Practical Considerations in Interoperability. The Unified Medical Language System

Practical Considerations in Interoperability The Unified Medical Language System Unified Medical Language System • Long Term Project of NLM (started...
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Practical Considerations in Interoperability The Unified Medical Language System

Unified Medical Language System • Long Term Project of NLM (started 1986) • Focus on Interoperability • Increasingly Standards Based

UMLS Purpose • Make it easy for health professionals and researchers to retrieve and integrate relevant information from disparate automated sources, e.g. – – – –

computer-based patient records factual databanks bibliographic databases and full-text expert systems

• Antedated and Anticipated the Web

UMLS Focus Conceptual Connections • Build knowledge sources that can be used by intelligent programs to overcome: – disparities in language used by different users and in different information sources; – difficulties in identifying which of many information sources is relevant

UMLS Knowledge Sources Multi-purpose Tools or “Intellectual Middleware” for System Developers • Metathesaurus • SPECIALIST lexicon and lexical programs • Semantic Network

UMLS Distribution • Annual updates, 1990 - • Free under license agreement with NLM – Need separate license agreements with vocabulary producers for some uses of some vocabularies in the Metathesaurus

• Available to licensed users (~2000) via Internet server and on CDs http://www.nlm.nih.gov/research/umls/

UMLS Metathesaurus Finely Granular Concepts • Concepts, terms, and attributes from many controlled vocabularies • New inter-source relationships, definitional information, use information • Scope determined by combined scope of source vocabularies • Strict definition of synonymy (=Identity)

Organization of Metathesaurus • Semantic Locality – – – –

Synonymy Contexts Co-Occurrences Asserted Relationships

• Analogous to Orthography

Concepts (MRCON) C0014834 C0014834 C0014834 C0014834 C0014834 C0014834 C0014834 C0014834

ENG ENG ENG FRE GER POR RUS SPA

P S S P P P P P

L0014834 L0004656 L0789289 L0166913 L0411596 L0325532 L0893188 L0343199

PF PF PF PF PF PF PF PF

S0038884 S0004045 S0864664 S0231394 S0535878 S0433837 S1097005 S0451504

Escherichia coli Bacterium coli E COLI ESCHERICHIA COLI ESCHERICHIA COLI ESCHERICHIA COLI ESCHERICHIA COLI ESCHERICHIA COLI

Sources (MRSO) C0014834 C0014834 C0014834 C0014834 C0014834 C0014834 C0014834 C0014834 C0014834 C0014834 C0014834 C0014834 C0014834 C0014834

L0004656 L0004656 L0014834 L0014834 L0014834 L0014834 L0014834 L0014834 L0166913 L0325532 L0343199 L0411596 L0789289 L0893188

S0004045 S0004045 S0038884 S0038884 S0038884 S0038884 S0038884 S0038884 S0231394 S0433837 S0451504 S0535878 S0864664 S1097005

SNM2 SNMI97 CSP94 LCH90 MSH98 RCD95 SNM2 SNMI97 INS97 BRMP98 BRMS98 DMD97 LNC10I RUS98

SY SY PT PT MH PT PT PT MH MH MH MH RN MH

E-1571 L-15601 0336-0160 U001655 D004926 X73K5 E-1571 L-15601 D004926 D004926 D004926 D004926 NOCODE D004926

Semantic Type (MRSTY) C0014834

T007

Bacterium

Definition (MRDEF) C0014834 MSH98

A species of gram-negative, facultatively anaerobic, rod-shaped bacteria commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce diarrhea and pyogenic infections.

Relationships And Contexts (MRREL & MRCXT) C0014834 C0014834 C0014834 C0014834 C0014834 C0014834 C0014834 C0014834 C0014834 C0014834 C0014834 C0014834 C0014834 ...

CHD CHD PAR PAR PAR PAR PAR RN RO RO RO RO SIB

C0376624 C0376625 C0014346 C0014833 C0014833 C0014833 C0014833 C0002054 C0148325 C0370139 C0370140 C0370141 C0315244

Escherichia coli O157-H7 Escherichia coli O157 Enterobacteriaceae Escherichia Escherichia Escherichia Escherichia Alkalescens-Dispar Group Verotoxin 2 Verotoxin 1 Verotoxin 1 Antibody Verotoxin 2 Antibody Escherichia hermannii

RCD95 MSH98 SNM2 CSP94 MSH98 RCD95 SNMI97 MTH MTH MTH MTH MTH RCD95

Lessons from UMLS • Context is Key • Face Validity a Problem in Many Systems • “Special” Meanings • Zipf’s Law

• Use Meaningless Identifiers • Let Concepts Persist

Observations • • • •

Multi-Purpose Tools Difficult to Use Semantic Locality Insufficient The Escher Phenomenon Other Terminological Paradoxes

Paradoxes in Terminology • Content seemingly defies logic • The way we use words often defies formal definitions – Wave-particle duality – The Escher phenomenon – Godel’s Theorem

• Logicians do not understand content – Categorical Names of Artifacts – Natural Objects (open lattice description)

Choices in Terminology • • • • • •

Want a Standard Understandable by Humans Reproducible for Machines Appropriate for Intended Use Update Model Low Cost

Standards in Models ƒ Doesn’t Vocabulary Alone Solve Problem? ƒ What is an Information Model? ƒ How Does it Relate to Terminology?

A Situation RECORD 1

RECORD 2

Male, 56, IDDM x 15 years, Graves’ Disease, Renal Failure, Admitted with Septic Shock.

Male, 56, IDDM x 15 years, Graves’ Disease Fam Hx of Renal Failure, Admitted with Septic Shock.

Decision Support If Renal Failure, do not give Aminoglycosides

Which Would be Appropriate Application of Rule?

What is an Information Model? ƒ ƒ ƒ ƒ

Example: MeSH in MEDLINE Recognition of Context Formalization of Implicit Design Formal Declaration of Intent

How Does it Relate to Terminology? ƒ Pre-Coordination versus Post Coordination • Use Requirements • Standards Efforts – HL7 for Clinical Records – Common Model Efforts • Gene Ontology • International Drug Harmonisation

Recent US Developments • Clinical Vocabularies – LOINC – SNOMED-CT – RxNorm

• Consolidated Health Informatics

SNOMED CT • ‘Most comprehensive international and multilingual clinical reference terminology available in the world’ • Latest release: Jan 31, 2004 – Concepts: 357,135 (298,090 current) – Descriptions: 957,349 (736,946 current) – Relationships: 1,374,955 (1,315,910 involve only current concepts)

SNOMED CT Data Structure • Concepts, Descriptions and Relationships – All Have Unique Identifiers – All Have Individual Attributes – Some Description Logic

• Mappings to ICD9CM • Original Format of Metathesaurus Incapable

Original Release Format (ORF) of Metathesaurus • Metathesaurus-Concept-Centric view • Concept -based Connections and Relationships • Most information at Concept (CUI) level

New Rich Release Format (RRF) • Source-Centric View (Source transparency) • Attributes and relationships at the Atom level – Denoted by AUI (Atom Unique identifier) – A string in a source

• New Fields for source specific identifiers (SCUI, SAUI, SRUI)

Different Theologies in Concept Organization • •

What is a concept? ‘A unit of thought’ In SNOMED CT: – –



Rigid hierarchies – mutually exclusive Define concepts by other concepts ( Description Logic)

In UMLS: – –

The working principle is ‘useful level of distinction for biomedical professionals eg. in clinical discourse’ May trade slight ambiguity in meaning for Improving localization

SNOMED CT Concept View

Acetaminophen (product)

Has-active ingredient

Is-a Acetaminophen 500 mg tablet (product)

Acetaminophen (substance)

Acetaminophen 80 mg suppository (product)

‘This patient is on acetaminophen.’ Useful clinical distinction? ‘Tylenol contains acetaminophen.’

SNOMED CT Concept View

Stab wound (disorder)

Has-associatedmorphology

Stab wound (morphologic abnormality)

‘The patient was admitted for a stab wound sustained during a fight.’ Useful clinical distinction? ‘On physical examination, there was a 3 cm stab wound in the right upper quadrant of the abdomen.’

Mapping Issues ƒ Few Able to Exploit Locality ƒ Direct Navigation Desirable ƒ From: ƒ Core Clinical Vocabularies ƒ To Other Important Terminologies

ƒ Directionality Important ƒ Complex Logical Expressions

Can Interoperability Be Achieved? • Desirable – What is Experience with Patients Like Mine? – Disease Surveillance

• UMLS a First Step • Semantic Web – No Standard – No Update Model

• Ars Longa, Vita Brevis

Thank you!

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