Hello,
I am a student researcher who just received access to the UK Biobank dataset. I am looking through the Research Analysis Platform and can't seem to find where the data relevant to my study is located.
Is there a codebook available for where data is located throughout the RAP? Much of the data that I need is related to physical measurements and the participant questionnaire (not genetic data). However, I can't seem to find this data in the "Bulk" data section of the RAP. I would appreciate any guidance on finding my relevant data.
Sincerely,
Anoop
In general the "Bulk" data folder contains quantitative measurements associated with participants - i.e. genomic sequencing data, imaging data, biometric data.
For phenotypic data associated with participants- i.e. diagnosis, sex, age you can use the "Cohort Browser" to search for this information and then export the data needed using "table exporter" or "dx extract dataset"
Thank you for your explanation. It seems that the "Cohort Browser" is not launching when I open my dataset. Do you know how else I may be able to access the browser?
Also, as @Anastazie Sedlakova? mentioned, you can search in the UKB showcase to find what the "Item Type" is for the data you're wanted. The "Bulk" folder on RAP should contain those where "Item Type" == Bulk or Records.
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Hi Anoop,
In general the "Bulk" data folder contains quantitative measurements associated with participants - i.e. genomic sequencing data, imaging data, biometric data.
For phenotypic data associated with participants- i.e. diagnosis, sex, age you can use the "Cohort Browser" to search for this information and then export the data needed using "table exporter" or "dx extract dataset"
https://dnanexus.gitbook.io/uk-biobank-rap/working-on-the-research-analysis-platform/accessing-phenotypic-data-as-a-file
Hi Alexandra,
Thank you for your explanation. It seems that the "Cohort Browser" is not launching when I open my dataset. Do you know how else I may be able to access the browser?
Sincerely,
Anoop
I think that based on showcase Item type attribute for each field, Bulk folder on RAP should contain fields with the following types: Bulk, Records https://biobank.ndph.ox.ac.uk/showcase/help.cgi?cd=item_type
This is how my screen appears after opening the dataset.![Image 2-6-23 at 1.13 PM]()
I think you need to click on the appXXX dataset to open the Cohort Browser: https://documentation.dnanexus.com/user/cohort-browser
Also, as @Anastazie Sedlakova? mentioned, you can search in the UKB showcase to find what the "Item Type" is for the data you're wanted. The "Bulk" folder on RAP should contain those where "Item Type" == Bulk or Records.
Thank you Alexandra and Anastazie for the guidance. That was very helpful!
Sincerely,
Anoop
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