An OGMS-based Model for Clinical Information

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This is the presentation of the paper presented on the early career symposium at the International Conference on Biomedical Ontology. http://www.unbsj.ca/sase/csas/data/ws/icbo2013/papers/ec/icbo2013_submission_56.pdf

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An OGMS-based Model for Clinical Information

  1. 1. Unrestricted © Siemens AG 2013. All rights reserved An OGMS-based Model for Clinical Information ICBO Early Career Symposium / July 2013 Heiner Oberkampf1,2, Sonja Zillner1, Bernhard Bauer2 and Matthias Hammon3 1 Siemens AG, Corporate Technology, Munich, Germany 2 Software Methodologies for Distributed Systems, University of Augsburg, Germany 3 Department of Radiology, University Hospital Erlangen, Germany
  2. 2. Unrestricted © Siemens AG 2013. All rights reservedPage 2 July 2013 Corporate Technology Agenda Clinical Data and Problem Description The Model for Clinical Information Storage and Queries Related Work
  3. 3. Unrestricted © Siemens AG 2013. All rights reservedPage 3 July 2013 Corporate Technology Clinical Data Unstructured, heterogeneous and complex. • Data is mostly unstructured • Data is not integrated • Different data needs to be combined for clinical decisions • Raw data needs to be interpreted to fasten clinical decisions (e.g. normal, abnormal, pathological …) • Clinicians do not use the full information contained in existing patient data Problems Structured • Diagnosis • Procedures • Lab values • Demographics • Medication • Provider Unstructured • Reports • Images • Omics data Data
  4. 4. Unrestricted © Siemens AG 2013. All rights reservedPage 4 July 2013 Corporate Technology Patient Data The development of our model is based on two datasets. Project: Data Intelligence for Clinical Solutions (6 manually selected melanoma patients) • Demographics • diagnoses (ICD-10 codes) • lab values (LOINC codes) • procedures (OPS codes) • drug administration (ATC codes) • radiology reports • pathology reports • all data timestamped Project: Theseus MEDICO (382 patients) • 2700 Radiological Reports • Image Annotations
  5. 5. Unrestricted © Siemens AG 2013. All rights reservedPage 5 July 2013 Corporate Technology Semantic Data Integration The Hospital in Erlangen integrates their data into an i2b2 data warehouse. Clinical Information Systems Model for Clinical Information i2b2 Data- Warehouse • Raw data • Vendor specific • Administration centric • BI applications (e.g. Oracle Health Data Model) • Structured data is mapped to standardized terminologies (ICD, LOINC, OPS…) • Identification of patient cohorts • Patient centric and granular data representation • Annotation of unstructured data • Use of medical ontologies and reasoning mechanisms
  6. 6. Unrestricted © Siemens AG 2013. All rights reservedPage 6 July 2013 Corporate Technology Questions to Answer In perspective we want to answer the following questions using Model of Clinical Information (MCI). Normal and abnormal structures • What findings about abnormalities do we have from the latest examination? Longitudinal data access • How does this finding evolved from last examination? Disease centric data access • Are there any cancer findings? Organ centric data access • What information do we have regarding the liver functioning? Decision support • What are likely diseases? • What examinations should be provided next?
  7. 7. Unrestricted © Siemens AG 2013. All rights reservedPage 7 July 2013 Corporate Technology Semantic Model for Clinical Information Agenda Clinical Data and Problem Description The Model for Clinical Information Storage and Queries Related Work
  8. 8. Unrestricted © Siemens AG 2013. All rights reservedPage 8 July 2013 Corporate Technology Technical Perspective Technical and Clinical Perspective Clinical Perspective • Provide a holistic view on the patient • Make the change of the patient‘s health status transparent • Point to missing information about symptoms and signs. • Allow efficient and integrated access to patient data • Provide a basis for clinical decision support systems • MCI integrates and structures clinical data and provides… • core concepts of clinical information • meta-information • interpretations • Clinical data is expressed using MCI in combination with established ontologies like SNOMED, RadLex, LOINC, ICD … • MCI is based on established upper level ontologies: BFO, OGMS, IAO … • Use of medical knowledge contained in ontologies through reasoning • Use of Linked Open Data: LinkedCT, SIDER, DrugBank, …
  9. 9. Unrestricted © Siemens AG 2013. All rights reservedPage 9 July 2013 Corporate Technology Big Picture Integrating different data and knowledge resources. Integrated Data Access Clinical Information Systems PACS, reports, treatment plans, lab values, administrative data … Data Repositories (factual knowledge) LinkedCT, DrugBank, SIDER, DBpedia, … Medical Ontologies (formalized knowledge) SNOMED CT, ICD, LOINC, ATC, RadLex, DOID, FMA, OPS, SYMP, … Model for Clinical Information (MCI)
  10. 10. Unrestricted © Siemens AG 2013. All rights reservedPage 10 July 2013 Corporate Technology Ontologies from the OBO Foundry MCI is based on established upper ontologies Basic Formal Ontology (BFO1.1) Completely domain independent Ontology for General Medical Science (OGMS) basic clinical concepts like, e.g., diagnosis, clinical finding, pathological anatomical structure … Ontology of Medically Related Social Entities (OMRSE) Patient role, healthcare provider role, gender role … Information Artifact Ontology (IAO) document, report, figure ... Relations Ontology (RO) has_part, has_participant, located_in … Units Ontology (UO) Subset: units for length, mass and time. Clinical Narrative Temporal Relation Ontology (CNTRO) (not from OBO Foundry) Subset: ObjectProperties before, after, overlap … Total MCI Classes 358 62 ObjectProperties 82 20 DatatypeProperties 19 14
  11. 11. Unrestricted © Siemens AG 2013. All rights reservedPage 11 July 2013 Corporate Technology Added Classes (I) Extensions under ‘obo:data item‘. mci:patient position mci:radiological examination _:re01 _:pp01 radlex:standing position mci:has examination modality _:ce01 obo:clinical encounter icd10:C79_8 obo:has specified output mci:main diagnosis _:md01 Examination modality Diagnosis rdf:type
  12. 12. Unrestricted © Siemens AG 2013. All rights reservedPage 12 July 2013 Corporate Technology Added Classes (II) Extensions under ‘obo:clinical finding‘ – interpretations of clinical findings. mci:approximately obo:length measurement datum 0.8^^xsd:decimal obo:has measurement unit label obo:image finding radlex:lymph node of thorax obo:is about mci:anatomical structure obo:has measurement value _:if01 _:as01 _:lmd01 uo:centimeter rdf:type…thoracic lymph node of ca. 0.8 cm.
  13. 13. Unrestricted © Siemens AG 2013. All rights reservedPage 13 July 2013 Corporate Technology Added Properties
  14. 14. Unrestricted © Siemens AG 2013. All rights reservedPage 14 July 2013 Corporate Technology mci:anatomical structure Example Representation of a Radiological Image Finding Spleen at hilum with diameter 10 x 4 cm mci:precisely 4^^xsd:decimal obo:has measurement unit label obo:image finding radlex:spleen obo:is about mci:anatomical structure obo:has measurement value _:if01 _:as01 uo:centimeter 10^^xsd:decimal _:lmd02 obo:has measurement value obo:length measurement datum _:lmd01 radlex:hilum of spleen _:as02 PATO:diameter _:q02 obo:is quality measurement of_:q01 mci:location specification
  15. 15. Unrestricted © Siemens AG 2013. All rights reservedPage 15 July 2013 Corporate Technology Semantic Model for Clinical Information Agenda Clinical Data and Problem Description The Model for Clinical Information Storage and Queries Related Work
  16. 16. Unrestricted © Siemens AG 2013. All rights reservedPage 16 July 2013 Corporate Technology Jena Fuseki Triple Store Datasets and Named Graphs are used to separate triples. /mci /radlex /patient23000PX1LH /ops /icd10 /atc 1) We transformed the the OPS hierarchy from in XML to RDF using XSLT. 2) We transformed ATC from Excel to RDF 1 2 Named Graphs for clinical encountersNamed Graphs for clinical encounters … /patient23000JJ43N Named Graphs for clinical encountersNamed Graphs for clinical encounters … … …
  17. 17. Unrestricted © Siemens AG 2013. All rights reservedPage 17 July 2013 Corporate Technology Querying the Model All findings about the gastrointestinal tract. obo:image finding obo:is about mci:anatomical structure _:if01 _:as01 radlex:wall of sigmoid colon Radlex:sigmoid colon radlex:gastro intestinal tract radlex:distal part of sigmoid colon SELECT ?f WHERE { SERVICE <http:localhost:3030/radlex/sparql> { SELECT ?partOfGastroIntest WHERE { # part of the gastroint. tract ?partOfGastroIntest radlex:Part_Of+ radlex:RID94 . } } ?f a obo:OGMS_0000014; # a obo:clinical finding obo:IAO_0000136 [ # which is about # some part of the gastroint. tract a ?partOfGastroIntest ]. }
  18. 18. Unrestricted © Siemens AG 2013. All rights reservedPage 18 July 2013 Corporate Technology SPARQL Update Queries Normal and abnormal status of findings about lymph nodes. INSERT { ?f a ?findingType . } WHERE { SERVICE <http:localhost:3030/radlex/sparql> { SELECT ?lymphNode WHERE { ?lymphNode rdfs:subClassOf radlex:RID13296 . } } ?f a obo:OGMS_0000014; # a obo:clinical finding obo:IAO_0000136 [ a ?lympNode ]; # which is about some lymph node (mci:MCI_0000056 | mci:MCI_0000057) [ # approximately or precisely a obo:IAO_0000408 ; # a length measurement datum obo:IAO_0000039 uo:UO_0000015; # has measurement unit label uo:centimeter obo:IAO_0000004 ?v; # has measurement value ?v ] . BIND( IF(?v <= 1), mci:MCI_0000034, # normal finding mci:MCI_0000035 ) # abnormal finding AS ?findingType) } mci:approximately obo:length measurement datum 0.8^^xsd:decimal obo:has measurement unit label obo:image finding radlex:lymph node of thorax obo:is about mci:anatomical structure obo:has measurement value _:if01 _:as01 _:lmd01 uo:centimeter obo:normal finding
  19. 19. Unrestricted © Siemens AG 2013. All rights reservedPage 19 July 2013 Corporate Technology Semantic Model for Clinical Information Agenda Clinical Data and Problem Description The Model for Clinical Information Storage and Queries Related Work
  20. 20. Unrestricted © Siemens AG 2013. All rights reservedPage 20 July 2013 Corporate Technology Related Work (I) Existing open data models. Model Motivation Status Difference to MCI HL7 Reference Information Model v3 • supplement to standards for messaging and clinical documents (CDA) • 2010: first owl-version • inconsistent definitions of concepts • MCI is based on established upper level ontologies IHE • cross institutional EHRs • mainly for data exchange • based on standards like HL7, XACML, SAML • granular access rights OpenEHR • interoperability and computability in e-health • formal representation of clinial data • archetypes and templates • use of external terminologies • not in RDF i2b2 SMART Data Model • supplement to the i2b2 datawarehouse • work in progress • should be the basis for i2b2 SMART applications • MCI is based on established upper level ontologies Translational Medicine Ontology (TMO) • data integration for clinical studies • actively worked on by the W3C HCLS interest group • focus on studies, especially with relation to omics data Computer based Patient Record (CPR) • creation of a semantic patient model based on BFO and BioTop • last modification in July 31th • MCI builds upon OGMS • BioTop is not included … … … …
  21. 21. Unrestricted © Siemens AG 2013. All rights reservedPage 21 July 2013 Corporate Technology Related Work (II) Existing data models from horizontal IT providers. Model Motivation Status Difference to MCI Oracle Healthcare Data Model • DWH • implement healthcare specific KPIs for reporting • extended model for BI • many temp. concepts • reporting • more concepts (many for adm.) • focus on hospital organization Teradata Healthcare Logical Data Model • DWH • framework for knowledge applications • “single view of your enterprise” • strategic business and clinical information • administration centric • focus on the hospitals organization IBM Healthcare Provider Data Model • DWH • health analytics • business insights • „innovate and improve the cost, quality and experience of healthcare” • connection to IBM warehousing platforms and BI applications • application modules for “patient care and insights” • administration centric • focus on hospital organization … … … …
  22. 22. Unrestricted © Siemens AG 2013. All rights reservedPage 22 July 2013 Corporate Technology Heiner Oberkampf PhD student Corporate Technology CT RTC BAM KMR-DE Otto-Hahn-Ring 6 81739 München, Deutschland Tel: +49 89 636-37566 Fax: +49 89 636-49438 Mobile: +49 176 49839029 E-mail: heiner.oberkampf.ext@siemens.com Questions ?

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