modeling biomedical systems IV

  1. FOL
    first order logic
  2. FOL quantifiers
    for all, there exists
  3. FOL logical connectives
    and, or, exclusive or, implies
  4. FOL predicates
    • Describe variables and relationships between variables
    • Diagnosis(X, anemia)
    • Male(Y)
    • Patient(Z)
  5. Six components of FOL
    • quantifiers
    • logical connectives
    • negation
    • predicates
    • variables
    • function
  6. OWL is what kind of knowledge representation?
    description logic
  7. for most ontologies, people use ____ to build them
  8. OWL
    Web Ontology Language
  9. Four advantages of description logic
    • Open-world assumption: Just because something hasn’t been said yet, doesn’t mean it is not true
    • Automatic classification of new concepts
    • Automatic identification of redundant concepts
    • Ease of customization when customers require specialized terms
  10. precise notation for representing noun phrases
    description logic
  11. fundamental ontology of description logics
    • conceptual model is populated by:
    • individuals
    • related by binary relationships (roles and features)
    • grouped into classes (concepts)
  12. Three uses of description logic:
    • 1. subsumption: is category C1 a subset of C2?
    • 2. classification: does object O belong to C?
    • 3. satisfiability: can category C ever be instantiated?
  13. Closed-world assumption, give an example
    • What is not known to be true must be false
    • Frame-based systems, rule-based systems, FOL
  14. open-world assumption, give an example
    • Unstated things are unknown
    • Just because someone hasn’t said it yet, doesn’t mean it isn’t true
    • Description logic uses an open-world assumption
  15. ​If we had an OWL (description logic) knowledge base that contained only a statement that said “all cats are animals”, what would we conclude about a new statement that says “all cats are soft”?
    This new statement is not entailed from the current knowledgebase, but it is not contradicted by it either. Since we’re using OWL, which is based in DL, and the open­world assumption holds in DL, then we accept the new statement into the knowledgebase as true, but can’t conclude anything more about animals.
  16. Many DLs are _________ of first-order logic (FOL).
    decidable fragments
  17. description logic: classification
    Classification takes a new Concept and automatically determines all subsumption relations between it and all other Concepts in the network
  18. true/false - description logic: Adds new links when new subsumption relations are discovered
  19. DL: automates the placement of new ______ in the taxonomy
  20. DL: The classifier takes care of where to place a new concept in the ______
  21. DL: All ________ are automatically propagated to the new concept
    inheritance relationships
  22. DL: Relationships among a new concept and other entities are automatically simplified by classifying the new concept as a ______ of existing concepts
  23. DL restrictions: Each individual of a concept will have certain _____ (aka Data Properties and Object Properties). We can put restrictions on the type of data and objects linked together with these ____
  24. DL cardinality restrictions
    minCardinality, maxCardinality: Must have at least/most X values entered
  25. DL is good for representing...
    discrete, clear descriptions of facts/relationships
  26. DL is not good for representing ...
    things like multi-valued relations and probabilistic relations (or anything other than descriptions)
  27. two examples of limitations of DL in biomedical applications
    • A patient may have some subset of symptoms but its not clear how many of the symptoms a patient needs before they reach a diagnosis. Some symptoms may be more important than others. 
    • A patient’s symptoms give clues about the probability of disease more often than they definitively denote a disease.
  28. Biomedical application that uses DL
  29. semantics and the "meaning triangle"
    • There is an object/thing in the real world (e.g. Down Syndrome)
    • We have a mental concept for what that object is
    • We have a symbol to represent that object and how we conceive it so that we can communicate the thought of the object to other people and to computers
    • For example, it could be an instance of the class Developmental Disease and have certain symptom properties
  30. model
    anything used to represent any subject matter in order to help us to understand this subject matter
  31. “Competency questions”
    • Provide a good start for building a model
    • Use to limit the scope of the model
    • Which wine characteristics should I consider when choosing a wine?
    • Is Bordeaux a red or white wine?
  32. What is MIAME?
    • Minimum Information About a Microarray Experiment
    • Describes the minimum information required to ensure that microarray data can be easily interpreted and that results derived from its analysis can be independently verified.
    • The ultimate goal of this work is to establish a standard for recording and reporting microarray-based gene expression data, which will in turn facilitate the establishment of databases and public repositories and enable the development of data analysis tools.
  33. The Problem-Oriented Medical Record
    • Elements of EHR
    • Dr. Larry Weed
    • Created new model based on patient problems
    • 1971
  34. What does SOAP stand for?
    • S: subjective data
    • O: objective data
    • A: assessment
    • P: plan
    • Every problem is numbered
    • Description of problem may change over time with new information
    • Number for each problem never gets recycled
  35. Controlled terminologies: diseases
    ICD-10, ICD-10-CM, DRG
  36. controlled terminologies: Procedures
    CPT-5, ICD-10-PCS
  37. controlled terminologies: laboratory tests
  38. controlled terminologies: nursing activities
    NIC, NOC, HHCC, Omaha
  39. controlled terminologies: drugs
    Multum, Micromedex, NDFRT
  40. controlled terminologies: biomedical literature
  41. controlled terminologies: clinical documentation
    Medcin, Purkinjie
  42. controlled terminologies: cross-references among terminologies
  43. What is SNOMED Clinical Terms (SNOMED CT)?
    A systematically organized collection of medical terms providing codes, terms, synonyms and definitions used in clinical documentation and reporting.
  44. SNOMED-CT uses ____ to relate terms
    description logic
  45. ______ system contains codes for diseases, signs and symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or diseases
    ICD code
  46. ICD codes are used for (5 uses)
    • Disease surveillance and public health
    • Institutional planning
    • Quality assurance
    • Economic modeling
    • Billing and reimbursement
  47. Current Procedural Terminology (CPT)
    • Provides a code for every type of medical procedure
    • Relationships between codes are implicit
    • Example: Code 93571 codes for an intravascular doppler measurement during a coronary angiogram. Then Code 93572 is the code for each additional vessel that you measure after measuring the first one. The definition of Code 93572 does not make any explicit mention of Code’s just implied.
  48. Logical Observations, Identifiers, Names and Codes (LOINC)
    • Standardized terminology for lab tests
    • Codes enumerate highly structured attributes of laboratory observations (e.g., substance measured, analytical method used)
    • No hierarchical organization
  49. Unified Medical Language System (UMLS)
    provides a way to unify all of the other ontologies (diseases, procedures, lab tests, etc)
  50. UML uses _____ semantics to define relative equivalence of concepts and relationships among concepts
  51. UML provides a metathesaurus of more than 40 “source terminologies,” with more than 331,000 terms. Provides a ____ for each entry
    Concept Unique Identifier (CUI)
Card Set
modeling biomedical systems IV
modeling biomedical systems