Improving column names

[vincent-octo]

We could discuss about changing the column names, as in my opinion some are a bit confusing at the moment. The idea is to be more consistent in the naming, and avoid implicitness.

The suggested renaming would be based on — and differentiate between — these concepts:

• a lab test, column prefix: TEST_
• a measurement for a lab test, column prefix: MEASUREMENT_
• a result for a lab test, column prefix: RESULT_

This would mean we will not have the same column names as in Kira's output, but that's OK.

Suggested column renaming:

• LAB_DATE_TIME => MEASUREMENT_DATE_TIME Would probably need to confirm the datetime here is about the measurement, and not about when the result arrived in Kanta system for example.

• LAB_SERVICE_PROVIDER => SERVICE_PROVIDER Though the variale for this might be missing in the FinnGen raw data.

• LAB_ID => TEST_ID

• LAB_ID_SOURCE => TEST_ID_SOURCE

• LAB_ABBREVIATION => TEST_NAME_ABBREVIATION

• LAB_VALUE => MEASUREMENT_VALUE

• LAB_UNIT => MEASUREMENT_UNIT

• LAB_ABNORMALITY => RESULT_ABNORMALITY

• ~MEASUREMENT_STATUS => RESULT_STATUS~ (keep MEASUREMENT_STATUS, see https://github.com/FINNGEN/kanta_lab_preprocessing/issues/15#issuecomment-2112011424)

• REFERENCE_VALUE_TEXT => TEST_REFERENCE_VALUE

So in the end, we would change from this header:

FINREGISTRYID   LAB_DATE_TIME   LAB_SERVICE_PROVIDER    LAB_ID  LAB_ID_SOURCE   LAB_ABBREVIATION    LAB_VALUE   LAB_UNIT    LAB_ABNORMALITY REFERENCE_VALUE_TEXT    MEASUREMENT_STATUS

to this header:

FINREGISTRYID   MEASUREMENT_DATE_TIME   SERVICE_PROVIDER    TEST_ID TEST_ID_SOURCE  TEST_NAME_ABBREVIATION  MEASUREMENT_VALUE   MEASUREMENT_UNIT    RESULT_ABNORMALITY  TEST_REFERENCE_VALUE    RESULT_STATUS

[piotor87]

Just one thing: for consistency with the input columns, I kept MEASUREMENT_STATUS because in the original column is grouped with the other ones:

'tutkimustulosarvo':              'MEASUREMENT_VALUE',
'tutkimustulosyksikko':           'MEASUREMENT_UNIT',
'tutkimusvastauksentila':         'MEASUREMENT_STATUS',
'tuloksenpoikkeavuus':            'RESULT_ABNORMALITY',