, Sapporo, Japan Graduate School of Medicine, Sapporo, Japan th International Prot The 8 th é g é Conference International Prot é g é Conference The 8 Madrid, Spain, July 20, 2005 Madrid, Spain, July 20, 2005
Classification of Views for Electronic Patient Records Classification of Views for Electronic Patient Records From Q.Zeng, et al. Journal of Biomedical Informatics. 2001;34(2):112-128
Concept- -Oriented Views Oriented Views Concept � Several studies have demonstrated that Several studies have demonstrated that � computer computer- -generated, concept generated, concept- -oriented views for oriented views for ’ clinical data can be used to reduce clinicians ’ clinical data can be used to reduce clinicians information overload and improve the accuracy information overload and improve the accuracy of clinical data retrieval. of clinical data retrieval. � However, the tasks for automating the However, the tasks for automating the � generation of concept- -oriented views are oriented views are generation of concept challenging. challenging.
Formal Concept Analysis Formal Concept Analysis � Formal concept analysis (FCA), a mathematical Formal concept analysis (FCA), a mathematical � approach to data analysis based on lattice theory, approach to data analysis based on lattice theory, has been advocated to represent and process has been advocated to represent and process medical knowledge in different topics related to medical knowledge in different topics related to decision support systems. decision support systems.
Example: A family Example: A family
Study Purpose Study Purpose � In the study, the potential role of formal In the study, the potential role of formal � concept analysis on concept concept analysis on concept- -oriented view oriented view generation for clinical data is explored. generation for clinical data is explored.
Materials Materials � Clinical Data Clinical Data � � A collection of 386 Japanese discharge summaries A collection of 386 Japanese discharge summaries � obtained from cardiovascular domain. obtained from cardiovascular domain. � Knowledge sources Knowledge sources � � The Japanese version of � The Japanese version of MeSH MeSH (MSHJPN) in (MSHJPN) in UMLS2005AA (54,550 entries). UMLS2005AA (54,550 entries). Developed by the NLM � Developed by the NLM � MEDIS version 2.3 � MEDIS version 2.3 -- --The Japanese standard The Japanese standard dictionaries of diagnosis terms (19,660 entries) and dictionaries of diagnosis terms (19,660 entries) and procedural terms (9,686 entries). procedural terms (9,686 entries). � Developed by the MEDIS Developed by the MEDIS- -DC in Japan DC in Japan
System Construction System Construction é g é - FCAView Tab: Tab: A Prot A Prot é g é � FCAView -2000 tab plug 2000 tab plug- -in in � A virtual patient records system � A virtual patient records system � A ontology- -based knowledge base based knowledge base � A ontology � Medical concepts � Medical concepts � Formal concept analysis � Formal concept analysis � A natural language processing (NLP) module � A natural language processing (NLP) module � A formal concept analysis (FCA) module � A formal concept analysis (FCA) module �
The structure of The structure of <?xml version="1.0" encoding="Shift_JIS"?> <!DOCTYPE DischargeSummary SYSTEM "DischargeSummary.dtd"> discharge summary discharge summary <DischargeSummary> <PatientDischargeSummary> represented by a represented by a <FileInformation> <FileID>pcdata</FileID> <PatientID>pcdata</PatientID> XML file XML file </FileInformation> <PatientInformation> <PatientAge>pcdata</PatientAge> <PatientSex>pcdata</PatientSex> <PatientOccupation>pcdata</PatientOccupation> </PatientInformation> <DateInformation> <AdmissionDate>pcdata</AdmissionDate> <DischargeDate>pcdata</DischargeDate> </DateInformation> <DiagnosisList> <PrimaryDiagnosis>pcdata</PrimaryDiagnosis> <SecondaryDiagnosis>pcdata</SecondaryDiagnosis> </DiagnosisList> <PatientSummary> <Complaint>pcdata</Complaint> <CurrentHistory>pcdata</CurrentHistory> <PastHistory>pcdata</PastHistory> <OtherHistory>pcdata</OtherHistory> <ExaminationRecords>pcdata</ExaminationRecords> <InvestigationRecords>pcdata</InvestigationRecords> <ProgressRecords>pcdata</ProgressRecords> </PatientSummary> </PatientDischargeSummary> </DischargeSummary>
An Example of the Virtual Patient Records An Example of the Virtual Patient Records
Ontology- -based Knowledge Base based Knowledge Base Ontology Class Slot Instance Case id
NLP Module NLP Module � ChaSen ChaSen version 2.3 version 2.3 � � A Japanese morphological analysis system A Japanese morphological analysis system � Open source Open source � Developed by Nara Institute of Science and Technology Developed by Nara Institute of Science and Technology � MACD MACD � � Morphological Analyzer Connectivity Driver Morphological Analyzer Connectivity Driver- -model model � As the Java interface of As the Java interface of ChaSen ChaSen � Developed by Nara Institute of Science and Technology Developed by Nara Institute of Science and Technology � User dictionaries: User dictionaries: � � MSHJPN MSHJPN � MEDIS version 2.3 MEDIS version 2.3
FCA Module FCA Module � The Java API of Concept Explorer version 1.2 The Java API of Concept Explorer version 1.2 � � Open source project Open source project � � To generate the concept oriented views for the To generate the concept oriented views for the � clinical data clinical data
Results (I) Results (I) � View generation for individual patient records View generation for individual patient records � � The items about the structure knowledge of the patient � The items about the structure knowledge of the patient records used as the formal objects records used as the formal objects � Primary diagnosis Primary diagnosis � Secondary diagnoses Secondary diagnoses � Chief Complaints Chief Complaints Current history � Current history � Past history Past history Other histories � Other histories � Examination records Examination records Investigation records � Investigation records � Progress records Progress records � The medical concepts extracted from each part used as The medical concepts extracted from each part used as � the formal attributes the formal attributes
Context of an Individual Case by Cross- -table table Context of an Individual Case by Cross Medical Structural Concepts Items
Concept- -Oriented View of an Individual Case by Lattice Oriented View of an Individual Case by Lattice Concept Effort Angina Impaired Shortness of breath, liver function A feeling of general fatigue
Results (II) Results (II) � View generation for the similar cases View generation for the similar cases � The similar cases indicated by the case ids � The similar cases indicated by the case ids � were used as the formal objects were used as the formal objects The medical concepts extracted from each � The medical concepts extracted from each � case were used as the formal attributes case were used as the formal attributes
Context of the Similar Cases by Cross- -table table Context of the Similar Cases by Cross Medical Concepts Case Ids
Concept- -Oriented View of the Similar Cases by Lattice Oriented View of the Similar Cases by Lattice Concept Effort Angina Shortness of Chest Pain Breath Chest Discomfort Hyperlipidemia Diabetes Mellitus Type II
Results (III) Results (III) � Implementation of information model for Implementation of information model for � practical use practical use Converting the lattice diagram into a concept � Converting the lattice diagram into a concept � tree tree Developing the filters to restrict the context size � Developing the filters to restrict the context size �
For Context Of For Context Of The Individual Case Effort Angina The Similar Cases Impaired Liver Function
Effort Angina � Context filter using Context filter using � Structure Knowledge Structure Knowledge � Primary diagnosis Primary diagnosis � Secondary diagnosis Secondary diagnosis � Chief complaints Chief complaints � Current history Current history � Past history Past history � Other history Other history � Examination records Examination records � Investigation records Investigation records � Progress records Progress records
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