Data types

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  Ondrej Klempir DNAnexus Team

  • 23 November 2022 13:35

  In order to get this info, I normally go to Cohort Browser and check details about each column, e.g.:

   

  It also contains a link to UKB Showcase, where this info is available as well.

   

  https://biobank.ctsu.ox.ac.uk/crystal/field.cgi?id=12143

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  Permanently deleted user

  • 23 November 2022 15:25

  Thanks, I am interested in a way to automate this for a potentially large number of columns. Ideally, I would need a per field summary table. Does anything like that exist?

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  Ondrej Klempir DNAnexus Team

  • 23 November 2022 15:40

  I believe you should be able to get this programatically with inspiration from this notebook:

  https://github.com/dnanexus/OpenBio/blob/master/dxdata/getting_started_with_dxdata.ipynb

   

  • "Field - Represents all other DataDictionary columns not covered by Entity and Edge
    • name (str): Field's internal name.
    • type (str): Primitive type name, e.g. "integer", "string", "date" ...
    • table_name (str): Database table where this field's data values are stored.
    • column_name (str): Database column where field values are stored.
    • coding (Coding): Coding instance that applies to this field's values.
    • is_multi_select (bool): Whether the field can contain multiple values per cell (array/set type)
    • is_sparse_coding (bool): Whether all data values should be covered by codings.
    • title (str): Optional.
    • description (str): Optional.
    • units (str): Optional.
    • concept (str): Optional.
    • linkout (str): Optional.
    • ** kwargs (dict of strings): Arbitrary additional attributes with string values.

   

  Do not forget to run Spark based JupyterLab.

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