-
Notifications
You must be signed in to change notification settings - Fork 11
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Map NCIT measurements #163
Comments
I agree these would be extremely useful for OBA. |
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? |
@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). |
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. |
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. |
This commit intends to * update imports, * update the `entity_attribute_location` pattern to allow broad and narrow synonyms as well `example of usage` comments to complement the computer generated text definitions, and thereby * fix QC errors. Resolve #163.
Here is a mapping table of 30 NCIT measurement terms:
|
Fix obsolete GO:0042133 neurotransmitter metabolic process component by removing EQ. Close #163
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
The text was updated successfully, but these errors were encountered: