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Non standard to Standard - Units

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#1

Hello Everyone,

I am trying to map our source data to CDM form. However, we have few units like (‘g/day’,‘mg/day’,‘cells/uL’) which doesn’t have a matching standard concept in Athena.

However I am able to find the matching non standard concepts for these 3 units ( 4124449, 4120731,4117642)

I believe we aren’t supposed to map it to a non-standard term.

So, the only way is to convert it to some other valid standard unit and avoid using non-standard concepts?

When a concept becomes standard and non-standard? What is required to convert a concept from non-standard to standard?

Thanks
Selva

#2

Hello!

2 Likes
#3

Hello @zhuk

With your help, I was able to find most of the units. However I am still not able to find the below terms. Will you be able to help?

  1. casts/uL
  2. TSI index
  3. GPL
  4. copies/mL
  5. kU/L - Is this 8810?

Thanks
Selva

#4

@SELVA_MUTHU_KUMARAN

4117808 casts/uL

4171221 GPL unit

8799 copies per milliliter

4118306 kU/L

Can you give more description on TSI index?

#5

Thank you @QI_omop. But I guess the ids that you gave are again non-standard…I am looking for standard terms for these units

1 Like
#6

@QI_omop - I mean except “copies per milliliter”, all other concept_ids are non-standard which I found already. I am looking for equivalent standard concept_ids

#7

casts/uL

Casts are measured per area. In general, you shouldn’t look for unit where the measurement itself is specified. Change your strategy - go throw measurements first, check LOINC to find measurement and unit, then go to UCUM. Example for casts.

TSI index

Why do you need any special units? As I can see here, any of units/volume can be used. Just find suitable for your use case.

GPL unit

The same situation here.

kU/L - Is this 8810?

Yes, if you mean kilounit per liter for ‘kU/L’

#8

I am trying with Christian develop a conversion ETL. Can you please describe how you deal with weight in pounds and kilograms. Our ETL goal is to have UPDATE statement that for each measurement defines convertable units (pounds) and single desired unit (kg). So when the update sql is executed, all weight is in the desired unit (and all other tests as well). Can you please comment on whether in your current data, you are trying to achieve that?

#9

Hello @Vojtech_Huser,

Thanks for the response

Currently our Source data has weight only in kg. So I just map it to kg. Yes, if it had been in pounds, I would have converted it it to retain same unit throughout. But I believe we might have to do this sort of conversion for other units in our data. As we are trying to compare between two data sources, we see differences in other measurement units (but not weight).

Did I answer your question?

#10

Our unit morphing ETL and knowledge base (draft) can be pre-viewed here. https://github.com/OHDSI/sandbox/tree/master/unitmorph

1 Like
#11

@Vojtech_Huser Thanks for sharing this

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