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Documenting the semantics of medical data

This paper discusses the MediGrid project, a modular application system for distributed processing of health-related data based on Grid technology. It explores the structure of medical data, including indicators and modules, as well as the description of data and their relations using traditional systems and ontologies. The MediGrid Documentation Service is introduced as a means of addressing the problem of unambiguous description of data and algorithms, serving as a network for sharing unique knowledge.

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Documenting the semantics of medical data

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  1. Documenting the semantics of medical data Adela Jarolimkova, Petr Lesny, Krystof Slaby, Helena Bouzkova, Jan Vejvalka 10th European Conference of Medical and Health Libraries, Cluj-Napoca, 11th - 16th September 2006

  2. MediGrid project • 2005 - 2009 • Partners • CESNET (Czech national research and education network operator) • Faculty Hospital Motol - Prague • Masaryk Hospital - Ustí nad Labem • Main goal • to propose and test MediGrid – a modular application system for distributed processing of health-related data based on Grid networkas the integrating technology 10th European Conference of Medical and Health Libraries, Cluj-Napoca, 11th - 16th September 2006

  3. MediGrid structure - data and indicators • Medical data are described as indicators – to underline their subjective nature • Why not data records? • the term data record is quite overloaded while we need a term with a clearly defined meaning • in the term indicator the subject taking the record is also reflected • Transformations • Indicator classes 10th European Conference of Medical and Health Libraries, Cluj-Napoca, 11th - 16th September 2006

  4. MediGrid structure - modules • Module • Automated tool for indicators tranformation • Relation among indicator classes • Each module implements one relation – algorithm, expert consultation, conference of experts • MediGrid structure • Modules • Sorter • Documentation service 10th European Conference of Medical and Health Libraries, Cluj-Napoca, 11th - 16th September 2006

  5. Description of data and their relations – traditional systems • Terminological and classification systems (MeSH, ICD etc.) • Hierarchical structure • Relations – taxonomic, synonymic, meronymic • Main problem – limited number of relation types, insufficient for describing complex relationships in algorithmic medicine 10th European Conference of Medical and Health Libraries, Cluj-Napoca, 11th - 16th September 2006

  6. Description of data and their relations - ontologies • Ontologies • „explicit specification of conceptualization“ • Medical ontologies • „old“ systems – SNOMED, UMLS • Cover the whole field of medicine, but contain many inconsistencies and inaccuracies as described in literature • „new“ systems – OpenGalen, On9 • Maintain formal ontology rules, but structured from the top, whereas concepts belonging to algorithmic medicine are typically very „low-level“ 10th European Conference of Medical and Health Libraries, Cluj-Napoca, 11th - 16th September 2006

  7. Description of data and their relations - example • Description of BMI module using UMLS MetaThesaurus and Semantic Network • Body Mass Index calculation • Inputs – body weight, body height • Output – body mass index • Corresponding Metathesaurus Concepts • Body mass index calculation – no such concept • Body weight - cui C0005910 • Body height - cui C0005890 • Body mass index - cui C1305855 10th European Conference of Medical and Health Libraries, Cluj-Napoca, 11th - 16th September 2006

  8. Description of data and their relations – example cont. • Corresponding semantic types • Organism attribute • Clinical attribute • Quantitative concept • Relations between semantic types • Is_a • Degree_of • Associated_with • X body_mass_index_calculation • X is_input_of, is_output_of 10th European Conference of Medical and Health Libraries, Cluj-Napoca, 11th - 16th September 2006

  9. MediGrid Documentation Service • Tasks • to address the problem of unambiguous description of data and algorithms • to prove evidence / credibility for modules • to serve as a mean of scientific communication between individual specialists • to serve as a network for sharing unique knowledge 10th European Conference of Medical and Health Libraries, Cluj-Napoca, 11th - 16th September 2006

  10. DS metadata • Basic entity categories • Modules • Indicator classes • Citations • Concepts (primarily UMLS, other controlled vocabularies are allowed)/ module title, author code, structured description with relevant citations • Kept in a machine-readable (database) format • Presented to users in application-specific views 10th European Conference of Medical and Health Libraries, Cluj-Napoca, 11th - 16th September 2006

  11. external resources PubMed modules documentation 1:11 fulltext citations indicator classes shared comments 1:1 DS scheme documentation service catalogue 10th European Conference of Medical and Health Libraries, Cluj-Napoca, 11th - 16th September 2006

  12. DS ontology • „ad-hoc“ ontology generated from the machine-readable documentation • Contains only entities(indicator classes and modules) currently existing and documented and their relationships • Changes every time a new knowledge element (algorithm) is implemented 10th European Conference of Medical and Health Libraries, Cluj-Napoca, 11th - 16th September 2006

  13. Citations in DS • used to confirm the value and credibility (evidence-base) of implemented algorithms • Application for citation handling similar to simple reference manager • allows to save a record of any published or unpublished information, both manually and by acquiring the record from an external database • to insert the citation into documentation • to interconnect the citation with some external resource 10th European Conference of Medical and Health Libraries, Cluj-Napoca, 11th - 16th September 2006

  14. Citation record format • Based on XML • Allows citing any published or unpublished information in any form (print or electronic) • Supports evaluation of quality and relevance • Conforms with Vancouver requirements • Allows arbitrary extending to meet the needs of DS • Compatible especially with PubMed 10th European Conference of Medical and Health Libraries, Cluj-Napoca, 11th - 16th September 2006

  15. Conclusion • Documentation service in this proposed form is now being implemented within the framework of the MediGrid project • Its functionality, especially the use of ad-hoc generated ontologies for processing of health-related data, will then be tested – as a novel approach to unambiguous representation of medical knowledge, readily available for exploitation in computerized information systems. 10th European Conference of Medical and Health Libraries, Cluj-Napoca, 11th - 16th September 2006

  16. Thank you for your attention Any questions? Contacts: http://www.medigrid.cz ajarolimkova@seznam.cz petr.lesny@lfmotol.cuni.cz 10th European Conference of Medical and Health Libraries, Cluj-Napoca, 11th - 16th September 2006

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