How to download HES files from UKBiobank and how to create phenotype file?
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2.5 years ago
anamaria ▴ 160

Hello,

I want to create pehonotype file with these defintions for cases and controls:

Case: 1.Eyesight questionnaire data field 6148 Diabetes related eye disease (case) (4,235) 2.Data-Field 41270 Diagnoses: - ICD10, Chapter IV Endocrine, nutritional and metabolic diseases: E10.3 (T1D with ophthalmic manifestations), E11.3 (T2D with ophthalmic manifestations), E14.3. Chapter VII Diseases of the eye and adnexa: H36.0 (diabetic retinopathy). Add together 1 and 2 to use as cases and remove duplicates.

Control: 1.Data-Field 2443 Diabetes diagnosed by doctor (control) Yes (29,572) 2.Data-Field 41270 Diagnoses:Chapter IV Endocrine, nutritional and metabolic diseases:E10.9, E11.9, E14.9 (diabetes without complications).Add together 1 and 2 to use as controls and remove duplicates.

I plan to use this software: https://github.com/saphir746/BiobankRead-Bash/blob/master/README.rst

It seems to me that I would need to run this script from there: extract_HES.py

for that I would need HES files downloaded? Does anyone know where I how I can download those?

I found this https://biobank.ndph.ox.ac.uk/showcase/label.cgi?id=2000 they have HES Data Dictionary and HES Table Structure, which one I would use?

also there is this other information for HES files here: http://biobank.ctsu.ox.ac.uk/showcase/exinfo.cgi?src=HESupdate

Any idea how to proceed with this?

Thanks Ana

ukbiobank • 1.2k views
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Hi,recently I am running the bio-reader, have you sovled the problems. During I run the commond line, it takes huge memory and didn't give the result. I guess somewhere I did wrong, but couldn't find the answer.

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15 months ago

Record-level inpatient data, "The record-level inpatient data is accessed via the online Data Portal (via a project's Download page)". https://biobank.ndph.ox.ac.uk/showcase/label.cgi?id=2000 Updates to the Data Portal- Table: https://biobank.ndph.ox.ac.uk/showcase/exinfo.cgi?src=timelines_all

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