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Term issue: glycated hemoglobin #208

Closed cstoeckert closed 4 years ago

cstoeckert commented 4 years ago

For PennTURBO and OBI, we'd like a term for human 'glycated hemoglobin' as the analyte measured in Hemoglobin A1c tests for blood sugar levels. It could be defined as: 'a form of hemoglobin (Hb) that is chemically linked to a sugar.' Definition source: https://en.wikipedia.org/wiki/Glycated_hemoglobin

nataled commented 4 years ago

Hi Chris,

Is it desired that the term be scoped to humans only, or is a broad taxonomic scope desired? We can accommodate either. Also, I presume from the name given by wikipedia that you are interested only in the most common form, adult hemoglobin A, and not other types (such as fetal or HbA2. Is that correct?

cstoeckert commented 4 years ago

Our primary interest is humans but it appears that the test is also available for dogs and cats (https://www.vmdtoday.com/news/a1c-test-now-available-for-cats-and-dogs) so broader would be good.
My interpretation like yours is that A1c is for HbA not HbF or HbA2.

nataled commented 4 years ago

Hi Chris,

Well, this was more involved than I expected! It seems that the definition of HbA1c has changed over the years. I'm not fully sure it has been fully standardized yet. Nonetheless, I defined it using what I believe is the latest standard, which involves a very specific amino acid modification to one of the subunits (see first term below). The second term is the requested term. Please verify that this is what you want.

[Term] id: PR:000050468 name: hemoglobin subunit beta N-1-deoxyfructosylated 1 def: "A hemoglobin subunit beta, initiator methionine removed form that has been N-1-deoxyfructosylated at the position equivalent to Val-2 of the sequence represented by UniProtKB:P68871-1 or a 1:1 ortholog thereof. [PRO:DAN] comment: Category=modification. synonym: "HBB/InitMet-/dFruc:1" EXACT PRO-short-label [PRO:DAN] synonym: "beta-N-1-deoxy fructosyl hemoglobin subunit" BROAD [PRO:DAN] is_a: PR:000020114 ! hemoglobin subunit beta, initiator methionine removed form

[Term] id: PR:000050469 name: hemoglobin A1c def: "A hemoglobin complex that is composed of at least one beta-N-1-deoxy fructosyl hemoglobin subunit, in which the glycan is attached to the N-terminal valine (after initiator methionine removal) of one or both beta subunits." [PRO:DAN, PMID:9732983, Wikipedia:Glycated_hemoglobin] comment: Category=complex. Requested by=PennTURBO. Note: The precise definition of hemoglobin A1c has evolved over time [https://medcraveonline.com/JNMR/laboratory-diagnosis-of-hba1c-a-review.html]. This PRO term is based on the most-precise definition currently in use. synonym: "HbA1c" EXACT PRO-short-label [PRO:DAN] synonym: "glycohemoglobin" BROAD [PMID:9732983] synonym: "glycated hemoglobin" BROAD [PMID:9732983] synonym: "HgbA1c" EXACT [PMID:9732983] is_a: GO:0005833 ! hemoglobin complex relationship: has_component PR:000050468 {minCardinality="1"} ! hemoglobin subunit beta N-1-deoxyfructosylated 1 relationship: has_component PR:000050468 {maxCardinality="2"} ! hemoglobin subunit beta N-1-deoxyfructosylated 1 relationship: has_component PR:000050026 {maxCardinality="1"} ! hemoglobin subunit beta relationship: has_component PR:000008456 {cardinality="2"} ! hemoglobin subunit alpha

cstoeckert commented 4 years ago

Hi Darren, Yes, the second term is what we want. Thanks!