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?