Process for updating the ontology with the RCMT data
The following steps are followed to add RCMT data into the ontology.
1. Identify the LOINC codes that are missing from the ontology on a disease-bydisease basis.
2. The ‘Terminology’ class has a new subclass ‘RCMT ValueSetClass’, which has
a new subclass ‘RCMT LOINC ValueSet’. Each new disease which has RCMT
codes that are not in the ontology must have a subclass created under this
one. The className for the new classes follows the naming convention of
“RCMT_disease_ValueSets”, and a label of “disease ValueSets”, where disease
is the name of the NND condition.
3. Under this valueSet class there are 1 to many classes containing the LOINC
codes. One class is created for each type of test, based on the LOINC
component name, and includes the method. The name of the class follows
the naming convention of “RCMT_Only_disease_uniqueTestString”, where
‘disease’ is the name of the NND condition, and ‘uniqueTestString’ is a string
based on the LOINC component that uniquely identifies a group of related
tests. This new class must get a label with the naming convention that
embodies a subset of the LOINC component that identifies a related group of
tests, and should include the method. For example, one of these value sets in
Plague is named “RCMT_Only_Plague_Ab” with a label of “Yersinia pestis Ab”,
one for Chancroid is named “RCMT_Only_Chancroid_DNA_by_probe” with a
label of “H. ducreyi DNA by probe”.
4. These value set classes each have a further subclass with the naming
convention “RCMT_Only_testgroupname_scale”, where ‘testgroupname’ is the
same as that used in the superclass, and ‘scale’ is the result type as defined in
LOINC (e.g. Nom, Ord, Qn, etc.). Each of these must have a label with the
naming convention “testgroupname – scale”.
5. Each of these value set classes contains the RCMT LOINC codes as members
that are not already contained in the CSTE portion of the ontology. For
example, the class “Yersinia sp DNA by probe – Nom” has as its member the
LOINC code 48646-4 Yersinia DNA XXX PCR; the class “Yersinia persis Ab –
Ord” contains as members the LOINC codes 33689-1, 33706-3, 45045-2, and
47518-6 all of which are the codes in RCMT for Y. pestis antibody tests with
an ordinal result.
6. Under the high level class “Lab OBX Criteria”, create a subclass with the
naming convention “RCMT_Only_disease_OBX” with a label of “disease RCMT
Only”, where ‘disease’ is the name of the NND condition. This enables both
the sequestering of the data and the sort sequencing to be correct in the
output and when browsing. This class must explicitly have an additional
Superclass added through the Add Superclass function using the Object
Restriction Creator to select ‘associated event’ and the Restriction Filler
control used to select the disease in the NNDSS class hierarchy; this connects
the RCMT value set to the NND. Each subclass below this will inherit this
connection.
7. Under this class, for each disease/condition, there must be one subclass for
the lab tests for this disease, having the naming convention
“NNDSS_nndID_RCMT_1” and a label of “RCMT disease Lab Tests”, where
nndID is the code for the disease (e.g. 10440 for Plague), and disease is the
NND condition name.
8. Under this class, there must be one subclass for each of the classes in the
RCMT LOINC value set class for the disease value sets. Each of these classes
should follow the naming convention “NNDSS_nndID_RCMT_m_#”, where
‘nndID’ is the condition code for the disease, and ‘#’ is a key number
associated with the value type of the lab result. These numbers are 1 for
Nominal, 2 for Ordinal, and 3 for Quantitative. ‘m’ is 1 for the first group of
similarly named tests, and increments for each type of test. The label for
each of these classes should follow the pattern “disease_testtype_ resultType”.
9. Each of these classes must have a rule expression setup under Equivalent
Classes using the Add Equivalent Class function. The first argument is the
Top Level Restriction Property using the Object Restriction Creator of
‘Observation Identifier’, the second argument is the restriction filler where
you browse to the value set class under Terminology->RCMT_ValueSetClass>RCMT_LOINC ValueSet->disease ValueSets->desired value set->bottom
value set containing the LOINC code members, and with a cardinality of
“Only”. Then using the Class Expression editor, the string “and ('Observation
Value' value 'quantitative value')” must be appended to the expression.
10. Repeat steps 8 and 9 for each of the classes of groups of LOINC tests defined
in the Terminology hierarchy.