diff --git a/docs/column_descriptions.md b/docs/column_descriptions.md index 234803f..39868c3 100644 --- a/docs/column_descriptions.md +++ b/docs/column_descriptions.md @@ -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)