I have a use case for modelling "Genetic risk level for colorectal cancer(observable entity)" in order to define clinical findings of carriers of genetic states such as Lynch syndrome and Familial adenomatous polyposis. I assume this would be a DISPOSITION types of observable but I need guidance on the definition. If I want to define an ORDINAL observable ((High, Medium, Low risk) would the proper modelling of a fully defined concept be:
Genetic risk level for developing colorectal cancer (observable entity)
ISA 419841000004102|Hereditary cancer risk observable|
INHERES IN 1350001000004100|Nucleotide sequence|
TOWARDS 363510005|Malignant tumor of large intestine|
SCALE TYPE Ordinal or quantitative value
TIME ASPECT Single point in time
By the way Farzaneh, this raises the case once more for nucleotide sequence(cell structure) being a subtype pf Chromosome structure because transloactions and other chromosomal reorganization also changes the nucleotide sequence and therefore it would argue that the nucleotide sequence is a more specific way of specifying a chromosomal structural change.
I obviously forgot one important PROPERTY! But I can't find any of what we discussed in terms of appropriate <<118598001|Measurement property| in the international release. Did all of our discussion on instruments and observations of risk/probability/likelihood go for naught?
Jim
Genetic risk level for developing colorectal cancer (observable entity)
ISA 419841000004102|Hereditary cancer risk observable|
INHERES IN 1350001000004100|Nucleotide sequence|
TOWARDS 363510005|Malignant tumor of large intestine|
PROPERTY some risk or probability or likelihood property
this discussion was never concluded in the spring, I assume that is the reason the content is missing, plus that LOINC linking has been put on hold.
I would challenge your observable definition by asking how you would define "risk level for developing colorectal cancer based on any method" and if you think that the modelling between different techniques of assessing the risk should be similar or not.
Further, as this is a future risk, I will opt to use the function (realizable) pattern (although I do not claim that a risk is a function).
| generic risk... | : ISA ... (does hereditary imply germ line mutation here??) | observable | PROPERTY = | Risk | INHERES IN = | Large intestine | (or one could argue the whole body or the patient...) HAS REALIZATION = | Colorectal cancer |
and then for | genetic risk level... | one could add TECHNIQUE = | genetic technique or something more specific | , (possibly) DIRECT SITE = | nucleotide sequence | etc.
3 Comments
James R. Campbell
I have a use case for modelling "Genetic risk level for colorectal cancer(observable entity)" in order to define clinical findings of carriers of genetic states such as Lynch syndrome and Familial adenomatous polyposis. I assume this would be a DISPOSITION types of observable but I need guidance on the definition. If I want to define an ORDINAL observable ((High, Medium, Low risk) would the proper modelling of a fully defined concept be:
Genetic risk level for developing colorectal cancer (observable entity)
ISA 419841000004102|Hereditary cancer risk observable|
INHERES IN 1350001000004100|Nucleotide sequence|
TOWARDS 363510005|Malignant tumor of large intestine|
SCALE TYPE Ordinal or quantitative value
TIME ASPECT Single point in time
By the way Farzaneh, this raises the case once more for nucleotide sequence(cell structure) being a subtype pf Chromosome structure because transloactions and other chromosomal reorganization also changes the nucleotide sequence and therefore it would argue that the nucleotide sequence is a more specific way of specifying a chromosomal structural change.
Jim
James R. Campbell
I obviously forgot one important PROPERTY! But I can't find any of what we discussed in terms of appropriate <<118598001|Measurement property| in the international release. Did all of our discussion on instruments and observations of risk/probability/likelihood go for naught?
Jim
Genetic risk level for developing colorectal cancer (observable entity)
ISA 419841000004102|Hereditary cancer risk observable|
INHERES IN 1350001000004100|Nucleotide sequence|
TOWARDS 363510005|Malignant tumor of large intestine|
PROPERTY some risk or probability or likelihood property
SCALE TYPE Ordinal or quantitative value
TIME ASPECT Single point in time
Daniel Karlsson
Hi Jim,
this discussion was never concluded in the spring, I assume that is the reason the content is missing, plus that LOINC linking has been put on hold.
I would challenge your observable definition by asking how you would define "risk level for developing colorectal cancer based on any method" and if you think that the modelling between different techniques of assessing the risk should be similar or not.
Further, as this is a future risk, I will opt to use the function (realizable) pattern (although I do not claim that a risk is a function).
| generic risk... | :
ISA ... (does hereditary imply germ line mutation here??) | observable |
PROPERTY = | Risk |
INHERES IN = | Large intestine | (or one could argue the whole body or the patient...)
HAS REALIZATION = | Colorectal cancer |
and then for | genetic risk level... | one could add TECHNIQUE = | genetic technique or something more specific | , (possibly) DIRECT SITE = | nucleotide sequence | etc.
Thoughts?
/Daniel