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Languages of Medicine

Languages of Medicine. Barry Smith http://ontology.buffalo.edu/smith. Organ. Tissue. 10 -1 m. Cell. Organelle. 10 -5 m. Protein. DNA. 10 -9 m. Organism. Holy Grail of Biomedical Informatics. New Golden Age of Classification. 30,000 genes in human 200,000 proteins

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Languages of Medicine

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  1. Languages of Medicine Barry Smith http://ontology.buffalo.edu/smith

  2. Organ Tissue 10-1 m Cell Organelle 10-5 m Protein DNA 10-9 m Organism Holy Grail of Biomedical Informatics

  3. New Golden Age of Classification • 30,000 genes in human • 200,000 proteins • 100s of cell types • 100,000s of disease types • 1,000,000s of biochemical pathways (including disease pathways)

  4. The problem is: • each (chemical, clinical, pathological, immunological, toxicological, pharmacological, anatomical …) database uses its own classification and its own data dictionary • How overcome the incompatibilities which become apparent when data from distinct sources are combined?

  5. we need to know where in the body we need to know what kind of disease process we need semanticannotation of data = common tags, labels, with definitions and logical structure

  6. cavities • conduits • containers

  7. Systems digestive respiratory circulatory immune skeletal musculatory

  8. What is a System? • quid? substance • quantum? quantity • quale? quality • ad quid? relation • ubi? place • quando? time • in quo situ? status/context • in quo habitu? habitus • quid agit? action • quid patitur? passion

  9. regulation

  10. Systems • have functions • can malfunction • disease • death

  11. pathways

  12. a new discipline is being born

  13. HMS Ontology

  14. The new ontology employs empirical methods Transcriptomics (MIAME Working Group) Proteomics (Proteomics Standards Initiative) Metabolomics (Metabolomics Standards Initiative) Genomics and Metagenomics (Genomic Standards Consortium) In Situ Hybridization and Immunohistochemistry (MISFISHIE Working Group) Phylogenetics (Phylogenetics Community) RNA Interference (RNAi Community) Toxicogenomics (Toxicogenomics WG) Environmental Genomics (Environmental Genomics WG) Nutrigenomics (Nutrigenomics WG) Flow Cytometry (Flow Cytometry Community)

  15. An Interdisciplinary Journal of Ontological Analysis

  16. industrial applications

  17. typical reactions to the founding of a new discipline (e.g. psychology) • struggle for resources • resistance from within philosophy • the new discipline is dismissed by the philosophical mother-discipline as ‘trivial’

  18. typical results of the founding of a new discipline • intensified international cooperation • genuine cooperative work with clear deadlines and goals • shorter deadlines for publication of research results

  19. disciplines are shaped by the age of their establishment: philosophy

  20. disciplines are shaped by the age of their establishment • multinational workgroups coordinated through teleconferences with web-support and working towards specific deadlines • use of fancy equipment (powerpoints ...)

  21. Ontologies are systems of annotationsmost successful example so far:The Gene Ontology(www.geneontology.org)

  22. what cellular component? what molecular function? what biological process?

  23. molecular function biological process cellular component GO’s three ontologies

  24. GO: asymmetric protein localization involved in cell fate commitment

  25. ontologies as graphs • with edges: • is-a (= is a subtype of ) • (copulation is-a biological process) • part-of • (cell wall part-of cell)

  26. GO = a set of standardized textual descriptions • used to annotate (‘tag’) the entities represented in the major biochemical databases which are intelligible to human beings and processable by computers • thereby integrating these databases

  27. Google hits Mar. 2007 (in millions) • ontology 14.2 • ontology + philosophy 1.2 • ontology + data 5.0 • ontology + medicine 1.3 • Gene Ontology 6.9

  28. Gene Ontology • Open Source • Cross-Species • Very useful, in ever new ways • But manifests a series of logical problems

  29. GO:0019836 hemolysis • Definition: The processes that cause hemolysis • X =def. the Y of X • this is worse than circular

  30. UMLS = Unified Medical Language Systemcreated by US National Library of Medicine out of 120 source vocabularies, including the GO

  31. UMLS Semantic Network

  32. UMLS Semantic Network

  33. UMLS Semantic Network • anatomical abnormality associated_with daily or recreational activity • educational activity associated with pathologic function • bacterium causes experimental model of disease

  34. UMLS Semantic Network • Drug Delivery Device contains Clinical Drug • Drug Delivery Device narrower_in_meaning_than Manufactured Object • The use-mention confusion: • “Swimming is healthy and has 8 letters”

  35. GenBank • National Center for Biotechnology Information, Washington DC • gene =def. a DNA region of biological interest with a name and that carries a genetic trait or phenotype

  36. An Ontological Horror Story

  37. HL7 RIM(Health Level 7 Reference Information Model)a set of standards for exchange, integration, sharing, and retrieval of electronic health information

  38. … based on speech act theory • the medical record is not a collection of facts, but "a faithful record of what clinicians have heard, seen, thought, and done" [based on] what is known as "speech-acts" in linguistics and philosophy.

  39. The Ontology of HL7 RIM • Act as statements or speech-acts are the only representation of real world facts or processes in the HL7 RIM. • The truth about the real world is constructed through a combination (and arbitration) of such attributed statements only,

  40. The Ontology of HL7 RIM • “… and there is no class in the RIM whose objects represent "objective states of affairs" or "real processes" independent from attributed statements. • As such, there is no distinction between an activity and its documentation. Every Act includes both to varying degrees.”

  41. HL7 RIM (Ballot September 2004) • Act = record of an Act (1.5.1) • Act = intentional action (3.1.1) • document is a subclass of structured document (2.2.3) • (Compare: number is a special type of prime number) • HL7 RIM approved on this basis as ISO Standard by the International Standards Organization

  42. HL7 RIM • Animal • Definition: A subtype of Living Subject representing any animal-of-interest to the Personnel Management domain. • LivingSubject • Definition: A subtype of Entity representing an organism or complex animal, alive or not.

  43. HL7 RIM • Person • Definition: A Living Subject representing single human being [sic] who is uniquely identifiable through one or more legal documents • – impossible to refer to undocumented persons

  44. HL7 RIM • Individual Allele =def. • Act of Observation of an Individual Allele • Disease =def. Act of observation of a disease • Diagnosis =def. Act of observation of an Act of observation • WHY IS THIS IMPORTANT?

  45. HL7 Corporate Sponsors:GE IBMMicrosoft Oracle SiemensSun MicrosystemsErnst & Young Eli Lillyetc. etc.

  46. HL7 International Affiliates

  47. HL7 Merchandizing

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