Subsumption test - Revision history

DavidStables at 09:00, 17 May 2020

2020-05-17T09:00:46Z

← Older revision		Revision as of 09:00, 17 May 2020
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	<div class="mw-collapsible-content">		<div class="mw-collapsible-content">
	~~<syntaxhighlight lang="JSON">~~
	<pre>		<pre>
	EquivalentClasses(		EquivalentClasses(

DavidStables at 09:00, 17 May 2020

2020-05-17T09:00:10Z

← Older revision		Revision as of 09:00, 17 May 2020
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	ObjectSomeValuesFrom(		ObjectSomeValuesFrom(
	:370135005 \|Pathological process (attribute)\|		:370135005 \|Pathological process (attribute)\|
	:441862004 \|Infectious process (qualifier value)\|		:441862004 \|Infectious process (qualifier value)\|)))))
	)
	)
	)
	)
	)
	</pre></div></div>		</pre></div></div>

DavidStables at 08:59, 17 May 2020

2020-05-17T08:59:19Z

← Older revision		Revision as of 08:59, 17 May 2020
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	To make this work it is usually necessary to have a concept Y, properly defined using an [https://en.wikepedia.or/wiki/axiom axiom] defined in something like the ontology language [https://www.w3.org/TR/owl2-syntax OWL2]		To make this work it is usually necessary to have a concept Y, properly defined using an [https://en.wikepedia.or/wiki/axiom axiom] defined in something like the ontology language [https://www.w3.org/TR/owl2-syntax OWL2]

	For example, the axiom (Manchester syntax) :		For example, the axiom (Manchester OWL syntax) :

	<span style="color:#8e44ad;">Covid 19 {</span><span style="color:#27ae60;">EquivalentTo</span><span style="color:#8e44ad;"> : Disease </span>		<span style="color:#8e44ad;">Covid 19 {</span><span style="color:#27ae60;">EquivalentTo</span><span style="color:#8e44ad;"> : Disease </span>
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	Thus a search for diseases that are infectious and have causative agents that are viruses would pick up Covid 19 because coronavirus 2 is a subclass of virus.		Thus a search for diseases that are infectious and have causative agents that are viruses would pick up Covid 19 because coronavirus 2 is a subclass of virus.

			The following show the same expression in the different syntaxes supported by Discovery

	<div class="toccolours mw-collapsible mw-collapsed">		<div class="toccolours mw-collapsible mw-collapsed">

DavidStables at 08:58, 17 May 2020

2020-05-17T08:58:08Z

← Older revision		Revision as of 08:58, 17 May 2020
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	)		)
	</pre></div></div>		</pre></div></div>


	<div class="toccolours mw-collapsible mw-collapsed">		<div class="toccolours mw-collapsible mw-collapsed">

DavidStables at 08:57, 17 May 2020

2020-05-17T08:57:27Z

@@ Line 72: / Line 72: @@
+	)
+)
 </pre></div></div>

DavidStables at 08:54, 17 May 2020

2020-05-17T08:54:34Z

← Older revision		Revision as of 08:54, 17 May 2020
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	"ObjectSome": {		"ObjectSome": {
	"Property":"246075003 \|Causative agent (attribute)",		"Property":"246075003 \|Causative agent (attribute)",
	"Class" : "840533007 \|Severe acute respiratory syndrome coronavirus 2 (organism) }},		"Class" : "840533007 \|Severe acute respiratory syndrome coronavirus 2 (organism)" }},
	{"ObjectSome": {		{"ObjectSome": {
	"Property":"370135005 \|Pathological process (attribute)",		"Property":"370135005 \|Pathological process (attribute)",

DavidStables at 08:54, 17 May 2020

2020-05-17T08:54:11Z

← Older revision		Revision as of 08:54, 17 May 2020
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	"EquivalentTo": {		"EquivalentTo": {
	"Intersection": [{		"Intersection": [{
	"Class": ":"64572001 \|Disease (disorder)",		"Class": "64572001 \|Disease (disorder)",
	"ObjectSome": {		"ObjectSome": {
	"Property": "609096000 \|Role group (attribute)",		"Property": "609096000 \|Role group (attribute)",

DavidStables at 08:53, 17 May 2020

2020-05-17T08:53:26Z

← Older revision		Revision as of 08:53, 17 May 2020
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	Thus a search for diseases that are infectious and have causative agents that are viruses would pick up Covid 19 because coronavirus 2 is a subclass of virus.		Thus a search for diseases that are infectious and have causative agents that are viruses would pick up Covid 19 because coronavirus 2 is a subclass of virus.

			<div class="toccolours mw-collapsible mw-collapsed">
			Discovery syntax

			<div class="mw-collapsible-content">
			<syntaxhighlight lang="JSON">
			{"iri" :" :840539006 \|Disease caused by severe acute respiratory syndrome coronavirus 2 (disorder)",
			"EquivalentTo": {
			"Intersection": [{
			"Class": ":"64572001 \|Disease (disorder)",
			"ObjectSome": {
			"Property": "609096000 \|Role group (attribute)",
			"Intersection" : [{
			"ObjectSome": {
			"Property":"246075003 \|Causative agent (attribute)",
			"Class" : "840533007 \|Severe acute respiratory syndrome coronavirus 2 (organism) }},
			{"ObjectSome": {
			"Property":"370135005 \|Pathological process (attribute)",
			"Class":"441862004 \|Infectious process (qualifier value)"}}]}}]}}
			</syntaxhighlight>

			</div></div>


			<div class="toccolours mw-collapsible mw-collapsed">
			OWL2 Functional syntax

			<div class="mw-collapsible-content">
			<syntaxhighlight lang="JSON">
			<pre>
			EquivalentClasses(
			:840539006 \|Disease caused by severe acute respiratory syndrome coronavirus 2 (disorder)\|
			ObjectIntersectionOf(
			:64572001 \|Disease (disorder)\|
			ObjectSomeValuesFrom(
			:609096000 \|Role group (attribute)\|
			ObjectIntersectionOf(
			ObjectSomeValuesFrom(
			:246075003 \|Causative agent (attribute)\|
			:840533007 \|Severe acute respiratory syndrome coronavirus 2 (organism)\|
			)
			ObjectSomeValuesFrom(
			:370135005 \|Pathological process (attribute)\|
			:441862004 \|Infectious process (qualifier value)\|
			)
			)
			)
			)
			)
			</pre></div></div>

	In practice, one of two types of techniques are employed when using subsumption testing in queries:		In practice, one of two types of techniques are employed when using subsumption testing in queries:

DavidStables at 08:47, 4 May 2020

2020-05-04T08:47:35Z

← Older revision		Revision as of 08:47, 4 May 2020
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	The challenge to overcome is that in most cases, the relevant concepts that are X are not within a hierarchy of codes as specified by Y. There is no classification of diseases organised by whether they are communicable AND caused by viruses. Instead it is necessary to use a process called  [https://en.wikepedia.org/wiki/inference inference] to determine whether something is subsumed by something.		The challenge to overcome is that in most cases, the relevant concepts that are X are not within a hierarchy of codes as specified by Y. There is no classification of diseases organised by whether they are communicable AND caused by viruses. Instead it is necessary to use a process called  [https://en.wikepedia.org/wiki/inference inference] to determine whether something is subsumed by something.

	To make this work it is usually necessary to have a concept Y, properly defined using an [https://en.wikepedia.or/wiki/axiom axiom] defined in the ontology language [https://www.w3.org/TR/owl2-syntax OWL2]		To make this work it is usually necessary to have a concept Y, properly defined using an [https://en.wikepedia.or/wiki/axiom axiom] defined in something like the ontology language [https://www.w3.org/TR/owl2-syntax OWL2]

	For example, the axiom (Manchester syntax) :		For example, the axiom (Manchester syntax) :
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	'''Is concept X subsumed by Y. ''' In this case the concept X definition is used against the concept Y definition, such  test usually including all other definitions in the ontology that are subsumed by Y.  This is more commonly used in decision support.		'''Is concept X subsumed by Y. ''' In this case the concept X definition is used against the concept Y definition, such  test usually including all other definitions in the ontology that are subsumed by Y.  This is more commonly used in decision support.

	Thus subsumption testing requires an information model that contains a properly authored ontology		Thus subsumption testing requires an information model that contains a properly authored ontology.

DavidStables at 08:45, 4 May 2020

2020-05-04T08:45:53Z

← Older revision		Revision as of 08:45, 4 May 2020
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	Subsumption testing is the mainstay of health record query. It is the major differentiator of health care records from conventional database records that have simple codes or data types as values.		Subsumption testing is the mainstay of health record query. It is the major differentiator of health care records from conventional database records that have simple codes or data types as values.

	To take an example, when examining an entry in a health record that purports to be a ~~diganosis~~, one could ask "is this diagnosis a communicable disease caused by a virus?".		To take an example, when examining an entry in a health record that purports to be a diagnosis, one could ask "is this diagnosis a communicable disease caused by a virus?".

	Conversely, one might be interested in finding all the entries in a population of health records that are "communicable diseases caused by a virus", or even a question against an ontology such as "Get me a list of all communicable diseases caused by a virus".		Conversely, one might be interested in finding all the entries in a population of health records that are "communicable diseases caused by a virus", or even a question against an ontology such as "Get me a list of all communicable diseases caused by a virus".
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	<span style="color:#8e44ad;">                </span><span style="color:#27ae60;">and</span><span style="color:#8e44ad;">(has_pathological_process </span><span style="color:#27ae60;">some</span><span style="color:#8e44ad;"> infectious_process)}.</span>		<span style="color:#8e44ad;">                </span><span style="color:#27ae60;">and</span><span style="color:#8e44ad;">(has_pathological_process </span><span style="color:#27ae60;">some</span><span style="color:#8e44ad;"> infectious_process)}.</span>

	Thus a search for diseases that are infectious and have causative agents that are viruses would pick up Covid 19 because ~~coranvirus~~ 2 is a ~~siubclass~~ of virus.		Thus a search for diseases that are infectious and have causative agents that are viruses would pick up Covid 19 because coronavirus 2 is a subclass of virus.

	In practice, one of two types of techniques are employed when using subsumption testing in queries:		In practice, one of two types of techniques are employed when using subsumption testing in queries: