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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.
Inferred relationships for concrete values, e.g. decimal, integer, string, or dateTime, should be included in a separate relationship file.
Rules for Determining Redundant Relationships
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Example for Class inclusion
Stated relationships
Inferred relationships before the removal of redundant relationshiprelationships
Inferred relationships after the reduction
For
, the relationship Concept ShowParts term t 12676007 |Fracture of radius|
= Concept ShowParts term t 363698007|Finding site|
is inherited from Concept ShowParts term t 299701004|Bone structure of radius and/or ulna|
, which is a redundant relationship because Concept ShowParts term t 65966004|Fracture of forearm|
is a subtype of Concept ShowParts term t 62413002|Bone structure of radius|
. The relationship Concept ShowParts term t 299701004|Bone structure of radius and/or ulna|
= Concept ShowParts term t 116676008|Associated morphology|
is inherited from Concept ShowParts term t 19130008|Traumatic abnormality|
, which is a redundant relationship because Concept ShowParts term t 429353004|Injury of radius|
is a subtype of Concept ShowParts term t 72704001|Fracture (morphologic abnormality)|
. Concept ShowParts term t 19130008|Traumatic abnormality|
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Example in OWL axiom refset and RF2 relationship file (NNF) |
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
Inferred relationships after reduction
For concept
, the relationship Concept ShowParts term t 7246002|Kidney biopsy|
= Concept ShowParts term t 363704007|Procedure site|
is inherited from Concept ShowParts term t 64033007|Kidney structure|
, which is a redundant relationship to Concept ShowParts term t 118851004|Procedure on kidney|
= Concept ShowParts term t 405813007|Procedure site - Direct|
because Concept ShowParts term t 64033007|Kidney structure|
is a subtype of Concept ShowParts term t 405813007|Procedure site - Direct|
. Because Concept ShowParts term t 363704007|Procedure site|
is a subtype of Concept ShowParts term t 64033007|Kidney structure|
and Concept ShowParts term t 122489005|Urinary system structure|
, the inherited relationships for Concept ShowParts term t 82849001|Retroperitoneal compartment structure|
are also redundant. Concept ShowParts term t 405813007|Procedure site - Direct|
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Example in OWL axiom refset and RF2 relationship file (NNF) |
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
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Attribute u is the same as or a subtype of t, and
D has a relationship to C via attribute s
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Example for property chain:
Stated relationships of
(the other model detail has been omitted): Concept ShowParts term t 323739006 |Product containing precisely amoxicillin (as amoxicillin sodium) 1 gram/1 vial powder for conventional release solution for injection (clinical drug)|
Stated relationships
of
Concept | ||||
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|
Inferred relationships before the removal of the redundant relationship
Inferred relationships after the reduction
For
, the relationship Concept ShowParts term t 422453004323739006 |Product containing ethyl morphineprecisely amoxicillin (as amoxicillin sodium) 1 gram/1 vial powder for conventional release solution for injection (clinical drug)|
= Concept ShowParts term t 127489000|Has active ingredient|
is inherited from Concept ShowParts term t 373529000372687004 |MorphineAmoxicillin|
. If the rule 1 for class inclusion was to applyapplied, the relationships would not be considered as redundant because Concept ShowParts term t 7357200927658006 |Product containing morphineamoxicillin|
is not a subconcept of Concept ShowParts term t 74905005427483001 |Ethylmorphine Amoxicillin sodium (substance)|
. Because Since Concept ShowParts term t 373529000372687004 |Morphine Amoxicillin (substance)| Concept ShowParts term t 74905005427483001 |Ethyl morphineAmoxicillin sodium| Concept ShowParts term t 738774007|Is modification of|
and property chain of of " Concept ShowParts term t 373529000372687004 |MorphineAmoxicillin|
and o Concept ShowParts term t 127489000|Has active ingredient|
" is a sub-property of Concept ShowParts term t 738774007|Is modification of|
, the rule 2 actually compares the anonymous concepts for subsumption, i.e. Concept ShowParts term t 127489000|Has active ingredient|
= Concept ShowParts term t 127489000|Has active ingredient (attribute)|
with Concept ShowParts term t 373529000 |Morphine (substance)372687004 |Amoxicillin|
= Concept ShowParts term t 127489000|Has active ingredient|
. Therefore, the inherited relationship is redundant and can be removed from the NNF. Their relationships and property chain can be demonstrated in the following diagram. Concept ShowParts term t 74905005427483001 |Ethyl morphineAmoxicillin sodium|
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Example in OWL axiom refset and RF2 relationship file (NNF) |
referencedComponentId | owlExpression (stated relationships) | Inferred Relationships in Necessary Normal Form | ||||||
sourceId | destinationId | relationshipGroup | typeId | 73572009|||||
27658006 | EquivalentClasses(: | 73572009 27658006 ObjectIntersectionOf(:763158003 ObjectSomeValuesFrom(:609096000 ObjectSomeValuesFrom(:127489000 : | 373529000372687004)))) | 7357200927658006 | 76488700590704004 | 0 | 116680003 | |
73572009 | 360204007 | 0 | 116680003 | |||||
27658006 | 372687004 | 73572009 | 3735290001 | 127489000 | 422453004||||
323739006 | EquivalentClasses(: | 422453004 323739006 ObjectIntersectionOf(:763158003 ObjectSomeValuesFrom(:609096000 ObjectSomeValuesFrom(: | 127489000 762949000 : | 74905005427483001)))) | 422453004323739006 | 7357200927658006 | 0 | 116680003 | 422453004
323739006 | 74905005427483001 | 1 | 127489000762949000 | |||||
127489000 | SubObjectPropertyOf(ObjectPropertyChain(:127489000 :738774007) :127489000)) | N/A | N/A | N/A | ||||
427483001 | SubClassOf(: | 74905005 427483001 ObjectIntersectionOf(:440327007 ObjectSomeValuesFrom(:738774007 : | 373529000372687004))) | 74905005427483001 | 440327007373298001 | 0 | 116680003 | 74905005|
427483001 | 373529000372687004 | 0 | 738774007 | |||||
427483001 | 768681000 | 0 | 726542003 |
Technical Implementation for Calculating the NNF
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Read the Stated Form from RF2 files.
The following files are required: Concept, Stated Relationship, OWL Ontology Reference Set, OWL Axiom Reference Set.
If the edition has any active stated relationships then the Stated Relationship and MRCM Attribute Domain Reference Set files are also required.
Use the OWL API to infer the class hierarchy
Build the Ontology object using:
Axioms from the OWL Axiom Reference Set, making a note of any Transitive property and Property Chain axioms.
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.
Use a reasoner to pre-compute the class hierarchy.
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Calculating the necessary normal form happens in two passes of the hierarchy.org.snomed.otf.owltoolkit.normalform
Walk the class hierarchy in a top-down, breadth first, order.
For each class visited gather the stated attributes of this class and each inferred parent.
Compare the attributes and remove those which are found to be redundant because they are less specific in terms of depth in the hierarchy.
During this first pass build a hierarchy for property chains and transitive properties.
Walk the class hierarchy again in the same order reducing the attributes of each class further.
Compare the attributes and remove those which are found to be redundant because they are less specific in terms of depth in one of the alternate hierarchies.
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All
relationships should be assigned in role group 0;Concept t 116680003 |Is a| Attribute that is not grouped, not a value of
or grouped=0 in MRCM, should be assigned in role group 0;Concept ShowParts term t 609096000 |Role group (attribute)| - Attribute that is grouped, value of
or grouped=1 in MRCM, should be assigned in a role group 1 or abovenumber that is not 0. EachConcept ShowParts term t 609096000 |Role group (attribute)|
in the OWL axiom should be presented by a unique role group number. Note, role group merging is not covered here.Concept ShowParts term t 609096000 |Role group (attribute)|
Concept | ||
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An example for the current diagram representation for attribute in role group 0 in the stated relationship file and concept model diagram
sourceId | destinationId | relationshipGroup | typeId |
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90708001 | 64033007 | 0 | 363698007 |
After the complete OWL axiom refset is implemented,
Concept | ||||
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referencedComponentId | owlExpression |
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90708001 | EquivalentClasses(:90708001 ObjectIntersectionOf(:64572001 ObjectSomeValuesFrom(:609096000 ObjectSomeValuesFrom(:363698007 :64033007)))) |
Representation of
Concept | ||||
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sourceId | destinationId | relationshipGroup | typeId |
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90708001 | 734045002 | 0 | 116680003 |
90708001 | 443820000 | 0 | 116680003 |
90708001 | 249578005 | 0 | 116680003 |
90708001 | 64033007 | 1 | 363698007 |