Subsumption test: Difference between revisions
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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 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 the ontology language [https://www.w3.org/TR/owl2-syntax OWL2] | ||
For example, the axiom (Manchester syntax) : <span style="color:#8e44ad;">Covid 19 {</span><span style="color:#27ae60;">EquivalentTo</span><span style="color:#8e44ad;"> : Disease </span><span style="color:#27ae60;">and</span><span style="color:#8e44ad;">(causative_agent </span><span style="color:#27ae60;">some</span><span style="color:#8e44ad;">coronavirus-2) </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> | For example, the axiom (Manchester syntax) : | ||
<span style="color:#8e44ad;">Covid 19 {</span><span style="color:#27ae60;">EquivalentTo</span><span style="color:#8e44ad;"> : Disease </span> | |||
<span style="color:#8e44ad;"> </span><span style="color:#27ae60;">and</span><span style="color:#8e44ad;">(causative_agent </span><span style="color:#27ae60;">some </span><span style="color:#8e44ad;">coronavirus-2)</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 coranvirus 2 is a siubclass 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: | ||
'''Generate a list of concepts of type Y. ''' In this case a function determines all of the possible concepts X1... Xn that are subsumed by Y | '''Generate a list of concepts of type Y. ''' In this case a function determines all of the possible concepts X1... Xn in the ontology that are subsumed by Y. This list is used as a join or test against concepts store in records. This is the commonest technique. Type Y is normally part of a value set. | ||
'''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 | ||
Revision as of 11:19, 1 May 2020
A subsumption test is the act of testing X to see if is subsumed by Y. The question can also be reversed by asking "Does Y subsume X?".
if X is subsumed by Y it means that all objects of type X are also objects of type Y. Class X is thus either a subclass of class Y, or is equivalent to class Y
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?".
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".
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 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 axiom defined in the ontology language OWL2
For example, the axiom (Manchester syntax) :
Covid 19 {EquivalentTo : Disease
and(causative_agent some coronavirus-2)
and(has_pathological_process some infectious_process)}.
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.
In practice, one of two types of techniques are employed when using subsumption testing in queries:
Generate a list of concepts of type Y. In this case a function determines all of the possible concepts X1... Xn in the ontology that are subsumed by Y. This list is used as a join or test against concepts store in records. This is the commonest technique. Type Y is normally part of a value set.
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