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DOC: add documentation for clinical_index (#137)
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fedorov authored Nov 13, 2024
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Expand Up @@ -116,3 +116,34 @@ the attributes exist with suffix `_code_designator_value_str` and
and CodeValue, or CodeMeaning. If this is new to you, a brief explanation on the
three-value based coding scheme in DICOM can be found at
https://learn.canceridc.dev/dicom/coding-schemes.

## `clinical_index`

Many of the image collections available in IDC are accompanied by clinical data.
Such clinical data is organized in one or more tables that are shared alongside
the images.

Each row in `clinical_index` corresponds to a column in a clinical table
available in IDC. You can use this index to find collections that have a
specific clinical attribute, compare availability of the clinical data across
collections, identify patients that have specific clinical characteristics.

Note that IDC does not perform any harmonization of the clinical data across
collections, or any validation of the content of the tables. We share clinical
data as it was provided by the submitter.

provides the list of all of the columns across all of the clinical tables
available in IDC. It contains the following items:

- `collection_id`: identifier of the collection where the given clinical data
attribute is available
- `short_table_name`: name of the clinical data table where the attribute is
encountered; the referenced table can be loaded into a Pandas DataFrame using
the `IDCClient.get_clinical_data()` call
- `table_name`: fully resolved name of the table in IDC Google BigQuery public
dataset (only relevant if you would like to search using BigQuery)
- `column`: name of the column that is available in the given clinical table
- `colum_label`: label of the column (this field may contain more extensive
information describing a given column)
- `values`: set of values defining the content of the column (relevant if the
column contains fixed list of values and not free text)

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