SNOMED CT OWL Guide

Search

SNOMED CT Document Library

    Loading...

Versions Compared

Old Version 3

changes.mady.by.user Yongsheng Gao

Saved on

compared with

New Version 4

changes.mady.by.user David Markwell

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

The logic definitions are represented by the OWL axiom refset that is a replacement of the RF2 stated relationship file. As a result, the nature of the inferred relationship file in the distribution normal form (DNF) has changed because the new DL features are not representable in the current relationships file. The inferred relationship file will maintain the same format and structure, but it is no longer equivalent to the stated form (containing all necessary and sufficient conditions). In fact, it is a collection of all the necessary conditions of precoordinated concepts and represents a subset of the full semantics.

Necessary Normal Form

The Necessary Normal Form (NNF) is a replacement for the Distribution Normal Form for inferred relationships. The NNF is a precalculated distribution form for practical purposes, for example, to support the continuity of existing implementations based on relational databases and queries by the expression constraint language.

...

The NNF does not include class disjointness, transitive properties, reflexive properties and sufficient conditions represented as General Concept Inclusions (GCIs) in the OWL axiom refset.

Rules for determining redundant relationships

Rule 1 - Class and Role inclusions


Given two relationships, A and B, A with r = C and B with s = D, within the same role group, A is redundant if:

...

Note, “crossover relationships”, where r is a supertype of s, and C is instead a subtype of D do not result in a redundant relationship.

Example for Class inclusion

Stated relationships


Inferred relationships before the removal of redundant relationship

...

referencedComponentId


owlExpression

(stated relationships)

Inferred Relationships in Necessary Normal Form

sourceId

destinationId

relationshipGroup

typeId

125605004

EquivalentClasses(:125605004 ObjectIntersectionOf(:64572001 ObjectSomeValuesFrom(:609096000 ObjectIntersectionOf(ObjectSomeValuesFrom(:116676008 :72704001) ObjectSomeValuesFrom(:363698007 :272673000)))))

125605004

284003005

0

116680003

125605004

72704001

1

116676008

125605004

272673000

1

363698007

12676007

EquivalentClasses(:12676007 ObjectIntersectionOf(:64572001 ObjectSomeValuesFrom(:609096000 ObjectIntersectionOf(ObjectSomeValuesFrom(:116676008 :72704001) ObjectSomeValuesFrom(:363698007 :62413002)))))

12676007

65966004

0

116680003

12676007

429353004

0

116680003

12676007

72704001

1

116676008

12676007

62413002

1

363698007

62413002

SubClassOf(:62413002 :299701004)

62413002

299701004

0

116680003

Example for Role inclusion

Stated relationships

Inferred relationships before the removal of redundant relationship

...

referencedComponentId


owlExpression

(stated relationships)

Inferred Relationships in Necessary Normal Form

sourceId

destinationId

relationshipGroup

typeId

118851004

EquivalentClasses(:118851004 ObjectIntersectionOf(:71388002 ObjectSomeValuesFrom(:609096000 ObjectSomeValuesFrom(:363704007 :64033007))))

118851004

71388002

0

116680003

118851004

64033007

1

363704007

7246002

EquivalentClasses(:7246002 ObjectIntersectionOf(:71388002 ObjectSomeValuesFrom(:609096000 ObjectIntersectionOf(ObjectSomeValuesFrom(:260686004 :129314006) ObjectSomeValuesFrom(:405813007 :64033007)))))

7246002

118851004

0

116680003

7246002

362995002

0

116680003

7246002

430212007

0

116680003

7246002

129314006

1

260686004

7246002

64033007

1

405813007

405813007

SubObjectPropertyOf(:405813007 :363704007)

405813007

363704007

0

116680003

Rule 2 - Property chains including transitive properties


Given attribute r, s and t with a property chain SubObjectPropertyOf(ObjectPropertyChain(t s) r), and two relationships A and B, A with r = C and B with u = D, within the same role group, A is redundant if:

...

     SubObjectPropertyOf(ObjectPropertyChain(r r) r) and thus it is a special case of the above.

Example for property chain:

Stated relationships

Inferred relationships before the removal of redundant relationship

...

referencedComponentId


owlExpression

(stated relationships)

Inferred Relationships in Necessary Normal Form

sourceId

destinationId

relationshipGroup

typeId

73572009

EquivalentClasses(:73572009 ObjectIntersectionOf(:763158003 ObjectSomeValuesFrom(:609096000 ObjectSomeValuesFrom(:127489000 :373529000))))

73572009

764887005

0

116680003

73572009

360204007

0

116680003

73572009

373529000

1

127489000

422453004

EquivalentClasses(:422453004 ObjectIntersectionOf(:763158003 ObjectSomeValuesFrom(:609096000 ObjectSomeValuesFrom(:127489000 :74905005))))

422453004

73572009

0

116680003

422453004

74905005

1

127489000

127489000

SubObjectPropertyOf(ObjectPropertyChain(:127489000 :738774007) :127489000))

N/A

N/A


N/A

74905005

SubClassOf(:74905005 ObjectIntersectionOf(:440327007 ObjectSomeValuesFrom(:738774007 :373529000)))

74905005

440327007

0

116680003

74905005

373529000

0

738774007


Technical implementation for calculating the NNF

This fairly complex process uses the stated form and the output of the reasoner to calculate the necessary normal form which is represented in the relationship RF2 file.

The most straightforward way to produce the necessary normal form would be to use the Snomed OWL Toolkit or the Classification Service REST API which is language agnostic.

High Level Process

Classification

  1. Read the Stated Form from RF2 files.

    1. The following files are required: Concept, Stated Relationship, OWL Ontology Reference Set, OWL Axiom Reference Set and MRCM Attribute Domain Reference Set.

  2. Use the OWL API to infer the class hierarchy

    1. Build the Ontology object using:

      1. Axioms from the OWL Axiom Reference Set, making a note of any Transitive property axioms.

      2. Axioms created by converting Stated Relationships to OWL Axioms using the MRCM Attribute Domain Reference Set for list of attributes which should not be grouped in the given domain.

    2. Use a reasoner to pre-compute the class hierarchy.

Necessary Normal Form Calculation

Calculating the necessary normal form happens in two passes of the hierarchy.

...