Describe variables and relationships between variables
Diagnosis(X, anemia)
Male(Y)
Patient(Z)
Six components of FOL
quantifiers
logical connectives
negation
predicates
variables
function
OWL is what kind of knowledge representation?
description logic
for most ontologies, people use ____ to build them
OWL
OWL
Web Ontology Language
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
precise notation for representing noun phrases
description logic
fundamental ontology of description logics
conceptual model is populated by:
individuals
related by binary relationships (roles and features)
grouped into classes (concepts)
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?
Closed-world assumption, give an example
What is not known to be true must be false
Frame-based systems, rule-based systems, FOL
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
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.
Many DLs are _________ of first-order logic (FOL).
decidable fragments
description logic: classification
Classification takes a new Concept and automatically determines all subsumption relations between it and all other Concepts in the network
true/false - description logic: Adds new links when new subsumption relations are discovered
true
DL: automates the placement of new ______ in the taxonomy
concepts
DL: The classifier takes care of where to place a new concept in the ______
hierarchy
DL: All ________ are automatically propagated to the new concept
inheritance relationships
DL: Relationships among a new concept and other entities are automatically simplified by classifying the new concept as a ______ of existing concepts
specialization
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 ____
roles
DL cardinality restrictions
minCardinality, maxCardinality: Must have at least/most X values entered
DL is good for representing...
discrete, clear descriptions of facts/relationships
DL is not good for representing ...
things like multi-valued relations and probabilistic relations (or anything other than descriptions)
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.
Biomedical application that uses DL
SNOMED-CT
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
model
anything used to represent any subject matter in order to help us to understand this subject matter
“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?
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.
The Problem-Oriented Medical Record
Elements of EHR
Dr. Larry Weed
Created new model based on patient problems
1971
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
Controlled terminologies: diseases
ICD-10, ICD-10-CM, DRG
controlled terminologies: Procedures
CPT-5, ICD-10-PCS
controlled terminologies: laboratory tests
LOINC
controlled terminologies: nursing activities
NIC, NOC, HHCC, Omaha
controlled terminologies: drugs
Multum, Micromedex, NDFRT
controlled terminologies: biomedical literature
MeSH
controlled terminologies: clinical documentation
Medcin, Purkinjie
controlled terminologies: cross-references among terminologies
UMLS
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.
SNOMED-CT uses ____ to relate terms
description logic
______ system contains codes for diseases, signs and symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or diseases
ICD code
ICD codes are used for (5 uses)
Disease surveillance and public health
Institutional planning
Quality assurance
Economic modeling
Billing and reimbursement
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 93571...it’s just implied.
Logical Observations, Identifiers, Names and Codes (LOINC)
