Hi @Christian, @Dymshyts,
in which cdm table codes under domain Spec Anatomic Site should go? I suppose it is cdm.observation, is it correct?
Thank you,
Irina
Yes, into observation.
But it’s somehow confusing why we have these “Spec Anatomic Site” concepts in a data.
Can you please give an example of the source table containing there concepts?
Good idea, but the specimen table should be filled by concepts from domain = ‘Specimen’
and the meaning of ‘Specimen’ domain and ‘Spec Anatomic Site’ is different, i.e.
Spicemen examples: “Tissue specimen from esophagus”, “Blood clot sample” are samples taken for further analysis (i.e. microscopy);
Spec Anatomic Site examples: “Bone and joint, CS”, “Rib part”, “Population of all monocytes in portion of fluid” are some parts of the human body,
so it’s unknown what actual meaning they have in a patient data.
This way by default they go to the Observation but we need to see what exactly is in a data, and then decide.
It is a source event table that contain Read codes (that map to Condition, Observation, Procedure, Measurement, but also to Place of Service, Race, Gender and among others Spec Anatomic Site)
specimen.anatomic_site_concept_id?
I understand your idea, it would work great if those ‘Spec Anatomic Site’ would related to any specimen.
@IYabbarova and myself looked on the data and we didn’t find any significant relationship to other facts. So the best way in this particular case is to ignore them