Sets and classes - Revision history

DavidStables at 10:37, 7 July 2021

2021-07-07T10:37:21Z

DavidStables at 10:28, 7 July 2021

2021-07-07T10:28:59Z

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DavidStables: DavidStables moved page Value sets to Sets and classes

2021-07-07T07:57:06Z

DavidStables moved page Value sets to Sets and classes

← Older revision	Revision as of 07:57, 7 July 2021
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DavidStables at 11:20, 26 May 2020

2020-05-26T11:20:33Z

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	<div class="mw-collapsible-content">		<div class="mw-collapsible-content">
	<syntaxhighlight lang="JSON">		<syntaxhighlight lang="JSON">
			Firstly the value set is semantically defined in the semantic ontology
	{ "Class":{		{ "Class":{
	"iri": ":VSET_NonHospFaceToFace",		"iri": ":VSET_NonHospFaceToFace",
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	"SubClassOf": {"Class":":VSET_GPConsultations"}} // The value set is a subclass of a set of value sets about GP consultations		"SubClassOf": {"Class":":VSET_GPConsultations"}} // The value set is a subclass of a set of value sets about GP consultations

			Then the value set is defined in the value set class
	{"ValueSet":{		{"ValueSet":{
	"iri": "VSET_NonHospFaceToFace",		"iri": "VSET_NonHospFaceToFace",

DavidStables at 11:19, 26 May 2020

2020-05-26T11:19:01Z

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	"SubClassOf": {"Class":":VSET_GPConsultations"}} // The value set is a subclass of a set of value sets about GP consultations		"SubClassOf": {"Class":":VSET_GPConsultations"}} // The value set is a subclass of a set of value sets about GP consultations

	{"ValueSet":{"iri": "VSET_NonHospFaceToFace",		{"ValueSet":{
	"Member":[{		"iri": "VSET_NonHospFaceToFace",
	"Intersection": [ ~~// AN~~ // AND~~....~~		"Member":[{
	{"Class": ":CM_OnPremiseEncounter"},		"Intersection": [ // AND
	{"Negation": { "Class": ":DM_HospitalOpdEntry"}}]}}]}]}} // BUT NOT...		{"Class": ":CM_OnPremiseEncounter"},
			{"Negation": { "Class": ":DM_HospitalOpdEntry"}}]}}]}]}} // BUT NOT...
	</syntaxhighlight>		</syntaxhighlight>

DavidStables at 11:17, 26 May 2020

2020-05-26T11:17:39Z

← Older revision		Revision as of 11:17, 26 May 2020
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	<div class="mw-collapsible-content">		<div class="mw-collapsible-content">
	<syntaxhighlight lang="JSON">		<syntaxhighlight lang="JSON">
	{ "iri": ":VSET_NonHospFaceToFace",		{ "Class":{
			"iri": ":VSET_NonHospFaceToFace",
	"name": ":face to face consultations excluding hospital outpatients",		"name": ":face to face consultations excluding hospital outpatients",
	"SubClassOf": ~~[{ // The value set is a subclass of..~~		"SubClassOf": {"Class":":VSET_GPConsultations"}} // The value set is a subclass of a set of value sets about GP consultations
	~~"Intersection": [ // AND~~
	{ "Class": ":VSET_GPConsultations" }~~, This~~ value set is a subclass of ~~another~~ value ~~set~~		{"ValueSet":{"iri": "VSET_NonHospFaceToFace",
	{ "~~ObjectSome~~":{		"Member":[{
	"~~Property~~": "~~:CM_hasMember~~",		"Intersection": [ // AN // AND....
	"Intersection": [ // AND....
	{"Class": ":CM_OnPremiseEncounter"},		{"Class": ":CM_OnPremiseEncounter"},
	{"Negation": { "Class": ":DM_HospitalOpdEntry"}}]}}]}]}} // BUT NOT...		{"Negation": { "Class": ":DM_HospitalOpdEntry"}}]}}]}]}} // BUT NOT...

DavidStables: /* Value set class and language */

2020-05-26T10:45:12Z

Value set class and language

← Older revision		Revision as of 10:45, 26 May 2020
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	All value sets and the class expressions use concepts from the semantic ontology and the following shows the relationship between the two.		All value sets and the class expressions use concepts from the semantic ontology and the following shows the relationship between the two.

	~~Avalue~~ set class definition~~ looks very much like a semantic~~ ontology class expression~~,  ~~in ~~that it uses similar grammar and syntax~~. ~~In fact~~ a value set ~~can also be defined~~ in ~~OWL2 language~~.		The main difference between a value set expression and its syntactically equivalent class definition in the ontology is the way the value set is used. Within an ontology the class expression is normally used as part of an axiom for use in reasoning. Within a query a value set is used to test the value of a concept in a record. Within a data model, a value set is used as a range of allowable or preferred values for a particular property where the values do not belong to one class.






			A value set class definition looks very much like a semantic ontology class expression,  in that it uses similar grammar and syntax. In fact a value set can also be defined in OWL2 language.

	In this example a non hospital face to face consultation value set is defined as		In this example a non hospital face to face consultation value set is defined as
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	== Value set definition vs ontology axiom ==		== Value set definition vs ontology axiom ==

	~~The~~ main difference between an ontological axiom and a value set definition is their purpose and the way they are used.		As discussed above, the main difference between an ontological axiom and a value set definition is their purpose and the way they are used.

	Members of a value set set may or may not shared similar properties and therefore may be semantically diverse.  Nevertheless each member of a value set is a class expression with semantic meaning. Each member is used to define a set of concepts so that a [[subsumption test]] can be applied to the care record concept instances.		Members of a value set set may or may not shared similar properties and therefore may be semantically diverse.  Nevertheless each member of a value set is a class expression with semantic meaning. Each member is used to define a set of concepts so that a [[subsumption test]] can be applied to the care record concept instances.

DavidStables: /* Value set class and language */

2020-05-26T10:41:02Z

Value set class and language

← Older revision		Revision as of 10:41, 26 May 2020
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	== Value set class and language ==		== Value set class and language ==

			[[File:Value set class.png\|Value set class\|alt=\|thumb]]
	A value set class is best conceptualised in UML terms as a package whose elements are class expressions.		A value set class is best conceptualised in UML terms as a package whose elements are class expressions.

	All value sets and the class expressions use concepts from the semantic ontology and the following shows the relationship between the two.~~[[File:Value set class.png\|Value set class\|alt=\|thumb]]~~		All value sets and the class expressions use concepts from the semantic ontology and the following shows the relationship between the two.

	Avalue set class definition looks very much like a semantic ontology class expression,  in that it uses similar grammar and syntax. In fact a value set can also be defined in OWL2 language.		Avalue set class definition looks very much like a semantic ontology class expression,  in that it uses similar grammar and syntax. In fact a value set can also be defined in OWL2 language.

DavidStables at 10:40, 26 May 2020

2020-05-26T10:40:28Z

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			[[File:Information model value sets.png\|thumb\|Value set package]]

	A value set definition, and it's run time counterpart- value set transitive closure  , is a set of [[Concepts_classes_and_properties\|class expressions]] collected together for a particular business purpose.		A value set definition, and it's run time counterpart- value set transitive closure  , is a set of [[Concepts_classes_and_properties\|class expressions]] collected together for a particular business purpose.
	~~[[File:Information model value sets.png\|thumb\|Value set package]]~~
	There are a range of purposes for a value set. Examples range from defining a data set according to a set of recorded concepts, indicating the expected range of a property in a health record, or testing the presence of a feature in a patient record.		There are a range of purposes for a value set. Examples range from defining a data set according to a set of recorded concepts, indicating the expected range of a property in a health record, or testing the presence of a feature in a patient record.

DavidStables at 10:39, 26 May 2020

2020-05-26T10:39:34Z

← Older revision		Revision as of 10:39, 26 May 2020
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	A value set definition, and it's run time counterpart- value set transitive closure  , is a set of [[Concepts_classes_and_properties\|class expressions]] collected together for a particular business purpose.		A value set definition, and it's run time counterpart- value set transitive closure  , is a set of [[Concepts_classes_and_properties\|class expressions]] collected together for a particular business purpose.
			[[File:Information model value sets.png\|thumb\|Value set package]]
			There are a range of purposes for a value set. Examples range from defining a data set according to a set of recorded concepts, indicating the expected range of a property in a health record, or testing the presence of a feature in a patient record.

	~~There~~ are ~~a range~~ of ~~purposes for a value set. Examples range from defining a data set according to a set of recorded concepts, indicating~~ the ~~expected range of a property in a health record, or testing~~ the ~~presence of a feature in a patient record~~.~~ ~~		Value sets are one of the main 5 packages within the common information model.

	~~Value sets are one of the main 4 packages within the common information model:[[File:IM Package Value set.jpg\|center\|400x250px\|IM Package Value set.jpg]]~~

	== Value set class and language ==		== Value set class and language ==
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	A value set class is best conceptualised in UML terms as a package whose elements are class expressions.		A value set class is best conceptualised in UML terms as a package whose elements are class expressions.

	All value sets and the class expressions use concepts from the semantic ontology and the following shows the relationship between the two.[[File:Value set class.png\|~~center~~\|~~800x600px~~\|~~Value~~ set class.~~png]]~~		All value sets and the class expressions use concepts from the semantic ontology and the following shows the relationship between the two.[[File:Value set class.png\|Value set class\|alt=\|thumb]]

			Avalue set class definition looks very much like a semantic ontology class expression,  in that it uses similar grammar and syntax. In fact a value set can also be defined in OWL2 language.






	A value set class definition looks very much like a semantic ontology class expression,  in that it uses similar grammar and syntax. In fact a value set can also be defined in OWL2 language.

	In this example a non hospital face to face consultation value set is defined as		In this example a non hospital face to face consultation value set is defined as

← Older revision		Revision as of 10:37, 7 July 2021
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	Sets are collections of things. Members of a set (items in a set) may or may not share properties with each other.		Sets are collections of things. Members of a set (items in a set) may or may not share properties with each other.

	Classes are collections of things with common properties. Members of a class all share ~~some~~ of ~~their properties~~. A member of a class which is specialised by dint of having additional properties to the class is considered a subclass.		Classes are collections of things with common properties. Members of a class all share the properties of the class definition. A member of a class which is specialised by dint of having additional properties to the class is considered a subclass.

	Sets are the single most significant structure used in health query. ~~A whole set of~~ terms are in common use to describe different sets. In the information model the terms "concept sets" and "value sets" are the ones used, the former being defined for use in query and the latter to define expected values of properties in records.		Sets are the single most significant structure used in health query. Many terms are in common use to describe different purposes of sets. In the information model the terms "concept sets" and "value sets" are the ones used, the former being defined for use in query and the latter to define expected values of properties in records.

	Snomed-CT uses the term 'reference set' which is semantically the same as a concept set.		Snomed-CT uses the term 'reference set' which is semantically the same as a concept set. Some use the term "code sets" when interested in the codes of the concepts in a set.

	'''''It should not noted that an entity may be explicitly defined as being both a class (e.g. a Snomed-CT concept), and a Set (e.g. Ethnic category - 2001 Census). In other words an entity ~~with~~ two types.'''''		'''''It should not noted that an entity may be explicitly defined as being both a class (e.g. a Snomed-CT concept), and a Set (e.g. Ethnic category - 2001 Census). In other words an entity can have two types.'''''

	(This creates an interesting twist as a search for the subclasses of '''''Ethnic category - 2001 Census''''' would produce different results from a search for all members of subsets of '''''Ethnic category - 2001 Census)''''' In other words, how the concept is treated is determined by the use case.		(This creates an interesting twist as a search for the subclasses of '''''Ethnic category - 2001 Census''''' would produce different results from a search for all members of subsets of '''''Ethnic category - 2001 Census)''''' In other words, how the concept is treated is determined by the use case and the query.

	Set definitions can be simple or complex and fall into 2 main patterns:		Set definitions can be simple or complex and fall into 2 main patterns:

	== Sets whose members are expressions ==		== Sets whose members are expressions ==
	This pattern forms the majority of ~~sets~~.		This pattern forms the majority of set definitions.

	The set is given an identifier (an IRI) and is defined as a concept in its own right. This set pattern then has two predicates:		The set is given an identifier (an IRI) and is defined as a concept in its own right. This set pattern then has two predicates:

	# has Members. Which is a collection of class expressions (e.g. simple concepts or complex expressions)		# has Members. Which is a collection of class expressions (e.g. simple concepts or complex expressions)
	# not Members. Which is a collection of class expressions that are excluded from the set i.e. those that would otherwise have been included as subclasses of the 'has member' collection.		# not Members. Which is a collection of class expressions that are excluded from the set i.e. those that would otherwise have been included as subclasses of the 'has member' collection
	<syntaxhighlight lang="turtle">
			For example, the following set definition for a positive family history has one member and one excluded member:<syntaxhighlight lang="turtle">
	im:VSET_RecordType_FamilyHistory // This is a value set for family history		im:VSET_RecordType_FamilyHistory // This is a value set for family history
	rdf:type [ im:ConceptSet ];		rdf:type [ im:ConceptSet ];
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	The set is given an identifier and has on predicate:		The set is given an identifier and has on predicate:

	# has Subset. Which is a collection of subsets which may be either member based sets or subset based ~~sets~~		# has Subset. Which is a collection of subsets which may be either member based sets or subset based set
	<syntaxhighlight lang="turtle">
			The following example lists two of the categories of the ethnic category set.<syntaxhighlight lang="turtle">
	sn:92381000000106 \|Ethnic category - 2001 census (finding)\|		sn:92381000000106 \|Ethnic category - 2001 census (finding)\|
	rdf:type [owl:Class im:ConceptSet];		rdf:type [owl:Class im:ConceptSet];
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	== Set definitions versus set expansions ==		== Set definitions versus set expansions ==
	Sets are usually defined with only a few members. Each member is a class definition.		Sets are usually defined with only a few members although in some cases can get quite large. Each member is a class definition. In general it is better to define sets with "high level" concepts so that when new child concepts are added in later the actual set used is updated.

	When used in query it is usually necessary to use the "expanded" set which is in effect all of the subclasses of each member, obtained via a transitive closure of the "isa" or "subClassOf" predicate.		When used in query it is usually necessary to use the "expanded" set which is in effect all of the instances of the subclasses of each member, obtained via a transitive closure of the "isa" or "subClassOf" predicate. (N.B a class is always a subclass of itself)

	Thus the following query would be used to expand a member based concept set as above. Note that the im:isA predicate is the same as the Snomed-CT "is a" relationship and the same as rdfs:subClassOf.<syntaxhighlight lang="sparql">		Thus the following query would be used to expand a member based concept set as above. Note that the im:isA predicate is the same as the Snomed-CT "is a" relationship and the same as rdfs:subClassOf.<syntaxhighlight lang="sparql">
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	== Sets and codes ==		== Sets and codes ==
	The health service still relies on codes to identify concepts ~~(classes) and concepts as sets~~.		The health service still relies on codes to identify concepts.

	As in the ontology as a whole, a concept may be associated with many codes from many schemes. These codes can then be used in categorising outputs		As in the ontology as a whole, a concept may be associated with many codes from many schemes. These codes can then be used in categorising outputs
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	The query says "get the concept and NHS Data Dictionary category code of the members of the ethnicity 2001 set".		The query says "get the concept and NHS Data Dictionary category code of the members of the ethnicity 2001 set".

	Logically this ~~SPQRQL~~ graph query traverses from the set identifier (2001 census ethnic categories) to its subsets (e.g. African) to the code of the subset (e.g. N) the scheme of the code being NHS Data dictionary Ethnic Categories 2001.<syntaxhighlight lang="sparql">		Logically this SPARQL graph query traverses from the set identifier (2001 census ethnic categories) to its subsets (e.g. African) to the code of the subset (e.g. N) the scheme of the code being NHS Data dictionary Ethnic Categories 2001.<syntaxhighlight lang="sparql">
	select ?concept ?category		select ?concept ?category
	where {		where {
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	An example of generated code from a mapped SQL operating on a relational model, which logically performs the same expansion could be<syntaxhighlight lang="sql">		An example of generated code from a mapped SQL operating on a relational model, which logically performs the same expansion, and extended to include the none core codes could be <syntaxhighlight lang="sql">
	select locals.code as localCode,tc.code as categoryCode		select locals.code as localCode,tc.code as categoryCode
	from entity e		from entity e