Update plausible unit concept ID list

[katy-sadowski]

Update all 3 concept-level threshold files to include some additional plausible unit concepts:

• The number and percent of records for a given CONCEPT_ID 3009201 (THYROTROPIN [UNITS/VOLUME] IN SERUM OR PLASMA) with implausible units (i.e., UNIT_CONCEPT_ID NOT IN (44777578,8719,9040,9093)). (Threshold=5%).
  • Missing concept ID https://athena.ohdsi.org/search-terms/terms/8860
• The number and percent of records for a given CONCEPT_ID 3010813 (LEUKOCYTES [#/VOLUME] IN BLOOD) with implausible units (i.e., UNIT_CONCEPT_ID NOT IN (44777588,8848,8961,9444)). (Threshold=5%).
  • Is missing https://athena.ohdsi.org/search-terms/terms/8647
• The number and percent of records for a given CONCEPT_ID 3007461 (PLATELETS [#/VOLUME] IN BLOOD) with implausible units (i.e., UNIT_CONCEPT_ID NOT IN (8848,8961,9444)). (Threshold=5%).
  • Is missing https://athena.ohdsi.org/search-terms/terms/32706

[katy-sadowski]

The number and percent of records for a given CONCEPT_ID 3010813 (LEUKOCYTES [#/VOLUME] IN BLOOD) with implausible units (i.e., UNIT_CONCEPT_ID NOT IN (44777588,8848,8961,9444)). (Threshold=5%).

Is missing https://athena.ohdsi.org/search-terms/terms/8647

[katy-sadowski]

The number and percent of records for a given CONCEPT_ID 3007461 (PLATELETS [#/VOLUME] IN BLOOD) with implausible units (i.e., UNIT_CONCEPT_ID NOT IN (8848,8961,9444)). (Threshold=5%).

Is missing https://athena.ohdsi.org/search-terms/terms/32706

[adelmestri]

Some more issues to be solved on UNIT_CONCEPT_ID:
Table = ‘Measurement’, category = ‘Plausibility’, Status = ‘Fail’

1. The number and percent of records for a given CONCEPT_ID 4148615 (NEUTROPHIL COUNT) with implausible units (i.e., UNIT_CONCEPT_ID NOT IN (8784,8848,8961)). (Threshold=5%).” UNIT_CONCEPT_ID = 9444 = ‘1 billion per liter’ should be added to the list (8784,8848,8961).
   In fact
   8848 = thousand per microliter = 10^3 per microliter
   1 billion = 10^9
   1 liter = 10^6 microliter
   1 billion per liter = thousand per microliter

2. The number and percent of records for a given CONCEPT_ID 4254663 (LYMPHOCYTE COUNT) with implausible units (i.e., UNIT_CONCEPT_ID NOT IN (8848)). (Threshold=5%).
   UNIT_CONCEPT_ID = 9444 = ‘1 billion per liter’ should be added to the list for the same reason as point above

3. The number and percent of records for a given CONCEPT_ID 4298431 (WHITE BLOOD CELL COUNT) with implausible units (i.e., UNIT_CONCEPT_ID NOT IN (8848,8961)). (Threshold=5%).
   UNIT_CONCEPT_ID = 9444 = ‘1 billion per liter’ should be added to the list for the same reason as point above

4. The number and percent of records for a given CONCEPT_ID 4030871 (RED BLOOD CELL COUNT) with implausible units (i.e., UNIT_CONCEPT_ID NOT IN (8734,8815,8931,9444)). (Threshold=5%).
   UNIT_CONCEPT_ID = 9445 = 'billion per milliliter' should be added:
   8734 = 'trillion per liter'
   Billion = trillion/10^3
   Milliliter = liter/10^3

5. The number and percent of records for a given CONCEPT_ID 4197602 (SERUM TSH MEASUREMENT) with implausible units (i.e., UNIT_CONCEPT_ID NOT IN (8719,9040,9093)). (Threshold=5%).
   8719 = ‘milliunit per milliliter’
   9040 = ‘milli-international unit per liter’
   9093 = ‘micro-international unit per milliliter’

The following should be added to the list of acceptable UNIT_CONCEPT_ID:
44777578 = ‘milliunit per liter’
8750 = ‘microunit per liter’
8923 = ‘international unit per liter’

[katy-sadowski]

More:

• The number and percent of records for a given CONCEPT_ID 4184637 (HEMOGLOBIN A1C MEASUREMENT) with implausible units (i.e., UNIT_CONCEPT_ID NOT IN (8554,8632,8737)). (Threshold=5%). - add 9579 - millimole per mole
• The number and percent of records for a given CONCEPT_ID 37393850 (MCHC - MEAN CORPUSCULAR HAEMOGLOBIN CONCENTRATION) with implausible units (i.e., UNIT_CONCEPT_ID NOT IN (8636,8713)). (Threshold=5%). - add 8554 - percent and 8753 millimole per liter
• The number and percent of records for a given CONCEPT_ID 4151358 (HEMATOCRIT DETERMINATION) with implausible units (i.e., UNIT_CONCEPT_ID NOT IN (44777604,8554)). (Threshold=5%). - add 8523 - ratio
• The number and percent of records for a given CONCEPT_ID 4197602 (SERUM TSH MEASUREMENT) with implausible units (i.e., UNIT_CONCEPT_ID NOT IN (8719,9040,9093)). (Threshold=5%). -add 44777578 - milliunit per liter; 44777583 - micro-international unit per liter; 8750 - microunit per liter
• The number and percent of records for a given CONCEPT_ID 3034639 (HEMOGLOBIN A1C [MASS/VOLUME] IN BLOOD) with implausible units (i.e., UNIT_CONCEPT_ID NOT IN (8713,8840)). (Threshold=5%). - add 9579 - millimole per mole and 8923 - international unit per liter
• The number and percent of records for a given CONCEPT_ID 4030871 (RED BLOOD CELL COUNT) with implausible units (i.e., UNIT_CONCEPT_ID NOT IN (8734,8815,8931,9444)). (Threshold=5%). - add 9445 - billion per milliliter
• The number and percent of records for a given CONCEPT_ID 3000034 (MICROALBUMIN [MASS/VOLUME] IN URINE) with implausible units (i.e., UNIT_CONCEPT_ID NOT IN (8576,8723,8751,8840,8859)). (Threshold=5%). - add 8636 - gram per liter
• The number and percent of records for a given CONCEPT_ID 3016723 (CREATININE [MASS/VOLUME] IN SERUM OR PLASMA) with implausible units (i.e., UNIT_CONCEPT_ID NOT IN (8840)). (Threshold=5%). - add 8749 - micromole per liter
• The number and percent of records for a given CONCEPT_ID 3024128 (BILIRUBIN.TOTAL [MASS/VOLUME] IN SERUM OR PLASMA) with implausible units (i.e., UNIT_CONCEPT_ID NOT IN (8840)). (Threshold=5%). - add 8749 - micromole per liter
• add 8753 - millimole per liter for:
  • The number and percent of records for a given CONCEPT_ID 3003338 (MCHC [MASS/VOLUME]) with implausible units (i.e., UNIT_CONCEPT_ID NOT IN (8713)). (Threshold=5%).
  • The number and percent of records for a given CONCEPT_ID 3022192 (TRIGLYCERIDE [MASS/VOLUME] IN SERUM OR PLASMA) with implausible units (i.e., UNIT_CONCEPT_ID NOT IN (8840)). (Threshold=5%).
  • The number and percent of records for a given CONCEPT_ID 3004501 (GLUCOSE [MASS/VOLUME] IN SERUM OR PLASMA) with implausible units (i.e., UNIT_CONCEPT_ID NOT IN (8840)). (Threshold=5%).
  • The number and percent of records for a given CONCEPT_ID 4191837 (CALCULATED LDL CHOLESTEROL LEVEL) with implausible units (i.e., UNIT_CONCEPT_ID NOT IN (8840)). (Threshold=5%).
• The number and percent of records for a given CONCEPT_ID 3037556 (URATE [MASS/VOLUME] IN SERUM OR PLASMA) with implausible units (i.e., UNIT_CONCEPT_ID NOT IN (8840)). (Threshold=5%). - add 8923 - international unit per liter
• add 9444 - billion per liter to:
  • The number and percent of records for a given CONCEPT_ID 40487382 (TOTAL LYMPHOCYTE COUNT) with implausible units (i.e., UNIT_CONCEPT_ID NOT IN (8784,8848,8961)). (Threshold=5%).
  • The number and percent of records for a given CONCEPT_ID 4298431 (WHITE BLOOD CELL COUNT) with implausible units (i.e., UNIT_CONCEPT_ID NOT IN (8848,8961)). (Threshold=5%).
  • The number and percent of records for a given CONCEPT_ID 4254663 (LYMPHOCYTE COUNT) with implausible units (i.e., UNIT_CONCEPT_ID NOT IN (8848)). (Threshold=5%).
  • The number and percent of records for a given CONCEPT_ID 4148615 (NEUTROPHIL COUNT) with implausible units (i.e., UNIT_CONCEPT_ID NOT IN (8784,8848,8961)). (Threshold=5%).

[katy-sadowski]

These were fixed in release 2.6.2 :)