Medical informatics

Lecture 2
Formalising clinical data and medical
knowledge, Clinical coding systems, Formal
knowledge representation
if time formalising research results

Creating and using medical

knowledge
Understanding
Understanding
diseases and
diseases and
their treatment
their treatment

Develop
Develop
and test
and test
treatments
treatments

Health
Records
Service delivery,
Service delivery,
performance
performance
assessment
assessment

Ensure right
Ensure right
Patients receive
Patients receive
right
right
intervention
intervention

 using medical knowledge

Understanding
Understanding
diseases and
diseases and
their treatment
their treatment

Develop
Develop
and test
and test
treatments
treatments

Health
Records
Service delivery,
Service delivery,
performance
performance
assessment
assessment

Ensure right
Ensure right
Patients receive
Patients receive
right
right
intervention
intervention

Standardising clinical terms

Very difficult to use ordinary medical language
in computer systems

Extremely complex vocabulary.

Terms often vague and imprecise.
Same disease known by several names or expressions
(synonymy).
A single term may have several meanings according
to the context (polysemy).

Addressed by adopting formal coding and

classification systems.

Formal coding and classification systems

Different systems use same code or term in same way
Unique codes, precisely defined coding process

Benefits include abilities to

Share data between many systems
Gather data about diseases/treatments from many sources.
Deliver reminders, alerts and other information to clinicians
based on standardised clinical patterns or situations
Identify eligible patients for recruitment into clinical trials based
on well-defined criteria
Search professional literature based on standard queries

and many other benefits

Coding systems
International Classification of Diseases (ICD)
Diagnosis Related Groups (DRGs)
Standard Nomenclature for Medicine (SNOMED)
Logical Observation Identifiers Names and Codes
(LOINC)
Medical Subject Headings (MeSH)
Specialised coding systems

National Cancer Institute

Centre for Disease Control

WHO ICD
The International Classification of Diseases has
been used since 1853 to classify diseases and
other health problems recorded on many types
of records, including death certificates and
health records
In addition to enabling the storage and retrieval
of diagnostic information for clinical,
epidemiological and quality purposes, ICD also
provides a basis for the compilation of national
mortality and morbidity statistics by WHO
Member States (e.g. AIDS, swine flu).

International Classification of Diseases

I. Certain infectious and parasitic diseases
II. Neoplasms
III. Diseases of the blood and blood-forming organs, immune mechanism
IV. Endocrine, nutritional and metabolic diseases
V. Mental and behavioural disorders
VI. Diseases of the nervous system
VII. Diseases of the eye and adnexa
VIII. Diseases of the ear and mastoid process
IX. Diseases of the circulatory system
X. Diseases of the respiratory system
XI. Diseases of the digestive system
XII. Diseases of the skin and subcutaneous tissue
XIII. Diseases of the musculoskeletal system and connective tissue
XIV. Diseases of the genitourinary system
XV. Pregnancy, childbirth and the puerperium
XVI. Certain conditions originating in the perinatal period
XVII.Congenital malformations, deformations and chromosomal abnormalities
XVIII.Symptoms, signs and abnormal clinical and laboratory findings, not elsewhere classified
XIX. Injury, poisoning and certain other consequences of external causes
XX. External causes of morbidity and mortality
XXI. Factors influencing health status and contact with health services
XXII.Codes for special purposes

ICD family of disease and health

related classifications
Primary
healthcare
Information
Support

Other
healthcare
related
classifications

3-character core

Speciality codes

Diagnoses
Symptoms
Abnormal Lab
findings
Injuries and
poisonings
External causes of
morbidity and
mortality
Factors influencing
health status

oncology

dentistry
dermatology
psychology
neurology
obstetrics & gynaecology
rheumatology &
orthopaedics
general medical practice

International
Nomenclature
of Diseases

ICD-10
Uses an alphanumeric code that indicates
the location of the concept within a
disease hierarchy.
L93 Lupus erythematosus.
Excludes exedens A18.4, vulgaris A18.4 . . .
Use additional external cause code, if drug
induced.

L93.0 Discoid lupus erythematosus

L93.1 Subcutae cutaneous lupus
erythematosus

Diagnosis Related Groups

DRGs developed for relating the type of patients
a hospital treats (case mix) to treatment costs
All discharged patients in US classified into a
DRG
a limited, clinically coherent set of patient classes
based on age, sex, principal diagnosis, secondary
diagnoses, surgical procedures, and discharge status

All patients are unique but groups of patients

have common demographic, diagnostic and
therapeutic attributes that determine resource
needs.

DRGs
1
2
24
25
26
1

HYPERTENSIVE ENCEPHALOPATHY
23NONTRAUMATIC STUPOR & COMA
SEIZURE & HEADACHE AGE >17 WITH COMPLICATIONS, COMORBIDITIES
(prior to 10-1-06)
SEIZURE & HEADACHE AGE >17 WITHOUT COMPLICATIONS,
COMORBIDITIES (prior to 10-1-06)
SEIZURE & HEADACHE AGE 0-17
TRAUMATIC STUPOR & COMA, COMA >1 HR

TRAUMATIC STUPOR & COMA, COMA <1 HR AGE

>17 WITH COMPLICATIONS, COMORBIDITIES

29 TRAUMATIC STUPOR & COMA, COMA <1 HR AGE >17 WITHOUT

COMPLICATIONS, COMORBIDITIES
30 TRAUMATIC STUPOR & COMA, COMA <1 HR AGE 0-17
31 CONCUSSION AGE >17 WITH COMPLICATIONS, COMORBIDITIES
32 CONCUSSION AGE >17 WITHOUT COMPLICATIONS, COMORBIDITIES

The Systematized NOmenclature of

MEDicine (SNOMED)
Intended to be a general purpose,
comprehensive and computerinterpretable terminology
To represent and index virtually all of the
events found in the medical record

SNOMED code for tuberculosis

DE-14800

X-referencing

Tuberculosis
Bacterial infections
E = Infections or parasitic diseases
D = Disease or diagnosis
X-ref e.g. living organism, morphology, function

Logical Observation Identifiers

Names and Codes (LOINC)
A database and universal standard for
identifying medical laboratory observations.
Applies universal code names and identifiers to
medical terminology
For use in
gathering of clinical results (such as laboratory tests,
clinical observations, outcomes management and
research)
electronic data exchange
electronic health records

LOINC
LOINC currently includes over 58,000 terms
A unique 6-part name is given to each test or
observation.
Each database record includes six fields
Component- what is measured, evaluated, or observed
Kind of property - e.g. length, mass, volume, time stamp
Time interval over which observation or measurement made
System - or specimen type within which observation was made
Scale - quantitative, ordinal, nominal or narrative
Method procedure used to make measurement or observation

Problems with coding systems

Terms are subjective, often vague, imprecise
Codes often ad hoc (e.g. no systematic
relationship between code and medical concepts
and their uses)
Context dependent (e.g. normal BP)
Evolve over time

Mapping between systems difficult

Computers dont understand them we need
to capture meaning rather than use ad hoc
codes

Formalising medical concepts

Understanding
Understanding
diseases and
diseases and
their treatment
their treatment

Develop
Develop
and test
and test
treatments
treatments

Health
Records
Service delivery,
Service delivery,
performance
performance
assessment
assessment

Ensure right
Ensure right
Patients receive
Patients receive
right
right
intervention
intervention

Formalising medical concepts

Models

Rules
breast cancer IS_A
reproductive system and breast disorder

Relationships

Concepts
DF-400DB

Symbols

breast cyst
breast lump
breast cancer

SNOMED CT
All concepts (except the root) are the
source of at least one ISA(subtype)
relationships

Concept
Concept

A concept is described
in one or more
descriptions

Relationship
Relationship

For example the concept "headache (finding)"

in SNOMED CT includes:

A conceptId (25064002),
A set of descriptions
Description
Description
("headache", "pain in head", etc.)
A set of relationships ("is a"="pain",
"finding site"="head structure", etc.).

Unified Medical Language System

Links the major international terminologies into a
common structure, providing a translation mechanism
between them.
Designed to aid in the development of systems that

retrieve and integrate electronic biomedical information from

a variety of sources
permit linkage between disparate systems, including electronic
patient records, bibliographic databases and decision support
systems.

UMLS is the Rosetta Stone of international

terminologies
A long term research goal is to enable computer systems
to understand medical concepts.

UMLS semantic network

The UMLS Semantic Network allows for the semantic
categorization of a wide range of terminologies in
multiple domains.
Major groupings of semantic types include

organisms,
anatomical structures,
biologic function,
chemicals,
events,
physical objects, and
concepts or ideas.

Links between semantic types represent important

relationships in the biomedical domain.

UMLS Meta-thesaurus
Uniform format for over 100 biomedical
vocabularies and classifications
Organised by concept as a web rather than a tree,
linking alternative names and views together and
identifying useful relationships.

Components retain original structure.

Each concept has attributes that define its meaning (e.g.
semantic types or categories to which it belongs, a
definition).
Clinical
concept

UMLS

ICD-10

SNOMED

SNOMED CT

Chronic
ischaemic
heart disease

448589

125.9

14020

84537008

UMLS semantic network

Links between semantic types represent
important relationships in the biomedical
domain.
Primary link:

the isa link which establishes the hierarchy of

types within the network
Secondary non-hierarchical relationships

grouped into five major categories: physically

related to, spatially related to, temporally related
to, functionally related to, conceptually related to.

UMLS semantic network

Content
For each semantic type:

a unique identifier, a tree number indicating

its position in an isa hierarchy, a definition,
and its immediate parent and children.
For each relationship:

a unique identifier, a tree number, a definition,

and the set of semantic types that can
plausibly be linked by this relationship.

Terms and ontologies

http://bioportal.bioontology.org/

Emulating clinical expertise

Expert systems offer an engineering discipline that involves integrating
[human] knowledge into computer systems to solve complex problems
normally requiring a high level of human expertise"

Successful early demonstrations were developed in chemistry, medicine, various

fields of engineering (e.g. Banares-Alcantaras work on design of chem eng.
plant).

Key features distinguished expert systems from conventional software.

Explicit, declarative representation of knowledge: capture what an agent needs to
know without assuming how that knowledge is to be used in any particular
situation.
Domain-specific heuristics rather than general algorithms; said to resemble human
expertise more closely than algorithmic methods.

Formalising medical concepts

Models
Lump and pre-menopausal implies possible breast cancer

Rules
breast cancer is_a
reproductive system and breast disorder

Relationships

Concepts
DF-400DB

Symbols

breast cyst
breast lump
breast cancer

Formalising medical concepts

Models

pre-menopausal woman has possible breast cancer (scenario)

investigation of possible breast cancer (process)

Lump and pre-menopausal implies possible breast cancer

Rules
breast cancer is_a
reproductive system and breast disorder

Relationships

Concepts
DF-400DB

Symbols

breast cyst
breast lump
breast cancer

Clinical research and

evidence-based medicine
NIH 1975

February 2010

Centre for Doctoral Training

Levels of evidence

February 2010

Centre for Doctoral Training

Evidence-based medicine
The practice of EBM has five steps:
1. Convert need for information about prevention,
diagnosis, prognosis, therapy, causation etc. into an
answerable question
2. Track down the best evidence to answer the question
3. Critically appraise the evidence for validity and
applicability
4. Integrate the critical appraisal with our clinical expertise
and our patients unique biology, values and
circumstances
5. Evaluate our performance.

Medical research, clinical practice

Understanding
Understanding
diseases and
diseases and
their treatment
their treatment

Develop
Develop
and test
and test
treatments
treatments

Health
Records
Service delivery,
Service delivery,
performance
performance
assessment
assessment

Ensure right
Ensure right
Patients receive
Patients receive
right
right
intervention
intervention

The clinical trial is the most definitive tool for

evaluation of the applicability of clinical research.

Phase I
Ascertain Maximum
Tolerated Dose (MTD)

Phase III
Assess the effectiveness
of a new intervention
February 2010

Phase II
Estimate effect and rate of
adverse events

Phase IV

Long-term studies of
licensed interventions

Centre for Doctoral Training

February 2010

Centre for Doctoral Training

IT for evidence-based medicine

Formalising research results

treatment comparison formulas

IT for evidence-based medicine

IT for evidence-based medicine

Medical research, clinical practice

Understanding
Understanding
diseases and
diseases and
their treatment
their treatment

Develop
Develop
and test
and test
treatments
treatments

Health
Records
Service delivery,
Service delivery,
performance
performance
assessment
assessment

Lecture 3
Ensure right
Ensure right
Patients receive
Patients receive
right
right
intervention
intervention