search

TheJacksonLaboratory / loinc2hpoAnnotation

loinc2hpo Annotation Data
https://github.com/monarch-initiative/loinc2hpo
Other
24 stars 11 forks source link

2502-3: Iron saturation [Mass Fraction] in Serum or Plasma #55

Open callahantiff opened 5 years ago

callahantiff commented 5 years ago

This LOINC term is annotated to HP:0040303 (Decreased serum iron). The test is measuring iron saturation, which is different than than a test which measures serum iron (e.g. LOINC 2498-4).

I may be interpreting this incorrectly, but serum iron and iron saturation appear to be two separate types of tests, although they are both used for making certain diagnoses. If you agree, I think a concept related to transferrin saturation may be more fitting?

kingmanzhang commented 5 years ago

I think the biology is different but the annotation is probably fine. Iron is transported by transferrin, so low saturation roughly means low serum iron (?).

https://emedicine.medscape.com/article/2087960-overview

callahantiff commented 5 years ago

I think my initial question was not worded clearly, sorry about that.

What I meant to ask was why increased and decreased iron saturation (2502-3) lab results were being annotated to HPO terms that measured iron serum? I am asking this because there are HPO terms (HP:0012464 and HP:0012463) that measure increased and decreased iron or transferrin saturation?

Annotating this LOINC lab to the saturation HPO terms rather than the serum HPO terms seems like a more accurate mapping. Or was there a specific reason why you did not annotate it to those terms?

kingmanzhang commented 5 years ago

In this case, annotating to your suggest HPO terms sounds more precise. I will relay this to @LCCarmody to see if she agrees. It is possible that your suggested classes are new.

callahantiff commented 5 years ago

Thanks Aaron, that sounds great. I'm wondering if I should add the dates that HPO terms were added when posting issues, but only if that would be helpful.