Annotating pulmonary function labs

[callahantiff]

There are several LOINC codes which are measures of pulmonary function (e.g. 20159-9, 20155-8, 19870-5, 19877-4, 19877-0, and 19935-6) that seem as if they would be best annotated to more than 1 HPO term.

For example, annotating LOINC 19875-4 (Forced vital capacity [Volume] Respiratory system --post bronchodilation) to:

• Abnormality On Pulmonary Function Testing (HP:0030878)
• Functional Respiratory Abnormality (HP:0002795)

This annotation was clinically verified by clinicians from CHCO, but @nicolevasilevsky and I have been talking about it and wanted to get feedback from @pnrobinson.

[callahantiff]

@nicolevasilevsky and I will create new terms for each of the pulmonary function tests and will only use Abnormality On Pulmonary Function Testing (HP:0030878) as an ancestor or when needed for annotating normal lab results.

[pnrobinson]

• [ ] 20159-0 Maximum voluntary ventilation (need new HPO term)
• [x] 20155-8FEV1 --post bronchodilation (Decreased post-bronchodilator forced vital capacity HP:0032357)
• [x] 19870-5Forced vital capacity [Volume] Respiratory system (https://hpo.jax.org/app/browse/term/HP:0032341)
• [x] 19877-0Forced vital capacity [Volume] Respiratory system --pre bronchodilation (Decreased pre-bronchodilator forced vital capacity HP:0032356)
• [x] 19935-6Maximum expiratory gas flow Respiratory system airway by Peak flow meter (Decreased peak expiratory flow HP:0032355)

[pnrobinson]

@callahantiff we should use the same term for the abnormal and normal results, because not having one of these items does not imply NOT Abnormality On Pulmonary Function Testing (HP:0030878) -- other abnormalities could be present!

[callahantiff]

OK, that makes perfect sense to me!