- Created by Farzaneh Ashrafi, last modified on 2018-Apr-09
The Substance project is considering a change, which if implemented, will affect the mapping of LOINC terms.
The suggested change is to deprecate the instances of Free X (substance) and replace them with X (substance). E.g 259355006 | Free testosterone (substance) | will be deprecated and replaced by 43688007 | Testosterone (substance) |
The modelling of Testosterone has changed to reflect the change:
January 2018 release:
July 2018 release:
Currently the mapping of the LOINC Parts to SNOMED CT is as following (based on confirmation with RII). The changes in substance hierarchy will have an effect on mapping of the LOINC parts, specifically Testosterone and Testosterone total:
PartNum | Part Type | PartName | Concept ID | FSN | Correlation |
LP18811-7 | COMPONENT | Testosterone.free | 259355006 | Free testosterone (substance) | Exact |
LP29116-8 | COMPONENT | Testosterone.bound | 720374004 | Testosterone bound to sex hormone-binding globulin (SHBG) (substance) | Exact |
LP15881-3 | COMPONENT | Testosterone.free+weakly bound | 710118001 | Bioavailable testosterone (substance) | Exact |
LP19233-3 | COMPONENT | Testosterone.weakly bound | 720355007 | Testosterone bound to albumin (substance) | Exact |
LP14045-6 | COMPONENT | Testosterone | 43688007 | Testosterone (substance) | Snomed CT broader |
LP32165-0 | DIVISORS | Testosterone.total | 43688007 | Testosterone (substance) | Snomed CT broader |
From LOINC website: Testosterone is an androgenic steroid and is the primary male sex hormone. Approximately half of circulating testosterone is tightly bound to a protein called sex hormone binding globulin (SHBG) and is biologically inactive. Another fraction is weakly bound to other proteins, such as albumin, and the remainder is unbound, or "free". Weakly bound and free testosterone together represent bioavailable testosterone. Both total and free testosterone levels decrease with age. Low testosterone is associated with many other conditions, including osteoporosis, Alzheimer’s disease, obesity, diabetes and ischemic heart disease.
Example LOINC terms:
Other examples:
PartNum | PartTypeName | PartName | ConceptId | FSN |
LP18655-8 | COMPONENT | Estradiol.free | 259349001 | Free estradiol (substance) |
LP32049-6 | DIVISORS | Estradiol.total | 126172005 | Estradiol (substance) |
LP32015-7 | DIVISORS | Carnitine.free (C0) | 709152004 | Free carnitine (substance) |
LP32016-5 | DIVISORS | Carnitine.total | 59888006 | Carnitine (substance) |
PartNum | PartTypeName | PartName | Primary_ConceptId | Primary_FSN |
LP29075-6 | COMPONENT | Insulin.free | 706937006 | Free insulin (substance) |
LP31777-3 | COMPONENT | Insulin.bound | 706973004 | Bound insulin (substance) |
LP14676-8 | COMPONENT | Insulin | 67866001 | Insulin (substance) |
LP70329-5 | DIVISORS | Insulin | 67866001 | Insulin (substance) |
PartNum | PartTypeName | PartName | ConceptId | FSN |
LP15448-1 | COMPONENT | Bilirubin | 79706000 | Bilirubin (substance) |
LP15447-3 | COMPONENT | Bilirubin.albumin bound | 73828001 | Bilirubin-albumin complex (substance) |
LP15446-5 | COMPONENT | Bilirubin.glucuronidated | 259498006 | Bilirubin glucuronide (substance) |
LP15445-7 | COMPONENT | Bilirubin.glucuronidated+Bilirubin.albumin bound | 54462003 | Direct reacting bilirubin (substance) |
LP15449-9 | COMPONENT | Bilirubin.non-glucuronidated | 37852002 | Indirect reacting bilirubin (substance) |
LP31996-9 | DIVISORS | Bilirubin.total | 79706000 | Bilirubin (substance) |
From LOINC website: "Bilirubin is an orange-yellow pigment produced by the normal breakdown of heme, a component of the hemoglobin found in red blood cells. It is processed by the liver and excreted in bile. Conditions that cause red blood cell breakdown or interfere with liver or bile processing can cause elevated levels of bilirubin. Bilirubin exists in many forms. Non-glucuronidated bilirubin (also called unconjugated or indirect) is the breakdown product of heme and is not water-soluble. Hemolytic anemias, which cause increased red blood cell breakdown, are one cause of elevated non-glucuronidated bilirubin. Glucuronidated bilirubin (also called conjugated) is a water-soluble form of bilirubin that is made in the liver by the addition of sugar molecules to non-glucuronidated bilirubin. Conditions that affect liver function (such as hepatitis, cirrhosis and liver tumors) or physically block the bile ducts (such as gallstones) can cause elevated levels of glucuronidated bilirubin. A third form of bilirubin is that which is bound to albumin, and it is also known as delta bilirubin because it was originally identified based on the unexpected difference between the total bilirubin level and the level of glucuronidated plus non-glucuronidated bilirubin in some patient samples. Prior to the discovery of albumin-bound bilirubin, the term "direct" bilirubin was used as a synonym for glucuronidated bilirubin, but direct bilirubin is actually glucuronidated PLUS albumin-bound bilirubin."
Contributors (2)
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2 Comments
James R. Campbell
During the E2O discussion this AM, the team expressed concern that the use case for "Bound X substance" was not clear or important. Questions were raised when the proposed changes to the substance model would be implemented?
Farzaneh Ashrafi
Hi James R. Campbell
I am afraid I don't understand the question fully. Is the concern that "Bound X substance" concepts are not required? Or is the concern related to their modelling?
As for implementation of the changes, the existing concepts were remodelled in 2018 as per existing guidelines:
As discussed earlier via email, the existing guidelines are the result of discussing the initial proposal by the Substance project as noted above (i.e. to deprecate the instances of Free X (substance) and replace them with X (substance)) with the Observable project group back in June and July 2018. The Observable project group didn't agree with this proposal. The group recommendation, as noted in the minutes of the 2018-07-16 call (https://confluence.ihtsdotools.org/display/OBSERVABLE/2018-07-16+-+OBSERVABLE+Meeting [confluence.ihtsdotools.org]), was as follows:
The recommendation was to support measurement of bioavailable/bioactive and total substances.
Is the E2O project recommending a change in the above guidelines?
Thanks,
Farzaneh
CC: Suzanne Santamaria