Map NCIT measurements

[cmungall]

Examples

NCIT:C51948 ! Leukocyte Count NCIT:C51949 ! Lymphocyte Count NCIT:C51950 ! Neutrophil Count NCIT:C51951 ! Platelet Count NCIT:C61015 ! Serum Albumin Measurement NCIT:C61016 ! Serum Alkaline Phosphatase Measurement NCIT:C61017 ! Serum Alanine Aminotransferase Measurement NCIT:C61018 ! Serum Aspartate Aminotransferase Measurement NCIT:C61019 ! Blood Urea Nitrogen Measurement NCIT:C61023 ! Serum Creatinine Measurement NCIT:C61027 ! Serum Glucose Measurement NCIT:C61029 ! Serum Sodium Measurement NCIT:C61031 ! Serum Total Bilirubin Measurement NCIT:C61033 ! Serum Total Protein Measurement NCIT:C61037 ! Serum Triglyceride Measurement NCIT:C61041 ! Serum HDL Cholesterol Measurement NCIT:C61042 ! Serum LDL Cholesterol Measurement NCIT:C64433 ! Alanine Aminotransferase Measurement NCIT:C64467 ! Aspartate Aminotransferase Measurement NCIT:C64470 ! Total Basophil Count NCIT:C64471 ! Basophil to Leukocyte Ratio NCIT:C64488 ! Calcium Measurement NCIT:C64495 ! Chloride Measurement NCIT:C64545 ! Carbon Dioxide Measurement NCIT:C64547 ! Creatinine Measurement NCIT:C64550 ! Eosinophil Count NCIT:C64604 ! Eosinophil to Leukocyte Ratio NCIT:C64796 ! Hematocrit Measurement NCIT:C64810 ! Nitrite Measurement NCIT:C64816 ! Urobilinogen Measurement

Note: as stated a few other places I don't think we should separate characteristics from measurements, it's the same concept

I believe this would be of value to cpath cc @nicolevasilevsky

[matentzn]

I agree these would be extremely useful for OBA.

[ramonawalls]

Just to make sure I understand, OBA does not include classes for measurements, right, an these would map (somehow) to the relevant quality that is being measured?

[matentzn]

@ramonawalls - while there is clearly a conceptual difference between "Total Basophil Count" measurement (an observation which has, for example, an observer), and "total basophil count" trait (an observable characteristic of an organism) we do not believe that having classes for both make any sense. It will take years to bridge "information" and "characteristic"-centric data models as they have proliferated widely, but it is our belief that only the "characteristic" itself should be represented as a named class (the "measurement" aspect of a characteristic is purely a "shadow" of the actual characteristic), and that the occurrence of either one (measurement or trait) should be, for most biomedical data integration use cases, "conflated" (i.e. you should pretend they are the same). So in this case here (as with our EFO alignment) we will create all of these as trait terms, but pretend, that they relate to the same thing (i.e yes, map across).

[ramonawalls]

Thanks, @matentzn . I agree completely that there should not be parallel hierarchies of traits and measurement types. Saying that there is "a conceptual difference" between the two types understates the importance of the difference, at least for the kind of work I have done, but I support the conflation approach for knowledge graph work. I just wanted to be sure that in OBA, qualities are logically defined as qualities, not processes or information, so that if we want to use more robust reasoning, we can.

C-Path should be able to commit some resources to the mapping, if you can let us know what needs to be done.

[matentzn]

I just wanted to be sure that in OBA, qualities are logically defined as qualities, not processes or information, so that if we want to use more robust reasoning, we can.

100%! This is what they are.

@rays22 hold of on this for a moment.

@ramonawalls basically what we need is simply a two column table for each of these NCIT terms, the first column being the appropriate PATO quality and the second the respective entity, i.e. Hematocrit etc. This is not always trivial, but I think its not too bad.

The ratio ones require a new pattern I think. @rays22 can you propose a simple logical pattern for capturing the ratio traits? It should be aligned with uPheno.

[rays22]

Here is a mapping table of 30 NCIT measurement terms:

NCIT Identifier	NCIT label	predicate	OBA ID	OBA label
NCIT:C64488	Calcium Measurement	skos:exactMatch	OBA:VT0010499	calcium amount
NCIT:C61033	Serum Total Protein Measurement	skos:exactMatch	OBA:VT0005567	blood total protein amount
NCIT:C61019	Blood Urea Nitrogen Measurement	skos:exactMatch	OBA:VT0005265	blood urea nitrogen amount
NCIT:C51951	Platelet Count	skos:exactMatch	OBA:VT0003179	platelet quantity
NCIT:C64550	Eosinophil Count	skos:exactMatch	OBA:VT0002602	eosinophil quantity
NCIT:C61031	Serum Total Bilirubin Measurement	skos:exactMatch	OBA:VT0001569	blood bilirubin amount
NCIT:C51949	Lymphocyte Count	skos:exactMatch	OBA:VT0000717	lymphocyte quantity
NCIT:C51950	Neutrophil Count	skos:exactMatch	OBA:VT0000222	neutrophil quantity
NCIT:C51948	Leukocyte Count	skos:exactMatch	OBA:VT0000217	leukocyte quantity
NCIT:C61023	Serum Creatinine Measurement	skos:exactMatch	OBA:2050096	serum creatinine amount
NCIT:C61015	Serum Albumin Measurement	skos:exactMatch	OBA:2050068	serum albumin amount
NCIT:C61017	Serum Alanine Aminotransferase Measurement	skos:exactMatch	OBA:2050062	serum alanine aminotransferase amount
NCIT:C64796	Hematocrit Measurement	skos:exactMatch	OBA:2045381	hematocrit
NCIT:C61037	Serum Triglyceride Measurement	skos:exactMatch	OBA:2045035	level of triglyceride in blood serum
NCIT:C61016	Serum Alkaline Phosphatase Measurement	skos:exactMatch	OBA:2040575	level of alkaline phosphatase, tissue-nonspecific isozyme in blood serum
NCIT:C64495	Chloride Measurement	skos:exactMatch	OBA:1000959	chloride amount
NCIT:C64545	Carbon Dioxide Measurement	skos:exactMatch	OBA:1000957	carbon dioxide amount
NCIT:C64470	Total Basophil Count	skos:broadMatch	OBA:VT0002607	basophil quantity
NCIT:C61018	Serum Aspartate Aminotransferase Measurement	skos:narrowMatch	OBA:2041767	level of aspartate aminotransferase, mitochondrial in blood serum
NCIT:C61018	Serum Aspartate Aminotransferase Measurement	skos:narrowMatch	OBA:2045394	level of aspartate aminotransferase, cytoplasmic type in blood serum
NCIT:C61029	Serum Sodium Measurement	skos:exactMatch	OBA:2045395	serum sodium level
NCIT:C61027	Serum Glucose Measurement	skos:exactMatch	OBA:2045396	serum glucose level
NCIT:C61041	Serum HDL Cholesterol Measurement	skos:exactMatch	OBA:2045397	serum high-density lipoprotein cholesterol level
NCIT:C61042	Serum LDL Cholesterol Measurement	skos:exactMatch	OBA:2045398	serum low-density lipoprotein cholesterol level
NCIT:C64433	Alanine Aminotransferase Measurement	skos:exactMatch	OBA:2045399	alanine aminotransferase level
NCIT:C64467	Aspartate Aminotransferase Measurement	skos:narrowMatch	OBA:2045400	level of aspartate aminotransferase, cytoplasmic type
NCIT:C64467	Aspartate Aminotransferase Measurement	skos:narrowMatch	OBA:2045401	level of aspartate aminotransferase, mitochondrial type
NCIT:C64547	Creatinine Measurement	skos:exactMatch	OBA:2045402	creatinine level
NCIT:C64816	Urobilinogen Measurement	skos:exactMatch	OBA:2045403	urobilinogen level
NCIT:C64810	Nitrite Measurement	skos:exactMatch	OBA:2045404	nitrite level
NCIT:C64471	Basophil to Leukocyte Ratio	skos:broadMatch	OBA:2045390	basophil ratio
NCIT:C64604	Eosinophil to Leukocyte Ratio	skos:broadMatch	OBA:2045391	eosinophil ratio