Introduction of SNOMED-CT and UMLS

1
Introduction of SNOMED-CT and UMLS

• Kimikazu Kashiwagi
• National College of Nursing

2
Patient Records
Numerical Data
Narrative Text

• International Classification of Diseases (ICD)

3
Adverse Reaction terminology

• WHO Adverse Reaction Terminology
• J-ARTJapanese Adverse Drug Reaction Terminology
• COSTARTCoding Symbol for Thesaurus of Adverse
  Reaction Terms (FDA)
• MedDRA Medical Dictionary for drug regulatory
  affairs (ICH)

4
Case Organ Plant Center

• Organ Plant Center Dialysis Center

Renal Transplant Database
Dialysis Database
Same Patient - Different Terminology
From. Ontology in Medicine
5
Question

• To find the patients who have a heart disease
  from both database, in order to evaluate the
  correlation between heart diseases and the renal
  transplant result.
• Renal transplant recipientTo check if they have
  heart diseases, renal diseases, lung diseases,
  and liver diseases for evaluation study.

6
Problem

• If disease doesnt have a link to body site, we
  cant find Lung Disease.

7
Relationship between Disease and Site

• ??????????????????????
• ??????????????????????

Disease
Has_site
Site
8
Simple Ontology
Diesease ??
Has_Lesion
Lesion ??
Has_site
Has_finding
Site ??
Finding ??
9
Narrative Text

• ?????????ST?????????24??????????????????

Dictionary
Natural Language Processing
??????????????ST?? 24????????????????
10
SNOMED-CT
11
SNOMED-CT??

• Systematized Nomenclature of Medicine
• ?????????(CAPThe College of American
  Pathologists)???
• ???????????????????????????????1?
• ???34?
• http//www.snomed.org/

12
SNOMED???(1)

• 1965???????????(SNOPSystematized Nomenclature of
  Pathology)
• 1974? SNOMED
• 2000?5? SNOMED-RT (Reference Terminology)

13
SNOMED???(2)

• 2002?1? ?????????????(NHSNational Health
  Service)?????Clinical Terms Version
  3(ReadCode)????????SNOMED-CT (Clinical Terms)
• ???1???????????????2003July?

14
SNOMED??????

• SNOMED????????????????????????????
• ????????????????????????????
• ?????????????2???????CD-ROM????????
• ????????????????????(CLUE)??

15
SNOMED-CT??????

• 2003?7?NLM(???????)?3240???(38?8800??1\120)?5?
  ?????????????SNOMED-CT?Core Content(??????US Drug
  Extension????????)??NLM???????UMLS??????????????
• ?????????2004???????UMLS2004AA??????

16
???SNOMED-CT??????

• UMLS?????SNOMED-CT????????????????????????
• UMLS????????????????????????????????

17
Object, Concept, Description
Description
Concept
Object
18
?????????(1)
??
???
??
??
Chair
19
?????????(2)
??
???
?
Gold
Friday
Money
20
???(Synonym)????

• SNOMED-CT???1?????????????????????????????????????
  
• SNOMED-CT??????3?????????
• 1)????? (Fully Specified Name)
• 2)???(Preferred)
• 3)???(Synonym)

21
?????
?????
??
incontinence of feces (finding)
?????
incontinence of feces
???
bowel incontinence
???
involuntary stool
???
bowels incontinent
???
22
Strict Hierarchy?Polyhierarchy
??
???
???
???
???
???
J.J.Cimino.Practical Considerations for Choosing
Terminologies in Health Care Applications. AMIA
2003 Symposium Tutorial
23
?(Entire face)?????
SNOMED CT Concept
body structure
anatomical concepts
physical anatomical entity
anatomical structure
body region structure
surface region
body part structure
upper body structure
body surface region
upper body part structure
head and neck structure
head structure
face and neck structure
head part
region of head
face structure
surface region of head
entire face
24
?????
???????
???????
is-a
is-a
??????? ??
25
???????
??
???????
???????
?????????
??
??
??????? ????
???
?
??
26
SNOMED-CT???

• ????????SNOMED CT Concept????????????????????

SNOMED CT Concept
?? Finding
?? Disease
?? Procedure

19??????

• ???????????????????????????????????????????19?????
  ?????????????????????

27
SNOMED-CT19?????

• ?? (Finding)
• ?? (Disease)
• ?? (Procedure)
• ???? (Observable entity)
• ???? (Body structure)
• ?? (Organism)
• ?? (Substance)
• ?? (Pharmaceutical /
• biologic product)
• ?? (Specimen)
• ? (Physical object)

??? (Physical force) ??? (Events) ????
(Environments and geographical locations) ?????
(Social context) ????????? (Context- dependent
categories) ?? (Staging and scales) ??
(Attribute) ???? (Qualifier value) ???? (Special
concept)
28
1.?? (Finding) 39,138??

• ????????????????????
• ?
• ?62315008 ?? diarrhea (finding) ?
• ?48694002 ?? anxiety (finding) ?

29
2.?? (Disease) 70,832??

• ???????????????
• ?
• ?74400008 ??? appendicitis (disorder)?
• ?127013003 ?????? diabetic renal disease
  (disorder)?
• ?????????????????????????????
• ?248255005 ???????? cannot sleep at all
  (finding)????
• ?193462001 ??? insomnia (disorder)????

30
3.?? (Procedure) 50,319??

• ?????????????????????
• ?
• ?6143009 ??????? diabetic patient education
  (regime/therapy)?
• ?10870009 ?????????????????????????? Repair of
  atrial septal defect in total repair of total
  anomalous pulmonary venous connection
  (procedure)?
• ?371754007 ???? discharge planning (procedure) ?
• ?2475000 24???? urine specimen collection? 24
  hours (procedure) ?

31
UMLS
32
UMLS??

• Unified Medical Language System
• ?????????
• ?????????(NLM)???
• ??????????????????????????
• ??????????
• ??34??????

33
UMLS???

• ?????????????????72???????????????
• ???????????????????????5???????????

34
UMLS????

• Metathesaurus
• ?????????????????
• Semantic Network
• ??????
• SPECIALIST Lexicon and Lexical Programs
• ???????????????

35
1.Metathesaurus

• 143???????????????
• ?100?????430???
• ?????????????????????????

36
UMLS???????????

• ICD-10
• ICPC The International Classification of Primary
  Care
• SNOMED Clinical Terms
• MedDRA Medical Dictionary for Regulatory
  Activities Terminology
• DSM-IV Diagnostic and Statistical Manual of
  Mental Disorders
• HL7 Health Level Seven Vocabulary
• MeSH Medical Subject Headings
• RxNorm
• Gene Ontology

37
UMLS????????

• ????
• NANDA nursing diagnoses
• Home Health Care Classification of Nursing
  Diagnoses and Interventions
• Patient Data Care Set (PCDS)
• ????????
• Current Procedural Terminology (CPT)
• Healthcare Common Procedure Coding System
  (HCPCS).
• ????????(??????)
• JAMAS Japanese Medical Thesaurus (JJMT)

38
UMLS??????????

• Basque Translation.
• Danish Translation.
• Dutch Translation.
• Finnish Translation.
• French Translation.
• German Translation.
• Hebrew Translation, Denmark
• Hungarian Translation.
• Italian Translation.
• Norwegian Translation.
• Australian Modification.
• Portuguese Translation.
• Spanish Translation.
• Swedish Translation.

14?????? ?????? ???????
The International Classification of Primary Care
(ICPC).
39
???????

• ????????????????????????????????????????????????
  ???
• ???MetamorphoSys

40
Metathesaurus?????????????????

• ????1
• ?????????????????????
• ????2
• ????1???????????????????????
• ???????????????
• ????3
• ?????????????????????????????(??????????????????)
• ????4(SNOMED-CT??)
• ?????????????????????

41
MetamorphoSys???
42
??????(1)
43
??????(2)
44
MetamorphoSys???????

• ???????
• ???????????????????
• Oracle
• MySQL
• ASCII???????????(UTF-8)

45
UMLS???
Concept (CUI) Terms (LUIs) Strings (SUIs) Atoms (AUIs)
C000000??? ???? ?? ??? L0000001??? ???? S0000001??? A0000001???(from ---)
C000000??? ???? ?? ??? L0000001??? ???? S0000001??? A0000002???(from ---)
C000000??? ???? ?? ??? L0000001??? ???? S0000002???? A0000003????(from-)
C000000??? ???? ?? ??? L0000002?? ??? S0000003?? A0000004?? (from -)
C000000??? ???? ?? ??? L0000002?? ??? S0000004??? A0000005???(from ---)
46
UMLS???
Concept
?????
??
Term
??
??
String
???
String
???
47
2.Semantic Network

• ??????????
• ???????Semantic Type 135??
• ??????Semantic Relation 54??
• Metathesaurus?????????????Semantic Type???????
• 1????????Semantic Type?????????????

48
Semantic Type?Semantic Relation??
Physical Object
Group
IS_A
??
Clinical Drug
????
Occupation
??
?????
Antibiotic
Disease
49
Semantic Type???
Semantic Type
Event
Entity
Phenomenon or Process
Activity
Physical Object
Conceptual Entity
50
Semantic Relation???
Semantic Relation
associated_with
isa
physically_related_to
spatially_related_to
functionally_related_to
temporally_related_to
conceptually_related_to
51
Semantic Group(Semantic Type??????)

1. Living Beings
2. Objects
3. Occupations
4. Organizations
5. Phenomena
6. Physiology
7. Procedures

1. Activities Behaviors
2. Anatomy
3. Chemicals Drugs
4. Concepts Ideas
5. Devices
6. Disorders
7. Genes Molecular Sequences
8. Geographic Areas

52
3.SPECIALIST Lexicon

• ??????????
• Remove Genitive
• Replace Punctuation With Space ??????
• Strip Stop Words ????????
• Strip Diacritics
• Split Ligatures
• Lowercase Words
• Uninflect Words
• Citation
• Sort Words By ASCII Order
• Symbol Name Synonmy

53
?????????????????MetaMap Transfer (MMTx)

• ?)????????? ?Obstructive Sleep Apnea?
• Meta Candidates (7)
• 1000 Sleep Apnea, Obstructive
• 901 Apnea, Sleep (Sleep Apnea Syndromes)
• 827 Apnea
• 827 Obstructive (Obstructed)
• 827 Sleep
• Meta Mapping (1000)
• 1000 Sleep Apnea, Obstructive Disease or
  Syndrome

54
Knowledge Source Server

• Metathesaurus?Semantic Network?
  SPECIALIST?????????????????????????????????
• ????????????????????????????????

55
(No Transcript)
56
?????(WSD Test Collection)

• I am taking aspirin for my cold.
• Let's go inside, I'm cold.
• ???Cold???????????(COLD)??????????????????????????
  
• ????????????????????????????????????????

57
???????????????