NOMENCLATURES IN E-HEALTH Drs. Sven Van Laere Personal Sven VAN LAERE 3 rd year PhD – Research in…

NOMENCLATURES IN E-HEALTHDrs. Sven Van Laere

Personal

• Sven VAN LAERE• 3rd year PhD– Research in nomenclatures in

eHealth systems in Belgium relatedto pharmacy

Promotor: Prof. Dr. M. Nyssen

• Previous– MSc in Engineering: Computer Science (2013)– Professional Bachelor in Applied Informatics (2010)

Content Table

• Definition

• Clinical ideas

• History

• Nomenclatures in e-health

• “Coding”

Definition

• Nomenclature– Nomen - name– Calare - to call

• Definition– A system of names used in a science, as of

anatomical structures or biological organisms

Clinical idea

• Clinical idea comprise everything we think we know about health, illness, prevention, investigation, and treatment

• Clinical ideas are the building blocks of a personal health record

• Connected clinical ideas are essential for a connected health service

Clinical idea?

• Diseases• Organisms• Operations• Procedures • Devices • Drugs • Part of the body• …

Working with clinical ideas• Anyone involved in delivering healthcare• Recognition, manipulation and interconnection of clinical

ideas is a necessary part of the practice of any clinical discipline

• Growth of knowledge requires new clinical ideas to be developed, expressed and tested

• Effective delivery of high-quality health care requires clinical ideas to be shared in ways that…– Enhance the quality of the patient care– Facilitate the growth of clinical knowledge– Demonstrably deliver value to money

Problem

• It seems very simple– Clinical ideas are important– We need to share them

• What’s the problem?– Hasn’t this problem already been solved?– Can coding help to this?

Background

• Coding is needed– Variety of representing a clinical concept

• Example: coronary heart disease– Diagnosis of myocardial infarction– Raised cardiac enzymes– Myocardial ischaemia– Tripple vessel coronary artery disease– …

Why

• Need for a uniform way of expressing– Audit– NLP has not reached the point where free text can

be automatically turned into codes– Scientific research– Clinical decision support– …

History – Text based records• 1970 – floppy disk invented

– IBM introduced a pilot system in GP practice in Exeter, UK• 1976 – inktjet printer invented, VHS video tape introduced

– ICL launched GP system in Otterly St Mary, Exeter, UK– 1980: Text based patient records stored on mainframe computer

• expensive pilot project– Patient records linked by landlines– Free text allowed users to express clinical ideas

• Easy for data entry• Problem with retrieval

History – Flags to indicate clinical ideas

• 1982 – compact disks first released– New Abies computer system– System allowed each practice to specify a set of 96

important clinical ideas and link them to a patient record

Shared codes for each practice?

History – Coding clinical ideas

• 1983 – Lotus 1-2-3 spreadsheet arrived– Memory got a bit cheaper– Dated coded entries are added to the system– The codes are symple mnemonics with no structure

Links between similar ideas?

=> Still hard to query the data

History – Organising clinical ideas

• 1984– Read Codes released (named after James Read)

• Hierarchical set of codes• Retriaval based on hierarchy

History – Organising clinical ideas

• 1986 – late 1990’s there was a wider use of clinical systems using coded data– Read codes in the UK, SNOMED in the US, ICD-9

classification codes in several countries– The scope of coverage was broadening according to

scientific improvements– Codes served a useful purpose and continued to be used– However growing awareness of limitations in simple

approaches to codes and hierarchies

History – Organising clinical ideas

• 1986 – late 1990’s there was a wider use of clinical systems using coded data– Read codes in the UK, SNOMED in the US, ICD-9

classification codes in several countries– The scope of coverage was broadening according to

scientific improvements– Codes served a useful purpose and continued to be used– However growing awareness of limitations in simple

approaches to codes and hierarchies

Limitations to code-based hierarchies

• In a code-based hierarchy errors cannot be corrected without changing the code– Either the hierarchy stays “wrong” or the code must

change• For example– The read code hierarchy suggest that otis media is a type

of “nervous system and sense organ disease”

F: Nervous system and sense organ diseaseF5: Ear disease

F52: Suppurative and unspecified otitis media

Limitations to code-based hierarchies

• Suppurative otitis media (middle ear infection) is not a disorder of the nervous system– The condition is not a disorder of the nerves or sensors of the ear– The middle ear belongs anatomically to the respiratory tract

Þ Logically middle ear infections are a type of respiratory tract infection

F: Nervous system and sense organ diseaseF5: Ear disease

F52: Suppurative and unspecified otitis media

Limitations to code-based hierarchies

• Idea of polyhierarchy popped up– A simple hierarchy is a tree

• Every node has one parent node– Exception: Most upper parent node (concept)

– Example• Suppurative acute otitis is… (POLYHIERARCHY)

– An ear disease– An infectious disease

F: Nervous system and sense organ diseaseF5: Ear disease

F52: Suppurative and unspecified otitis media

Limitations to code-based hierarchies

• Need for non-hierarchical relations– Suppurative otitis media

• Is caused by “bacteria”but … is not a type of bacteria

• Occurs in the “middle ear”but … is not a type of middle ear

F: Nervous system and sense organ diseaseF5: Ear disease

F52: Suppurative and unspecified otitis media

ICPC

• International Classification of Primary Care

• Author: WONCA Int. Class. Committee

• Two versions:– 1987: ICPC-1– 1998: WHO

(accepted within WHO)

ICPC structure

• bi-axial

• One axis: 17 chapters with an alpha code based on body systems/problem areas

• Second axis: 7 identical components, with rubrics bearing a two-digit numeric code

ICPC’s 17 chapters• A General and unspecified

• B Blood, blood forming organs, lymphatics, spleen

• D Digestive

• F Eye

• H Ear

• K Circulatory

• L Musculoskeletal

• N Neurological

• P Psychological

• R Respiratory

• S Skin

• T Endocrine, metabolic and nutritional

• U Urology

• W Pregnancy, childbirth, family planning

• X Female genital system and breast

• Y Male genital system

• Z Social problems

ICPC’s componentsSymptoms and complaints 1-29Diagnostic and preventive procedures 30-49Treatment procedures, medication 50-59Test results 60-61Administrative 62Referral and other reasons for encounter 63-69Diseases: 70-99

- infectious diseases- neoplasms- injuries

- congenital anomalies- other specific diseases

ICPC example

• HeartburnCode: D03

Chapter D: DigestiveComponent 1: Symptom / Complaint

• PneumoniaCode: R81

Chapter R: RespiratoryComponent 7: Disease

Read Codes• Set of clinical codes designed for Primary Care to record

the every day care of a Patient

• Used in United Kingdom

• Developed by Dr James Read (GP, Loughborough)

• Recognized standard for General Practice

• Hierarchical structure

Key aspects of Read Codes

• Sorted into categories and chapters

• Hierarchical structure

• Combination of letters and numbers

• CaSe-SeNsItIve

• Version 1: Maximum of 4 characters (1983)Version 2: Maximum of 5 characters (1985)

Read Code chapters• Diagnoses

– Codes all begin with a capital letter– e.g. H33 (Asthma), C10E (Type 1 diabetes mellitus)

• Processes of Care– Codes all begin with a number– Used to record history, symptoms, examinations, tests, screening, operations and

patient administration, etc– e.g. 44P (Serum cholesterol), 65E (Influenza vaccination)

• Medication– Codes all begin with a small case letter– Automatically entered into the patient record when any treatment is prescribed– e.g. bu25 (Aspirin 75mg tablets)

Read Code chaptersExample:C Endocrine, nutritional, metabolic and immunity disordersC1 Other endocrine gland diseasesC10 Diabetes mellitusC10E Type 1 diabetes mellitusC10E7 Type 1 diabetes mellitus with retinopathy

• Could refer to these as “families” of codes – Parent and Child Codes• C10 is a parent code to C10E. It is also a child code to C1• Each code begins the same way as the one before but contains an

extra layer of detail• This pattern repeats across all chapters• Enables data to be entered at the required level of detail

Read version 3, Clinical Terms

• 1994: CTv3– Read version 3, clinical terms– Clinical Terms version 3

• Intention: develop terminology that could include specialist practice

• Used in small minority in UK

• Merged with SNOMED => SNOMED CT

ICD

• International Classification of Diseases (and Health Related Problems)

• Long history and many revisions

• Possibly suffixes– CM: Clinical Modifications (e.g. ICD-9-CM)– PCS: Procedure Classification System(e.g. ICD-10-PCS)

ICD

• End 2014- begin 2015: step-over to ICD-10– Start in Belgium: January, 2015

SNOMED

• In 1965– SNOP was developed by the College of American

Pathologists (USA)• Next 50 years– several changes on …

• … the number of concepts• … the covered domains • … the underlying representation formalism…

• Result: Systematized Nomenclature of Medicine, Clinical Terms (SNOMED CT) released in 2002

SNOMED CT

• Controlled coded clinical terminology for use in Electronic Health Records

• Helps in adding meaning to the HER

• SCT maintained and distributed by the IHTSDO since 2007

SNOMED CT

• Controlled coded clinical terminology for use in Electronic Health Records

• Helps in adding meaning to the EHR

• SCT maintained and distributed by the IHTSDO since 2007

SNOMED CT

• Concept components– Concepts– Descriptions– Relationships

• Concepts CONCEPT

Fully Specified Name (FSN)Identifier

SNOMED CT

• Concept – Own unique identifier• Numeric identifier of up to 18 digits• Used to refer between concepts

• Description types– All concepts have …• At least one fully specified name• At least one synonym

CONCEPT80146002

Preferred terms

SNOMED CT

• Relationships– Each concept is associated with other concepts by a set of

relationships– Expressing the defining characteristics of a concept

CONCEPT CONCEPT

CONCEPT

is a subtype of

[attribute] has value

SNOMED CT

• Relationships– Subtype relationships

• Create a hierarchy linking each concept to more general concepts• Enable retrieval of specific concepts in response to general concepts

All the supertypes of appendectomy

SNOMED CT

• Relationships– Attribute relationships• Provide additional defining information about concepts

– Why is it different from its supertype– E.g. sites, causative agents, …

SNOMED CT

• Pre- and post-coordination– Pre-coordination

Terminology producer provides a single conceptid for the meaning

• 31978002–means “fracture of tibia”

SNOMED CT

• Pre- and post-coordination– Post-coordination

A user composes a combination of conceptids to representthe meaning

• 31978002 : 272741003 = 7771000– (fracture of tibia : laterality = left)– In human readable form …

“fracture of left tibia”

SNOMED CT

• Which one is best to use?

?

SNOMED CT

• Which one is ‘best’ to use?

Pre-coordination Post-coordination

PRO’s

CON’s

- Single term use- Syntax is linked to semantics

- Overuse of terms- Long uninterpretable strings

- Need for powerful engine (complex)

- Short vocabulary: each concept once- Terms are easier to understand

Relationship All included in UMLS

All crossed with Snomed-Ct

ICPCICD9

ICD10

“Coding”

• Code…… is a representation applied to a term so that it can be more readily processed.

• Classification…… is an arrangement of all elements of a domain, into groups according to established criteria.

• Nomenclature…… is an arrangement of concepts, that can be combined according to specific rules to form more complex concepts.

2005, S. De Ludignan: Codes, classifications, terminologies and nomenclatures

“Coding”

Codes

Classifications

Nomenclatures

+ logical groupings(…is a… relationship)

+ polymorphism+ characteristics

Codes

Classifications

Nomenclatures

ICPC

Read

ICD

SNOMED

Sources• Papers

– 2005, S. De Ludignan: Codes, classifications, terminologies and nomenclatures

– 2006, R. Cornet: A framework for characterizing terminological systems

• Presentations– IHTSDO: Why Clinical Terminology Matters– Health Informatics: Terminology and classification

• Videos– What is ICD 10? https://www.youtube.com/watch?v=ZPDgtDDTc8k