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Need help with mapping to correct ontologies for kidney snRNA-seq dataset #42

Closed pnejad closed 4 years ago

pnejad commented 5 years ago

@zoependlington (or @zperova ?) could you help me map my fields to the correct ontologies? I'm unsure about some, but I've attempted to map some myself -- please let me know if any are incorrect!

mshadbolt commented 5 years ago

I'm not expert but maybe some of these would work:

hypertensive disorder:MONDO_0005044 - there are more specific child terms of this

hereditary hemochromatosis: MONDO_0006507

AKI is listed as a synonym for acute kidney failure:MONDO_0002492

depressive disorder:MONDO_0002050

ventricular tachycardia:MONDO_0005477

Maybe kidney neoplasm would work for renal mass if you don't know further information about the kind of tumor it is?

inherited lipid disorder:MONDO_0002525 has dyslipidemia as a synonym

maybe pleural effusion would be either pleurisy or pleuropneumonia? or maybe there needs to be a new term, there is already a pericardial effusion but doesn't seem to be one for pleura

zoependlington commented 4 years ago

Brain dump to look back over:

Renal mass = MONDO:0021163 (if no other information is provided) Acoustic neuroma = MONDO:0001569 OSA = MONDO:0007147 Hypertension = MONDO:0005044 AKI = MONDO:0002492 pleural effusion = new term request benign prostatic hyperplasia = MONDO:0010811 diverticulitis = MONDO:0004235 anxiety = MONDO:0011918 depression = MONDO:0002050 arthritis = MONDO:0005578 GERD = MONDO:0007186 lyme disease = MONDO:0019632 right renal mass = see renal mass type 2 diabetes = MONDO:0005148 adrenal mass = MONDO:0021227 NASH = MONDO:0007027 hemochromatosis = MONDO:0006507 SVT = ? IBS = MONDO:0005052 chest discomfort = ? hiatal hernia = MONDO:0007721 prostate cancer = MONDO:0008315 dyslipidemia = MONDO:0002525? hx VRE infection = new term PAF = MONDO:0018608 hyperlipidemia = MONDO:0021187

section = EFO:0009744

pnejad commented 4 years ago

@zoependlington Thank you for looking over this! I submitted this dataset already (part of the czi travel incentive). I will compare your suggestions with what I submitted and then do an AUDR next month after the meeting:)