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TheJacksonLaboratory / loinc2hpoAnnotation

loinc2hpo Annotation Data
https://github.com/monarch-initiative/loinc2hpo
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Review LOINC 4625-0 #112

Closed kingmanzhang closed 2 years ago

kingmanzhang commented 5 years ago

The H term is not correct

kingmanzhang commented 5 years ago

@callahantiff

callahantiff commented 5 years ago

The high result for this lab is annotated to (HP:0045057) HbS Hemoglobin. Why is that not correct? The sources I found state that a normal result is 0%. So in this case wouldn't we treat the high and low lab results the same? Perhaps I am misunderstanding.

kingmanzhang commented 5 years ago

oh, this is beyond my ability. I initially thought this was a simple error by judging what the terms reads like... I created this ticket because you put a flag on it, so I thought you request someone to double check. I will hand this to you and @nicolevasilevsky.

callahantiff commented 5 years ago

@kingmanzhang I spoke with @nicolevasilevsky and given that anything >0% is abnormal, we think the annotations could be:

I think the same annotations would also need to be made for LOINC:32683-5. What do you think @kingmanzhang? If you agree, then the low result annotations for both of these labs (LOINC:4625-0 and LOINC:LOINC:32683-5) would need to be removed.

kingmanzhang commented 5 years ago

I agree with this revision.

On Tue, Feb 26, 2019 at 5:50 PM Tiffany J. Callahan < notifications@github.com> wrote:

@kingmanzhang https://github.com/kingmanzhang I spoke with @nicolevasilevsky https://github.com/nicolevasilevsky and given that anything >0% is abnormal, we think the annotations could be:

  • Normal: NOT(HP:0045057)
  • High: HP:0045057
  • Low: None

I think the same annotations would also need to be made for LOINC:32683-5 https://s.details.loinc.org/LOINC/32683-5.html?sections=Comprehensive. What do you think @kingmanzhang https://github.com/kingmanzhang? If you agree, then the low result annotations for both of these labs (LOINC:4625-0 and LOINC:LOINC:32683-5) would need to be removed.

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pnrobinson commented 2 years ago

There currently is no HPO term for increased hemoglobin S (which is the sickle cell hemoglobin). I will make a term request. https://github.com/obophenotype/human-phenotype-ontology/issues/7201

pnrobinson commented 2 years ago

The term already existed as HP:0045047

pnrobinson commented 2 years ago

I added the correct annotation