Verification Category Examples for Conditions, Labs, Observations, and Procedures

[callahantiff]

@mgkahn, following up on our conversation yesterday, can you verify these examples? As a reminder, a partial match is one which requires special domain knowledge.

Phenotype: Peanut Allergy (Observations) Input String: “peanut” Source Code: SNOMED_91935009: Allergy to peanuts

• This source code is a good match because its label “allergy to peanuts”, contains the input string.
• This makes sense clinically as a realistic observation source code that would be assigned to a patient who had a diagnosed peanut allergy.

Conclusion: “Exactly Matches Definition String + Clinically Relevant”

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Phenotype: Peanut Allergy (Conditions) Input String: “peanut” Source Code: SNOMED_17212311000001107: Lifestyle gluten free peanut butter cookies (Ultrapharm Ltd)

• This source code is a good match because its label “allergy to peanuts”, contains the input string.
• This might NOT make sense clinically as a realistic diagnosis or condition code to use as evidence that a patient has been diagnosed with a peanut allergy.

Conclusion: “Exactly Matches Definition String + NOT Clinically Relevant”

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Phenotype: Systemic Lupus Erythematosus (Measurements) Input String: “antinuclear ab” Source Code: LOINC_11090-8: Smith extractable nuclear Ab [Units/volume] in Serum

• This source code is a good partial (and appropriate) match to the phenotype definition because smith extractable nuclear Ab is an autoantibody to the smith antigen (PMID:19121207).
• This code makes sense clinically as this lab test is specifically used to detect systemic lupus erythematosus (PMID: 5932578).

Conclusion: “Partially (and Appropriately) Matches Definition String + Clinically Relevant”

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Phenotype: Hypothyroidism (Measurements) Input String: “free t4” Source Code: LOINC_3022-1: Thyroxine free index in Serum or Plasma

• This source code is a good match because its label “Thyroxine free index in Serum or Plasma” contains the input string.
• This might NOT make sense clinically as this LOINC code has been deprecated and a different lab, LOINC_32215-6: Thyroxine (T4) free index in Serum or Plasma by calculation, is now preferred.

Conclusion: “Partially (and Appropriately) Matches Definition String + NOT Clinically Relevant”

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Phenotype: Crohn’s Disease (Conditions) Input String: “SLE” Source Code: CIEL_126366: Sleep-Related Bruxism

• This source code would NOT be a good match because “Sleep-Related Bruxism” has no well-known connection to “SLE” and was only included because it contained the string “SLE”.
• This would NOT make sense clinically as a diagnosis or condition code assigned to a Crohn’s disease patient, especially if it were being used as a way to rule out a secondary diagnosis of “SLE” or systemic lupus erythematosus.

Conclusion: “Does NOT Match Definition + NOT Clinically Relevant”

[callahantiff]

@mgkahn, I will assume that no response is a good thing 😄 and will close this unless you feel something else is needed.