I am building out a LOINC-on-OWL ontology for consumption bythe community of LOINC users. Laboratory and pathology are in pretty good shape and I am progressing through a frequency analysis of clinical observables concepts deployed and in use in US healthcare records. This is the top 20 list from UNMC and Intermountain.
LOINC_NUM
LONG_COMMON_NAME
Total
8867-4
Heart rate
349847977
9279-1
Respiratory rate
241742000
8480-6
Systolic blood pressure
228900486
8462-4
Diastolic blood pressure
226008756
8478-0
Mean blood pressure
168467673
8310-5
Body temperature
71671221
3141-9
Body weight Measured
33262360
8302-2
Body height
26433880
39156-5
Body mass index (BMI) [Ratio]
24710685
3151-8
Inhaled oxygen flow rate
12131789
9267-6
Glasgow coma score eye opening
7694651
9270-0
Glasgow coma score verbal
7679923
9268-4
Glasgow coma score motor
7676466
38208-5
Pain severity - Reported
7569094
50064-5
Ideal body weight
7297147
9187-6
Urine output
6453291
9269-2
Glasgow coma score total
5572112
I have been mapping to the LOINC codes and came up short in blood pressure. 99% of blood pressures done worldwide are a pair of measurements made with a blood pressure cuff on a peripheral artery and 8480-6 mapped nicely to 72313002|Systolic arterial pressure|, I was good with the definition which CHARACTERIZES SYSTOLIC PHASE, PROPERTY PRESSURE, INHERES IN ARTERIAL STRUCTURE. Systolic pressure measurements in general INHERE IN CARDIOVASCULAR STRUCTURE. When I researched diastolic pressure, I found no observable for 'Diastolic arterial pressure' and all diastolic pressures have a consistent definition and INHERE IN CARDIOVASCULAR STRUCTURE. Unfortunately, the fourth most common clinical observable does not exist in SNOMED CT but I would be willing to bet that we have LOTS of systems worldwide have been using 271650006|Diastolic blood pressure| to record that measurement over the years. That would argue for changing the FSN of 271650006 and defining it properly but the best strategy alludes me. Clearly the observables model supports proper definition of the LOINC concept but what should the map be in Nebraska Lexicon?
We are working on a computable phenotype for Alzheimers disease. The pathology observables are not mysterious although there are a lot of new attribute/value pairs we need to add. The clinical portion of the dataset will be heavily oriented towards neurocognitive examinations. Building out the scoring of the Folstein minimental status exam, I am seeking some advice:
72106-8 Minimental Status examination of cognitive function - total score(observable entity)
ISA =311465003|Cognitive functions(observable entity)|
INHERES IN =Cerebral structure
TECHNIQUE =Assessment scale\NEW Folstein minimental status examination
HAS REALIZATION = 719982003 Process\NEW Mental process(qualifier) \NEW |Cognition(qualifier)|
Just one quick suggestion would be a PROPERTY = Ability or Function or similar, given that this is an observation to assess cognitive ability or function. Sometimes these tests are for finding presence of disease rather than normal function, not sure about this one.
Further, whether this INHERES IN = CNS is also something to consider.
I was looking for a template for the FUNCTION observables but could not find one. Please give me a pointer if it exists. I agree that INHERES IN is not an intuitive choice here, but arguably, if you remove the cerebrum, you certainly ablate cognition. Frontal lobes and parieto-temporal and occipital regions are the most important in the case of cognitive function.
I want to model a couple observables for results of assessment scales for Pain severity and Chest pain. Has there been preparatory work in what Observables flavor to use?
I have appended to the last meeting page the presentation from today to the Anesthesiology CRG on Glasgow Coma Scale and machine learning using the neurological exam
7 Comments
James R. Campbell
I am building out a LOINC-on-OWL ontology for consumption bythe community of LOINC users. Laboratory and pathology are in pretty good shape and I am progressing through a frequency analysis of clinical observables concepts deployed and in use in US healthcare records. This is the top 20 list from UNMC and Intermountain.
I have been mapping to the LOINC codes and came up short in blood pressure. 99% of blood pressures done worldwide are a pair of measurements made with a blood pressure cuff on a peripheral artery and 8480-6 mapped nicely to 72313002|Systolic arterial pressure|, I was good with the definition which CHARACTERIZES SYSTOLIC PHASE, PROPERTY PRESSURE, INHERES IN ARTERIAL STRUCTURE. Systolic pressure measurements in general INHERE IN CARDIOVASCULAR STRUCTURE. When I researched diastolic pressure, I found no observable for 'Diastolic arterial pressure' and all diastolic pressures have a consistent definition and INHERE IN CARDIOVASCULAR STRUCTURE. Unfortunately, the fourth most common clinical observable does not exist in SNOMED CT but I would be willing to bet that we have LOTS of systems worldwide have been using 271650006|Diastolic blood pressure| to record that measurement over the years. That would argue for changing the FSN of 271650006 and defining it properly but the best strategy alludes me. Clearly the observables model supports proper definition of the LOINC concept but what should the map be in Nebraska Lexicon?
Jim
James R. Campbell
Given that the height (length) of the body is from sole to crown, would we define this as
ISA BODY HEIGHT MEASURE
PROPERTY LENGTH
SCALE TYPE QUANTITATIVE
TIME ASPECT SINGLE POINT IN TIME
GROUP 1 INHERES IN CROWN OF HEAD(SURFACE REGION)
GROUP 2 SOLE OF FOOT(SURFACE REGION)?
James R. Campbell
We are working on a computable phenotype for Alzheimers disease. The pathology observables are not mysterious although there are a lot of new attribute/value pairs we need to add. The clinical portion of the dataset will be heavily oriented towards neurocognitive examinations. Building out the scoring of the Folstein minimental status exam, I am seeking some advice:
72106-8 Minimental Status examination of cognitive function - total score(observable entity)
ISA =311465003|Cognitive functions(observable entity)|
INHERES IN =Cerebral structure
TECHNIQUE =Assessment scale\NEW Folstein minimental status examination
HAS REALIZATION = 719982003 Process\NEW Mental process(qualifier) \NEW |Cognition(qualifier)|
SCALE =Quantitative
TIME ASPECT =Single point in time
Daniel Karlsson
Just one quick suggestion would be a PROPERTY = Ability or Function or similar, given that this is an observation to assess cognitive ability or function. Sometimes these tests are for finding presence of disease rather than normal function, not sure about this one.
Further, whether this INHERES IN = CNS is also something to consider.
James R. Campbell
I was looking for a template for the FUNCTION observables but could not find one. Please give me a pointer if it exists. I agree that INHERES IN is not an intuitive choice here, but arguably, if you remove the cerebrum, you certainly ablate cognition. Frontal lobes and parieto-temporal and occipital regions are the most important in the case of cognitive function.
Jim
James R. Campbell
I want to model a couple observables for results of assessment scales for Pain severity and Chest pain. Has there been preparatory work in what Observables flavor to use?
Jim
James R. Campbell
I have appended to the last meeting page the presentation from today to the Anesthesiology CRG on Glasgow Coma Scale and machine learning using the neurological exam