Table 2.

Examples of phenotypic information represented using our proposed annotation scheme

COPD Phenotypes	Automatically recognized underlying concepts	Automatically linked ontological concepts
chronic airways obstruction	chronic airways obstruction	chronic (PATO:0001863) respiratory airway (UBERON:0001005) obstructed (PATO:0000648)
parenchymal destruction	parenchymal destruction	parenchyma (UBERON:0000353) damaged (PATO:0001167)
decrease in rate of lung function	decrease in rate lung function	decreased rate (PATO:0000911) lung (UBERON:0002048) function (PATO:0000173)
chronic bronchitis	N/A	chronic bronchitis (DOID:6132)
myocardial infarction	N/A	myocardial infarction (DOID:5844)
enhanced response to inhaled corticosteroids	enhanced response to corticosteroids	enhanced (PATO:0001589) response to (PATO:0000077) corticosteroid (ChEBI:50858)
FEV1 45% predicted	FEV1	Forced Expiratory Volume 1 Test (NCIT:C38084)
alpha1 antitrypsin deficiency	alpha1 antitrypsin deficiency	alpha-1-antitrypsin (PR:000014678) decreased amount (PATO:0001997)