umls semantic networkfeb 29, 2008 · structure fully formed anatomical structure embryonic...
TRANSCRIPT
UMLS Semantic Network
Dr. Olivier Bodenreider
Lister Hill National Centerfor Biomedical CommunicationsBethesda, Maryland - USA
http://www.nlm.nih.gov/research/umls/umlswebcasts/index.html
UMLS Webcasts seriesFebruary 29, 2008
2Lister Hill National Center for Biomedical Communications
Acknowledgments
Alexa T. McCrayHarvard Medical SchoolBoston, Massachusetts
3Lister Hill National Center for Biomedical Communications
Outline
The UMLS: A two-level structureUMLS Semantic Network
What is it?Semantic typesSemantic relationshipsSemantic relations
How to use it?Where it get it from?
Future directions
4Lister Hill National Center for Biomedical Communications
Unified Medical Language System
SPECIALIST Lexicon360,000 lexical itemsPart of speech and variant information
Metathesaurus6M names from over 100 terminologies1.5M concepts8M relations
Semantic Network135 high-level categories7000 relations among them
Lexicalresources
Ontologicalresources
Terminologicalresources
The UMLS
A two-level structure
Heart
Concepts
Metathesaurus
Esophagus
Left PhrenicNerve
HeartValves
FetalHeart
Medias-tinum
SaccularViscus
AnginaPectoris
CardiotonicAgents
TissueDonors
AnatomicalStructure
Fully FormedAnatomical
StructureEmbryonicStructure
Body Part, Organ orOrgan Component Pharmacologic
Substance
Disease orSyndrome
PopulationGroup
Semantic Types
SemanticNetwork
isa isa
isaadjacent_to
developmental_form_of
disrupts
location_of
PAR
CHD
SIBRO
Concepts
Metathesaurus
Esophagus
Left PhrenicNerve
HeartValves
FetalHeart
Medias-tinum
SaccularViscus
AnginaPectoris
TissueDonors
AnatomicalStructure
Fully FormedAnatomical
StructureEmbryonicStructure
Disease orSyndrome
PopulationGroup
Semantic Types
SemanticNetwork
isa isa
isaadjacent_to
developmental_form_of location_of
PAR
CHD
SIB
Body Part, Organ orOrgan Component Pharmacologic
Substancedisrupts
Heart CardiotonicAgents
RO
8Lister Hill National Center for Biomedical Communications
Concept categorization
High-level categories (semantic types)Assigned by the Metathesaurus editorsIndependently ofthe hierarchies inwhich these conceptsare located
Glycyrrhiza
Plant Families and Groups
Plants
Fabaceae
Angiosperms
http://en.wikipedia.org/wiki/Glycyrrhiza
Plant
MetathesaurusSemanticNetwork
UMLS Semantic Network
What is it?
10Lister Hill National Center for Biomedical Communications
Semantic network
Semantic types: NodesSemantic relationships:LinksSemantic relations: Triples (node1, link, node2)
AnatomicalStructure
Fully FormedAnatomical
StructureEmbryonicStructure
Body Part, Organ orOrgan Component Pharmacologic
Substance
Disease orSyndrome
isa isa
isaadjacent_to
developmental_form_of
disrupts
location_of
11Lister Hill National Center for Biomedical Communications
Semantic types
Semantic types (135)tree structure2 major hierarchies
Entity– Physical Object– Conceptual Entity
Event– Activity– Phenomenon or Process
12Lister Hill National Center for Biomedical CommunicationsHierarchical structure Entity
Entity■ Physical Object■ ■ Organism■ ■ ■ Plant■ ■ ■ ■ Alga■ ■ ■ Fungus■ ■ ■ Virus■ ■ ■ Rickettsia or Chlamydia■ ■ ■ Bacterium■ ■ ■ Archaeon■ ■ ■ Animal■ ■ ■ ■ Invertebrate■ ■ ■ ■ Vertebrate■ ■ ■ ■ ■ Amphibian■ ■ ■ ■ ■ Bird■ ■ ■ ■ ■ Fish■ ■ ■ ■ ■ Reptile■ ■ ■ ■ ■ Mammal■ ■ ■ ■ ■ ■ Human■ ■ Anatomical Structure■ ■ ■ Embryonic Structure■ ■ ■ Anatomical Abnormality■ ■ ■ ■ Congenital Abnormality■ ■ ■ ■ Acquired Abnormality■ ■ ■ Fully Formed Anatomical Structure■ ■ ■ ■ Body Part, Organ, or Organ Component■ ■ ■ ■ Tissue■ ■ ■ ■ Cell■ ■ ■ ■ Cell Component■ ■ ■ ■ Gene or Genome
■ Physical Object [continued]■ ■ Manufactured Object■ ■ ■ Medical Device■ ■ ■ Research Device■ ■ ■ Clinical Drug■ ■ Substance■ ■ ■ Chemical■ ■ ■ ■ Chemical Viewed Functionally■ ■ ■ ■ ■ Pharmacologic Substance■ ■ ■ ■ ■ ■ Antibiotic■ ■ ■ ■ ■ Biomedical or Dental Material■ ■ ■ ■ ■ Biologically Active Substance■ ■ ■ ■ ■ ■ Neuroreactive Substance or Biogenic Amine■ ■ ■ ■ ■ ■ Hormone■ ■ ■ ■ ■ ■ Enzyme■ ■ ■ ■ ■ ■ Vitamin■ ■ ■ ■ ■ ■ Immunologic Factor■ ■ ■ ■ ■ ■ Receptor■ ■ ■ ■ ■ Indicator, Reagent, or Diagnostic Aid■ ■ ■ ■ ■ Hazardous or Poisonous Substance■ ■ ■ ■ Chemical Viewed Structurally■ ■ ■ ■ ■ Organic Chemical■ ■ ■ ■ ■ ■ Nucleic Acid, Nucleoside, or Nucleotide■ ■ ■ ■ ■ ■ Organophosphorus Compound■ ■ ■ ■ ■ ■ Amino Acid, Peptide, or Protein■ ■ ■ ■ ■ ■ Carbohydrate■ ■ ■ ■ ■ ■ Lipid■ ■ ■ ■ ■ ■ ■ Steroid■ ■ ■ ■ ■ ■ ■ Eicosanoid■ ■ ■ ■ ■ Inorganic Chemical■ ■ ■ ■ ■ Element, Ion, or Isotope■ ■ ■ Body Substance■ ■ ■ Food
Entity [continued]■ Conceptual Entity■ ■ Idea or Concept■ ■ ■ Temporal Concept■ ■ ■ Qualitative Concept■ ■ ■ Quantitative Concept■ ■ ■ Functional Concept■ ■ ■ ■ Body System■ ■ ■ Spatial Concept■ ■ ■ ■ Body Space or Junction■ ■ ■ ■ Body Location or Region■ ■ ■ ■ Molecular Sequence■ ■ ■ ■ ■ Nucleotide Sequence■ ■ ■ ■ ■ Amino Acid Sequence■ ■ ■ ■ ■ Carbohydrate Sequence■ ■ ■ ■ Geographic Area■ ■ Finding■ ■ ■ Laboratory or Test Result■ ■ ■ Sign or Symptom■ ■ Organism Attribute■ ■ ■ Clinical Attribute■ ■ Intellectual Product■ ■ ■ Classification■ ■ ■ Regulation or Law■ ■ Language■ ■ Occupation or Discipline■ ■ ■ Biomedical Occupation or Discipline■ ■ Organization■ ■ ■ Health Care Related Organization■ ■ ■ Professional Society■ ■ ■ Self-help or Relief Organization■ ■ Group Attribute■ ■ Group■ ■ ■ Professional or Occupational Group■ ■ ■ Population Group■ ■ ■ Family Group■ ■ ■ Age Group■ ■ ■ Patient or Disabled Group
13Lister Hill National Center for Biomedical CommunicationsHierarchical structure Event
Event [continued]■ Phenomenon or Process■ ■ Human-caused Phenomenon or Process■ ■ ■ Environmental Effect of Humans■ ■ Natural Phenomenon or Process■ ■ ■ Biologic Function■ ■ ■ ■ Physiologic Function■ ■ ■ ■ ■ Organism Function■ ■ ■ ■ ■ ■ Mental Process■ ■ ■ ■ ■ Organ or Tissue Function■ ■ ■ ■ ■ Cell Function■ ■ ■ ■ ■ Molecular Function■ ■ ■ ■ ■ ■ Genetic Function■ ■ ■ ■ Pathologic Function■ ■ ■ ■ ■ Disease or Syndrome■ ■ ■ ■ ■ ■ Mental or Behavioral Dysfunction■ ■ ■ ■ ■ ■ Neoplastic Process■ ■ ■ ■ ■ Cell or Molecular Dysfunction■ ■ ■ ■ ■ Experimental Model of Disease■ ■ Injury or Poisoning
Event■ Activity■ ■ Behavior■ ■ ■ Social Behavior■ ■ ■ Individual Behavior■ ■ Daily or Recreational Activity■ ■ Occupational Activity■ ■ ■ Health Care Activity■ ■ ■ ■ Laboratory Procedure■ ■ ■ ■ Diagnostic Procedure■ ■ ■ ■ Therapeutic or Preventive Procedure■ ■ ■ Research Activity■ ■ ■ ■ Molecular Biology Research Technique■ ■ ■ Governmental or Regulatory Activity■ ■ ■ Educational Activity■ ■ Machine Activity
14Lister Hill National Center for Biomedical Communications
“Biologic Function” hierarchy (isa)
Biologic Function
Pathologic FunctionPhysiologic Function
Disease orSyndrome
Cell orMolecular
Dysfunction
ExperimentalModel ofDisease
OrganismFunction
Organor TissueFunction
CellFunction
MolecularFunction
Mental orBehavioral
Dysfunction
NeoplasticProcess
MentalProcess
GeneticFunction
15Lister Hill National Center for Biomedical Communications
Semantic type information
T047Disease or SyndromeB2.2.1.2.1A condition which alters or interferes with a normal process, state, or activity of an organism. It is usually characterized by the abnormal functioning of one or more of the host's systems, parts, or organs. Included here is a complex of symptoms descriptive of a disorder.Diabetes Mellitus; Dumping Syndrome; Malabsorption Syndromes; Nephrotic SyndromeAny specific disease or syndrome that is modified by such modifiers as "acute", "prolonged", etc. will also be assigned to this type. If an anatomic abnormality has a pathologic manifestation, then it will be given this type as well as a type from the 'Anatomical Abnormality' hierarchy, e.g., "Diabetic Cataract" will be double-typed for this reason.dsyn
IDNameTree numberDefinition
Examples
Usage note
Abbreviation
16Lister Hill National Center for Biomedical Communications
Semantic relationships
Semantic network relationships (54)Hierarchical (isa = is a kind of)
among types– Animal isa Organism– Enzyme isa Biologically Active Substance
among relations– treats isa affects
Associative (non-hierarchical)Sign or Symptom diagnoses Pathologic FunctionPharmacologic Substance treats Pathologic Function
17Lister Hill National Center for Biomedical Communications
Associative relationship hierarchy
associated with
physicallyrelated to
spatiallyrelated to
temporallyrelated to
functionallyrelated to
conceptuallyrelated to
associated with
physicallyrelated to
part of
consists of
contains
connected to
interconnects
branch of
tributary of
ingredient of
spatiallyrelated to
location of
adjacent to
surrounds
traverses
temporallyrelated to
co-occurs with
precedes
functionallyrelated to
conceptuallyrelated to
associated with
physicallyrelated to
spatiallyrelated to
temporallyrelated to
functionallyrelated to
conceptuallyrelated to
affects
brings about
performs
occurs in
uses
manifestation of
indicates
result of
manages
treats
disrupts
complicates
interacts with
prevents
produces
causes
carries out
exhibits
practices
process of
associated with
physicallyrelated to
spatiallyrelated to
temporallyrelated to
functionallyrelated to
conceptuallyrelated to
degree of
analyzes
measurement of
measures
diagnoses
property of
derivative of
method of
conceptual part of
issue in
assesses effect of
developmental form of
evaluation of
21Lister Hill National Center for Biomedical Communications
Semantic relationship information
T202ingredient_ofR1.8Is a component of, as in a constituent of a preparation.IGhas_ingredient
IDNameTree numberDefinitionAbbreviationInverse rel.
22Lister Hill National Center for Biomedical Communications
Semantic relations
612 assertions558 (type1, relationship, type2)
Hierarchical– Animal isa Organism– Enzyme isa Biologically Active Substance
Associative– Sign or Symptom diagnoses Pathologic Function– Pharmacologic Substance treats Pathologic Function
54 (relationship1, isa, relationship2)– treats isa affects
23Lister Hill National Center for Biomedical Communications
Semantic relations (subset)Organism
process of
EmbryonicStructure
AnatomicalAbnormality
CongenitalAbnormality
AcquiredAbnormality
Fully FormedAnatomicalStructure
AnatomicalStructure
part of
OrganismAttribute
property of
BodySubstance
contains,produces
conceptualpart of
evaluation of
Body Systemconceptualpart of
part of
Body Part, Organ orOrgan Component
part of
Tissue
part of
Cell
part of
CellComponent
Gene orGenome
Body Spaceor Junction
adjacent to
location of
location of
evaluation ofFinding
Laboratory orTest Result
Sign orSymptom
BiologicFunction
PhysiologicFunction
PathologicFunction
Body Locationor Region
conceptualpart of
conceptualpart of
Injury orPoisoning
disrupts
disrupts
co-occurs with
24Lister Hill National Center for Biomedical Communications
Inheritance
Disease or Syndrome
Pathologic Function
isa
isaBody Part, Organ,
or Organ Component
isa
Biologic FunctionFully FormedAnatomical
Structure
location of
25Lister Hill National Center for Biomedical Communications
Semantic relations (inherited)
6864 assertions6752 (type1, relationship, type2)
Hierarchical– Mammal isa Organism (from: Animal isa Organism)– Enzyme isa Chemical
(from: Enzyme isa Biologically Active Substance)Associative
– Body Part, Organ, or Organ Componentlocation_of Disease or Syndrome(from: Fully Formed Anatomical Structurelocation_of Biologic Function)
112 (relationship1, isa, relationship2)– treats isa functionally_related_to (from: treats isa affects)
26Lister Hill National Center for Biomedical Communications
Semantic relation information
Fully Formed Anatomical Structurelocation_ofBiologic FunctionD
Sem. Type1
RelationshipSem. Type2
Link status
UMLS Semantic Network
How to use it?
28Lister Hill National Center for Biomedical Communications
Why a semantic network?
Semantic Types serve as high level categories assigned to Metathesaurus concepts, independently of their position in a hierarchy
A relation between 2 Semantic Types (ST) indicates a possible link between 2 concepts that have been assigned to those STs
The relationship may or may not hold at the concept levelOther relationships may apply at the concept level
29Lister Hill National Center for Biomedical Communications
Identify concepts for a given category
Semantic typeList of all conceptshaving this semantic type
ConceptList of all descendants
30Lister Hill National Center for Biomedical Communications
Source of domain knowledgeOrganism
process of
EmbryonicStructure
AnatomicalAbnormality
CongenitalAbnormality
AcquiredAbnormality
part of
OrganismAttribute
property ofevaluation of
conceptualpart of
part ofpart of
part of part of
adjacent to
location of
location of
evaluation ofFinding
Laboratory orTest Result
Sign orSymptom
BiologicFunction
PhysiologicFunction
PathologicFunction
disrupts
co-occurs with
Fully FormedAnatomicalStructure
AnatomicalStructure
Body Part, Organ orOrgan Component
Tissue Cell CellComponent
Gene orGenome
BodySubstance
contains,produces
conceptualpart of
Body System Body Spaceor Junction
Body Locationor Region
conceptualpart of
conceptualpart of
Injury orPoisoning
disrupts
31Lister Hill National Center for Biomedical Communications
Semantics of Metathesaurus relations
Semantic Network
Metathesaurus
AdrenalCortex
AdrenalCortical
hypofunction
Disease or SyndromeBody Part, Organ,
or Organ Component
Pathologic Functionisa
Biologic Function
isa
Fully FormedAnatomical
Structure
isa
location of
location of
UMLS Semantic Network
Where to get it from?
33Lister Hill National Center for Biomedical Communications
UMLS distribution
Part of the UMLS distributionInstalled by MetamorphoSys (option)
Select this option
34Lister Hill National Center for Biomedical Communications
UMLS Semantic Network website
No intellectual property restrictions on the Semantic NetworkAvailable outside UMLS license agreementUMLS Semantic Network websitehttp://semanticnetwork.nlm.nih.gov/
35Lister Hill National Center for Biomedical Communications
UMLS Semantic Network website
http://semanticnetwork.nlm.nih.gov/
36Lister Hill National Center for Biomedical Communications
Semantic Network files
37Lister Hill National Center for Biomedical Communications
Semantic Network documentation
http://www.nlm.nih.gov/research/umls/meta3.html
UMLS Semantic Network
Future directions
39Lister Hill National Center for Biomedical Communications
Future directions
Harmonize with other top-level ontologies of biomedicine
Semantic types (e.g., with BioTop)Semantic relationships (e.g., with the OBO Relation Ontology, with relationships in GALEN)
40Lister Hill National Center for Biomedical Communications
BioTophttp://www.ifomis.org/biotop
41Lister Hill National Center for Biomedical Communications
OBO relations
http://www.obofoundry.org/ro/
42Lister Hill National Center for Biomedical Communications
GALEN relations isIngredientOf
http://opengalen.org
43Lister Hill National Center for Biomedical Communications
Future directions
Harmonize with other top-level ontologies of biomedicine
Semantic types (e.g., with BioTop)Semantic relationships (e.g., with the OBO Relation Ontology, with relationships in GALEN)
Align relationships between Metathesaurus and Semantic Network
affects
has directmorphology
has directsubstance
associated with
physicallyrelated to
spatiallyrelated to
temporallyrelated to
functionallyrelated to
conceptuallyrelated to
affects
brings about
performs
occurs in
uses
manifestation of
indicates
result of
manages
treats
disrupts
complicates
interacts with
prevents
produces
causes
carries out
exhibits
practices
process of
encodes encodesgene product
has indirectmorphology
metabolicsite of
metabolizes
pathological process of
has physio-logic effect
has specimenprocedure
interprets
Draft
causative agent ofcause of
definitionalmanifestation of
exhibits
may prevent
may treat
occurs in
occurs after
treats
process of
access instrument ofinstrument of
direct device of
indirect device of
procedure device of
inv
45Lister Hill National Center for Biomedical Communications
References
McCray AT, Nelson SJ.The representation of meaning in the UMLS.Methods Inf Med 1995;34(1-2):193-201McCray AT.An upper level ontology for the biomedical domain.Comp Funct Genom 2003; 4:80-4.McCray AT, Bodenreider O.A conceptual framework for the biomedical domain.In: Green R, Bean CA, Myaeng SH, editors. The semantics of relationships: an interdisciplinary perspective.Dordrecht; Boston: Kluwer Academic Publishers; 2002. p. 181-198.
http://semanticnetwork.nlm.nih.gov/
MedicalOntologyResearch
Olivier Bodenreider
Lister Hill National Centerfor Biomedical CommunicationsBethesda, Maryland - USA
Contact:Web: