Background
SNOMED CT and the ontology
SNOMED CT and the database
SNOMED CT and top-level ontologies
Methods
SCT to OGMS mapping process
Modeling pre-coordinated expressions
Modeling of post-coordinated expressions
-
The attribute name is a concept that is a subtype of 246,061,005|attribute|.
-
The refinement attribute value is a concept or expression that is appropriate to the attribute name as specified by the SCM. In most cases, any subtype child or descendant of a concept that is permitted as an attribute value of an attribute is also permitted as an attribute value.
-
Refinements may be grouped to represent interdependencies between them in the same way as super-type relationship groups.
Results
SCT description logic
Name | OWL syntax | Syntax | Semantics |
---|---|---|---|
Top | Thing | ⊤ |
∆
I
|
Bottom | Nothing | ⊥ | ∅ |
Atomic class | Class | C | CI |
Primitive role | Object and data property | R | RI |
Existential quantification | ObjectSomeValuesFrom | ∃R. C | {x ∈ ∆I| ∃y ∈ ∆I : (x, y) ∈ R ⋀ y ∈ CI} |
General class inclusion | SubClassOf | C ⊑ D | CI ⊆ DI |
Role inclusion | SubObjectPropertyOf | R ⊑ S | {x, y ∈ ∆I| (x, y) ∈ RI → (x, y) ∈ SI} |
Class equivalence | EquivalentTo | C ≡ D (C ⊑ D, D ⊑ C ) | CI = DI |
Conjunction | ObjectIntersectionOf | C ⊓ D | CI ∩ DI |
Domain restriction | ObjectPropertyDomain | ∃R. ⊤ ⊑ C | {x ∈ ∆I| (x, y) ∈ RI} ⊆ CI} |
Range restriction | ObjectPropertyRange | ⊤ ⊑ ∀ R. C | {y ∈ ∆I| (x, y) ∈ RI} ⊆ CI} |
Disjointedness | DisjointWith | C ⊓ D ⊑ ⊥ | CI ∩ DI = ∅ |
SCT compositional grammar | OWL construct | DL construct |
---|---|---|
expression, subExpression | Axiom | Axiom |
sctid = conceptReference = conceptid = term | String | String |
numericalValue | Float/integer | Float/integer |
Plus | objectIntersectionOf | ⊓ |
definitionStatus (<<<, ===) | subClassOf, equivalentClasses | ⊑, ≡ |
focusConcept | Class |
C
|
refinement | some, objectIntersectionOf | ∃, ⊓ |
attributeGroup | objectIntersectionOf | ⊓ |
attributeSet | objectIntersectionOf | ⊓ |
attributeValue | Data property, object property | Roles |
expressionValue | objectIntersectionOf | ⊓ |
Steps for building an SCT OWL 2 upper-level ontology
Determining SCT top-level concepts
Determining the OGMS concepts
Modeling SCT relationships and relationship groups
Class:
‘heart disease’
SubClassOf:
AND
disorder of mediastinum
AND
disorder of cardiovascular system’
AND
(
has_finding_site
ONLY
‘finding site’
)
ObjectProperty: has_finding_site
Domain:
‘clinical finding’
Range:
‘finding site’
ObjectProperty: has_location
Domain:
‘finding site’
Range:
‘body structure’
class:
‘finding site’
SubClassOf:
AND (has_location SOME
‘heart structure’
) AND (has_relationshipId ONLY
“2034997023”
) AND (has_moduleId ONLY
‘900000000000207008’
) AND (has_ typeId ONLY
“363698007”
) AND (has_ characteristicTypeId ONLY
‘900000000000011006’
) AND (has_ modifierId ONLY
‘900000000000451002’
)
DataProperty: has_...
Domain:
‘finding site’
Range: xsl:string
Class:
‘closed skull fracture with intracranial injury’
EquivalentTo:
‘closed injury of head’
and
‘closed fracture of skull’
and
IsSourceOf some
(((Relationship_destinationId some
‘intracranial structure’) and
(Relationship_typeId some
‘finding site’)) and Grouped_Relations exactly 1
((Relationship_destinationId some
‘closed traumatic abnormality’) and
(Relationship_typeId some
‘associated morphology’))))and
IsSourceOf some
(((Relationship_destinationId some
‘bone structure of cranium’) and
(Relationship_typeId some
‘finding site’)) and Grouped_Relations exactly 1
((Relationship_destinationId some
‘fracture, closed’) and
(Relationship_typeId some
‘associated morphology’))))Refinement of concept semantics
DisjointClasses
:
'pharmaceutical / biologic product' 'physical force' 'linkage concept' 'environment or geographical location' 'qualifier value' 'observable entity' 'record artifact' procedure, event specimen substance 'staging and scales' 'physical object' 'clinical finding' organism
axiom
1
or … or axiom
15
), one for each branch of Fig. 10. The axiom for the finding site of Fig. 10 can be represented as.
axiom
1
≡ (IsSourceOf some ((Relationship_destinationId some (
'acquired body structure'
or
'anatomical structure'
)) and (Relationship_typeId some
'finding site'
)))
Modeling of pre-coordination and post-coordination
-
concept name C as primitive concept (C ⊑ Ci) or defined concept (C ≡ Ci);
-
conjunctions of concept names: C1 ⊓ C2… ⊓ Cn;
-
conjunction of concept names with exists-restrictions and grouped exists-restrictions: C1 ⊓ C2… ⊓ Cn ⊓ ∃ R. C… ⊓ {∃R. C ⊓ …} ⊓ …
Class
: ‘Diabetes mellitus’SubClassOf
: ‘disorder of glucose metabolism’ and
‘disorder of endocrine system’ and
IsSourceOf some
((Relationship_destinationId some
‘structure of endocrine system’) and
(Relationship_typeId some
‘finding site’)).Class
: ‘salpingo-oophorectomy, with laser excision of the right ovary and diathermy excision of the left fallopian tube’SubClassOf
:IsSourceOf some
((((Relationship_destinationId some
‘excision - action’) and
(Relationship_typeId some
‘method’)) and Grouped_Relations exactly 1
((Relationship_destinationId some
‘structure of right ovary’) and
(Relationship_typeId some
‘procedure site - direct’))) and Grouped_Relations exactly 1
((Relationship_destinationId some
‘laser device’) and
(Relationship_typeId some
‘using device’)))IsSourceOf some
(((Relationship_destinationId some
‘diathermy excision - action’) and
(Relationship_typeId some
‘method’)) and Grouped_Relations exactly 1
((Relationship_destinationId some
‘structure of left fallopian tube’) and
(Relationship_typeId some
‘procedure site - direct’))))The resulting SCTO
Property | Definition | Domain | Range |
---|---|---|---|
Has_description | Determines a description for a class. | SNOMED CT Concept | SNOMED CT Description |
IsDescriptionOf | Is the inverse of Has_description. | SNOMED CT Description | SNOMED CT Concept |
Relationship_destinationId | Identifies the class that is the destination of the relationship. Set to an identifier of a concept in the Concept file. | SNOMED CT Relationship | SNOMED CT Concept |
Relationship_sourceId | Identifies the source concept of the relationship. Set to an identifier of a concept in the Concept file. | SNOMED CT Relationship | SNOMED CT Concept |
Relationship_typeId | A concept enumeration value from the metadata hierarchy that identifies the semantic type of the relationship. It is a subtype of 410,662,002 |Concept model attribute|. | SNOMED CT Relationship | Linkage Concept |
IsSourceOf | Determines the source of a relationship. It is the inverse of Relationship_sourceId. | SNOMED CT Concept | SNOMED CT Relationship |
IsDestinationOf | Determines the destination of a relationship. It is the inverse of Relationship_destinationId. | SNOMED CT Concept | SNOMED CT Relationship |
Grouped_Relations | Used to explicitly determine the grouped relationships | SNOMED CT Relationship | SNOMED CT Relationship |
Total number of object properties | 8 |
Property | Definition | Domain | Range |
---|---|---|---|
Concept_Id | The unique SNOMED CT Identifier for this Concept. | SNOMED CT Concept | String |
Description_term | The description’s text value, represented in UTF-8 encoding. | SNOMED CT Description | String |
Description_typeId | Identifies whether the description is an FSN, synonym, or other description type. | SNOMED CT Description | String |
Relationship_relationshipGroup | Groups together relationship versions that are part of a logically associated relationship group. | SNOMED CT Relationship | Integer |
Relationship_active | Specifies whether the relationship’s state is active or inactive. | SNOMED CT Relationship | Boolean |
Relationship_characteristicTypeId | A concept enumeration value that identifies the characteristic type of the relationship. | SNOMED CT Relationship | String |
…
| |||
Total number of data properties
|
20
|
Metric | Value |
---|---|
Number of classes | 304 |
Axioms | 2400 |
Object properties | 8 |
Data properties | 20 |
Maximum number of parents | 3 |
Average number of siblings | 3.62 |
Maximum number of children | 66 |
Average number of children | 3 |
Classes with more than 25 children | 1 |
Classes with a single child | 25 |
Maximum number of siblings | 66 |
Subclass axioms | 330 |
Annotations | 1555 |
Maximum depth | 8 |
Discussion
The study | Format | The base | Top-level ontology | Description logic | Modeled hierarchies | Publicly available | Size | Can model pre-coordinated concepts | Can model post-coordinated concepts | Handled semantics |
---|---|---|---|---|---|---|---|---|---|---|
Proposed SCTO | Ontology | SCM | BFO and OGMS | EL++ | Whole SCT | OWL format | Top-level concepts | Yes | Yes | Complete OWL axioms for all top-level SCT concepts |
SCT Perl script [3] | Ontology | No | No | EL++ | Whole SCT | Perl script | Low-level concepts | Yes | No | SCT taxonomy |
Schulz & Martínez-Costa [31] | Ontology | No | BioTopLite2 | OWL DL | Whole SCT | No | Top-level concepts | Yes | No | SCT taxonomy and basic relations |
Campbell et al. [20] | Graph database | No | No | No | Whole SCT | No | Low-level concepts | Yes | No | SCT taxonomy |
Martínez-Costa and Schulz [59] | Ontology | SCT context model | BioTopLite | OWLDL | Clinical findings | No | Low-level concepts | Yes | Yes | SCT taxonomy and basic relations |
Cheetham et al. [60] | Ontology | No | BioTopLite2 | OWLDL | Disorders | No | Low-level concepts | Yes | Yes | SCT taxonomy and basic relations |
Bodenreider [61] | Ontology | No | No | OWL EL | Disorders, procedures | No | Low-level concepts | Yes | No | SCT taxonomy |
Hogan [62] | Ontology | No | BFO | OWL EL | Whole SCT | No | Top-level concepts | No | No | SCT taxonomy |
Ochs et al. [63] | Abstraction network | No | No | No | Observable entity | No | Low-level concepts | Yes | No | SCT taxonomy |