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Where to store metabolites/metabolomics data?

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(Akshay Kumar) #1

Hello OHDSI experts,

Along with our EHR data, we also have metabolomics data.

Though the data looks like it can fit in measurement data with custom concepts, Am I right to understand that OMOP CDM at this moment does’t provide an option to store metobolomics data?

Can help us with this?


(Christian Reich) #2

@Akshay:

Map to LOINC and SNOMED whatever you can find. The rest list here and we can think what to do. Obviously, there is a potentially huge number of metabolites, but you probably have a small subset of those that you are collecting.


(Selva) #3

Hi @Christian_Reich,

We also have metabolomic - which has amino and acylcarnitine data. I sharing our source terms based on your response above. Yes we have only 104 terms. Apologies if I am sharing very limited information (without term description). We only have these terms and their value as of now… waaiting to know receive their descriptions. These terms shown below aren’t available in ATHENA right?

Gly 1
Ala 1
Ser 1
Pro 1
Val 1
Leu 1
Ile 1
Orn 1
Met 1
His 1
Phe 1
Arg 1
Cit 1
Tyr 1
Asp 1
Glu 1
Trp 1
C2
C3
C4
C5:1
C5
C4-OH
C6
C5-OH/C3-DC
C4-DC,C6-OH
C8:1
C8
C5-DC
C8:1-OH/C6:1-DC
C8-OH/C6-DC
C10:3
C10:2
C10:1
C10
C7-DC
C8:1-DC
C8-DC
C12:2
C12:1
C12
C12:2-OH/C10:2-DC
C12:1-OH
C12-OH/C10-DC
C14:3
C14:2
C14:1
C14
C14:3-OH/C12:3-DC
C14:2-OH
C14:1-OH
C14-OH/C12-DC
C16:3
C16:2
C16:1
C16
C16:3-OH/C14:3-DC
C16:2-OH
C16:1-OH/C14:1-DC
C16-OH
C18:3
C18:2
C18:1
C18
C18:3-OH/C16:3-DC
C18:2-OH/C16:2-DC
C18:1-OH/C16:1-DC
C18-OH/C16-DC
C20:4
C20:3
C20:2
C20:1
C20
C20:3-OH/C18:3-DC
C20:2-OH/C18:2-DC
C20:1-OH/C18:1-DC
C20-OH/C18-DC
C22:5
C22:4
C22:3
C22:2
C22:1
C22
C24
C26
C28
Gly 1_Conc(ratio/slope)
Ala 1_Conc(ratio/slope)
Ser 1_Conc(ratio/slope)
Pro 1_Conc(ratio/slope)
Val 1_Conc(ratio/slope)
Leu 1_Conc(ratio/slope)
Ile 1_Conc(ratio/slope)
Orn 1_Conc(ratio/slope)
Met 1_Conc(ratio/slope)
His 1_Conc(ratio/slope)
Phe 1_Conc(ratio/slope)
Arg 1_Conc(ratio/slope)
Cit 1_Conc(ratio/slope)
Tyr 1_Conc(ratio/slope)
Asp 1_Conc(ratio/slope)
Glu 1_Conc(ratio/slope)
Trp 1_Conc(ratio/slope)


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