Standards and Terminologies

S. Trent Rosenbloom, MD MPH

Associate Professor and Vice ChairDepartments of Biomedical Informatics, Internal Medicine and PediatricsVanderbilt University Medical Center

September 21, 2015Department of Biomedical InformaticsBMIF 6300

Standards and Terminologies

Standards are principles and rules designed to ensure that methods used and products created reliably and consistently conform to expectations

Software Standards Detail: minimum set of functions provided methods used to achieve those functions formatting of the data structure

Standards and Terminologies

minimum set of functions provided“Content standards”

methods used to achieve those functions“Functional standards”

formatting of the data structure“Syntactic standards” ← Messaging, e.g., HL7 XML“Semantic standards” ← Terminology, e.g., SNOMED CT

Terminologies can provide formal and machine-computable representations of knowledge and data

Such representation can facilitate interoperability, dissemination, decision support, research

Terminologies

Terminologies are formal representations of entities and their interrelationships. Embodied as concepts, terms, linkages

▪ Concepts are the cognitive representation of entities or meanings

▪ Terms are evocative words or phrases

▪ Linkages are explicitly defined relationships

Terminologies

Concept - ischemic injury and necrosis of heart muscle cells resulting from absent or diminished blood flow in a coronary artery

Terms –▪ Myocardial Infarction▪ Heart Attack

Linkage – ▪ is_a Disease of the Heart▪ has_severity Severities

Terminologies

Morning Star

Evening Star

The second planet from the sun, having an average radius of 6,052 kilometers (3,761 miles), a mass 0.815 times that of Earth, and a sidereal period of revolution about the sun of 224.7 days at a mean distance of approximately 108.2 million kilometers (67.2 million miles).

Morning Star

Evening Star

The second planet from the sun, having an average radius of 6,052 kilometers (3,761 miles), a mass 0.815 times that of Earth, and a sidereal period of revolution about the sun of 224.7 days at a mean distance of approximately 108.2 million kilometers (67.2 million miles).

Conceptual ExperienceRepresentative Terms

Venus

Adapted from Campbell, ‘Representing thoughts, words, and things in the UMLS’, 1998.

Physical Entity

Venus

Mercury

Earth

Jupiter

Saturn

Neptune

Planets of the Solar System

inside outside

Concept: Myocardial Infarction CUI: C0027051 Semantic Type: Disease or Syndrome

Entity: Gross necrosis of the myocardium, as a result of interruption of the blood supply to the area. (Dorland, 27th ed)

Representative Terms (synonyms): Myocardial Infarction Attack coronary Cardiac infarction Heart attack Infarction of heart MI MI - Myocardial infarction Myocardial Infarct Myocardial infarction (disorder) Myocardial infarction syndrome myocardium; infarction

More Specific Concepts (children): Acute myocardial infarction Old myocardial infarction Microinfarct of heart True posterior wall infarction Aborted myocardial infarction Other specified anterior myocardial infarction Silent myocardial infarction Subsequent myocardial infarction Postoperative myocardial infarction First myocardial infarction Myocardial infarction with complication Non-Q wave myocardial infarction

Adapted from the UMLS Metathesaurus.

There are a lot of terminologies

In 2003, the National Committee on Vital Health and Statistics (NCVHS) recommended a subset of existing terminologies as:

“uniform data standards for patient medical record information (PMRI) and the electronic exchange of such information”

Terminologies

PMRI standards: SNOMED CT (as licensed by the National Library of Medicine)

- for the exchange, aggregating, and analysis of patient medical information.

Logical observation Identifiers Names and Codes - for the representation of individual laboratory tests

Federal Drug Terminologies:▪ RxNorm;▪ The representations of the mechanism of action and physiologic effect

of drugs from NDF-RT; ▪ Ingredient name, manufactured dosage form and package type form

the FDA

UMLS (Unified Medical Language System)

The UMLS is a terminology collection Concepts are unique No formal relationships among concepts

present, per se

Using the UMLS: Semantics and relationships from source

terminologies lost (or implied) May mix up different levels of detail from

different terminologies Can loose link with source terminology, which

can hinder maintenance

Terminology [old] History Classification scheme for the London Bills of

Mortality - 16th century John Gaunt’s refinement - middle of the 17th

century International Classification of Diseases (ICD) -

first adopted in Paris in 1900 Multi-axial Standardized Nomenclature of

Diseases (SND) – 1928 Standardized Nomenclature of Diseases and

Operations (SNDO) - 1933

Terminology History

“Modern era for clinical descriptions” With SND and SNDO

▪ Multiaxial: users could model complex concepts by constructing them from more primitive building blocks

▪ Designed to classify diseases based on:EtiologyManifestations Relationships between them

Terminology Desiderata

Statement of purpose, scope, and comprehensiveness Complete coverage of domain specific content Use of concepts rather than terms, phrases and words (concept

orientation) Concepts do not change with time, view or use (concept consistency) Concepts must evolve with change in knowledge Concepts identified through nonsense identifiers (context-free identifier) Representation of concept context consistently from multiple hierarchies Concepts have single explicit formal definitions Support for multiple levels of concept detail Absence of or methods to identify duplication, ambiguity, and synonymy Integration with other terminologies Mapping to administrative terminologies

Adapted from Cimino, ‘Desiderata for controlled medical vocabularies in the twenty-first century’, 1998.

Coverage achieved by one of two ways

▪ Post-coordination - complex concepts from different levels of detail are composed as needed from fundamental concepts (e.g., ‘chest pain’ composed from the concepts ‘chest’ and ‘pain’ when

needed)

▪ Pre-coordination - all levels of detail are modeled with distinct concepts (e.g., ‘chest pain’, ‘substernal chest pain’, and ‘crushing substernal

chest pain’ are all in the terminology)

Completeness measured by Coverage:

▪ coverage calculated as the proportion of concepts covered by a terminology

▪ multiple studies: post-coordinated terminologies generally have better coverage than pre-coordinated terminologies

Post-coordination versus Pre-coordination

Select One Flavor

Select One Topping

Select One Cone

…or…Select One Favorite

Post-Coordination▪ Flexible▪ Wide choice▪ Rules implied▪ Explicit relationships▪ Inefficient▪ Permits Inappropriate

combinations

Pre-Coordination▪ No flexibility▪ Limited choice▪ Asserted knowledge▪ Implied relationships▪ Efficient▪ Only appropriate

combinations

Consequences of post-coordination:

▪ Inefficient post-coordination: “too cumbersome for complex problem entry”

▪ Nonsensical Concepts

▪ Concept duplication

D5-46210 01 Acute appendicitis, NOS G-A231 01 Acute D5-46100 01 Appendicitis, NOS

M-41000 01 Acute inflammation, NOSG-CO06 01 InT-59200 01 Appendix, NOS

G-A231 01 AcuteM-40000 01 inflammation, NOSG-CO06 01 InT-59200 01 Appendix, NOS

Table. Duplication due to compositionality: four ways to compose ‘Appendicitis’ in SNOMED, from the CANON Group

Rigorous development may produce terminologies unusable by healthcare providers for routine clinical tasks.

Rector: tension between clinical usability and meticulous knowledge representation mirrors the conflict -

▪ human users require flexible, expressive terminologies that model common colloquial phrases

▪ computer programs are generally designed to process formally defined concepts having rigidly defined interrelationships.

Rector’s six tasks for terminologies: 1) support efficient data entry and query formulation2) record and archive clinical information3) support sharing and reuse of clinical information4) infer and suggest knowledge according to decision

support algorithms5) support terminology maintenance6) create a natural language output from manual structured

input

Generally a set of flexible, user friendly, colloquial terms displayed in via computer programs.

Use assertional medical knowledge to support efficiency, size and focus

Have been used for problem list entry, clinical documentation, provider order entry

Rosenbloom ST, et al. Interface terminologies: facilitating direct entry of clinical data into electronic health record systems. J Am Med Inform Assoc. 2006 May-Jun;13(3):277-88..

Interface Terminologies

SNOMED CT 2012AA in the UMLS contains:▪ over 311,000 unique concepts, 10% are diagnoses▪ almost 800,000 descriptions▪ approximately 1,360,000 links

S-CT

Terminology Subsets

SNOMED CT CORE subset in the UMLS contains:▪ about 5,000 unique concepts, primarily diagnoses▪ covers 95% of diagnoses recorded from 7 healthcare sites

(Beth Israel Deaconess Medical Center, Intermountain Healthcare, Kaiser Permanente, Mayo Clinic, Nebraska University Medical Center, Regenstrief, Hong Kong Hospital Authority)

S-CT

CORE

Fung KW, Rosenbloom ST, et al. Testing Three Problem List Terminologies in a simulated data entry environment. AMIA Annu Symp Proc .2011:445-54.

Terminology Subsets

SNOMED CT VA-KP subset in the UMLS contains:▪ about 17,000 unique concepts▪ primarily contains precoordinated concepts from the

“Clinical Finding” hierarchy

S-CT

CORE

VA-KP

Terminology Subsets

Institutional subsets / supersets▪ can be created locally as SNOMED CT extensions▪ can be created locally without regard to SNOMED CT▪ may or may not follow standard formalisms

S-CT

CORE

VA-KP

local

Terminology Subsets

S-CT

CORE

VA-KP

CCPSS302,537 12,675

2,437

1,449

1,756527

9862475

9510

* Statistics thanks to Lina Sulieman

Terminology Subsets