NTR: Terms needed for BioData Catalyst Harmonization Pilot

[diatomsRcool]

I need the following terms for a BioData Catalyst harmonization pilot that is due this summer. BDC is a clinical data repository. I have looked through OBA and OBA issues to see if these terms existed already or had already been requested and I could not find them, but I could have missed something. I am also unsure if everything here is in scope for OBA, such as the dietary intake measurements.

• 8-epi-PGF2a in urine (8-Epi-Prostaglandin F2 Alpha) http://purl.obolibrary.org/obo/CHEBI_34505
• activity of LP-PLA2 in blood (Lipoprotein-Associated Phospholipase A2) http://purl.obolibrary.org/obo/GO_0004623 at least I think its this....is Lipoprotein-Associated Phospholipase A2 activity the same as Phospholipase A2 activity?
• AHI (Apnea-Hypopnea Index): AHI is calculated by adding the number of apneas and hypopneas per hour of sleep.
• Albumin creatinine ratio in urine - albumin is PR:000003918 and creatinine is CHEBI:16737
• Alcohol servings/week - http://purl.obolibrary.org/obo/NBO_0000131
• AST (aspartate aminotransferase) also known as SGOT (serum glutamic-oxaloacetic transaminase): measures the level of AST in the blood
• BUN Creatinine ratio: The BUN (blood urea nitrogen) to creatinine ratio is a blood test that measures the levels of two waste products in the blood: urea (BUN) and creatinine
• CAC Score (coronary artery calcium) score: Measure of calcium build-up in the coronary arteries. CAC scores are expressed as a number ranging from 0 to 400. Higher scores indicate a greater amount of calcium buildup and a higher risk of heart disease.
• CAC volume: Measures volume of calcium deposits in coronary arteries
• Cigarette smoking status: current, former, never - http://purl.obolibrary.org/obo/NBO_0015007
• D-Dimer in blood - PR:000050369
• EGFR (estimated glomerular filtration rate): eGFR is calculated using a formula that takes into account your blood creatinine levels, age, sex, and sometimes race
• FEV1 FVC ratio: Forced Expiratory Volume to Forced Vital Capacity ratio
• FVC - Forced Vital Capacity: total volume of air a person can exhale after taking a deep breath
• Fruits servings/week
• Hemoglobin A1c: I'm actually surprised I can't find this. Am I missing it?
• ICAM1 in blood (intercellular adhesion molecule 1): is this this same as cellular adhesion molecule 1?
• Interleukin 10 in blood - PR:000001471
• Interleukin 18 in blood - PR:000001376
• PR interval: time it takes for the electrical signal to travel from the atria to the ventricles
• QT interval: time it takes for the heart's ventricles to depolarize and repolarize
• red cell distribution width: Measurement of the ratio of variation in width to the mean width of the red blood cell (rbc) volume distribution curve taken at +/- 1 CV, known as red cell distribution width (RDW). - EFO:0009188
• Sodium intake: via diet - mg/day
• troponin in blood: I see measurements for troponin I and troponin T, but nothing for both types - GO:0005861
• Vegetables servings/week
• Waist-hip ratio
• CESD score (Center for Epidemiological Studies Depression) Scale: self-report questionnaire that give an integer score - EFO:0007006
• Fasting lipids: I see lipids, but not fasting lipids
• Medication adherence: How well is someone sticking to their doctor prescribed medication schedule?
• Medication use: Is someone using medication? Yes, No, Unknown

[rays22]

@diatomsRcool
Could you kindly provide identifiers (from OBO Foundry ontologies) for the component terms that I could use to define the terms you request?

ENTITY/PROCESS	POTENTIAL DOMAIN ONTOLOGY	ONTOLOGY IDENTIFIER
8-epi-PGF2a (8-Epi-Prostaglandin F2 Alpha)	ChEBI or other ontology identifier?
activity of LP-PLA2 in blood (Lipoprotein-Associated Phospholipase A2)	GO process/function term?
apnea	process term?
hypopnea	process term?
Albumin	PR or ChEBI term?
creatinine	PR or CheBI term?
Alcohol servings/week	NBO process term?
AST also known as SGOT (serum glutamic-oxaloacetic transaminase)	PR or ChEBI term?
Cigarette smoking status	NBO process term?
D-Dimer	PR, ChEBI identifier?
EGFR (estimated glomerular filtration rate)	GO biological process term?
FEV1 FVC ratio: Forced Expiratory Volume to Forced Vital Capacity ratio	PATO or other term?
Fruits servings/week	NBO process term?
Hemoglobin A1c	PR or ChEBI id?
ICAM1	PR or ChEBI id?
Interleukin 10	PR or ChEBI id?
Interleukin 18	PR or ChEBI id?
PR interval: time it takes for the electrical signal to travel from the atria to the ventricles	GO or other process term?
QT interval: time it takes for the heart's ventricles to depolarize and repolarize	GO or other process term?
red cell distribution width: Measurement of the ratio of variation in width to the mean width of the red blood cell (rbc) volume distribution curve taken at +/- 1 CV, known as red cell distribution width (RDW).	PATO term?
Sodium intake: via diet - mg/day	NBO term?
troponin	PR or ChEBI term?
Vegetables servings/week	NBO process term?
CESD score (Center for Epidemiological Studies Depression)	NBO process or other term?
Fasting lipids	PATO term?
Medication adherence	NBO process term?
Medication use	NBO process term?

[diatomsRcool]

Unfortunately, I can't edit your table to add the ontology terms, so I will add them to my initial comment as i find them.

[diatomsRcool]

@rays22
A few things

• Am I restricted to using PR, CheBI, PATO, GO, and NBO?
• Apnea and hypopnea are already in OBA under abnormal pattern of respiration and they are also in HPO. Can the AHI be created using these terms?
• GFR is already in OBA - should I use this for estimated GFR?
• FEV1 and FVC are volumes of air being exhaled and is a measure of lung function. Would air in respirator system be helpful here ? http://purl.obolibrary.org/obo/UBERON_0034874
• Could fruit and vegetable servings per week be subclasses of eating behavior which is already in OBA? OBA:VT0001431. FOODON uses FOODON:03315615 for fruit and FOODON:00001261 for vegetable and I think we can use CHEBI:26710 for sodium
• CESD has an EFO term but there is depression behavior in NBO? NBO:0000085
• Here is lipid CHEBI:18059 and here is fasting OBI:0003653
• There is a medication adherence behavior in EFO EFO:0006344
• Are we allowed to use BCIO:015093 for medication use?