diff --git a/README.md b/README.md index 0eab45dd7544f9d70ba82149613a8c17a1e96465..358b96de7f5980df141f322362534fd78cc342e2 100644 --- a/README.md +++ b/README.md @@ -158,10 +158,10 @@ The `"concept_sets"` object defines the structure and rules for grouping input c - **`version`**: Identifies the version of the concept set definitions being used. This can help track changes over time. -- **`columns`**: Describes the mapping of specific column names in the CSV file to attributes of the concept sets. Supported keys are: - - **`concept_set_name`**: Maps to the column specifying the name of the concept set. - - **`concept_set_status`**: Maps to the column indicating the status of the concept set. Only concept sets the **"AGREED"** status will be outputted! - - **`metadata`**: A list of additional columns in the CSV file that should be copied to the output for descriptive or contextual purposes. +- **`concept_set`**: Defines a list of concept_set objects along with their attributes: + - **`concept_set_name`**: Specifies the name of the concept set. + - **`concept_set_status`**: Indicates the status of the concept set. Only concept sets the **"AGREED"** status will be outputted! + - **`metadata`** (optional): A list of additional properties that will be copied into the output. Can be used for descriptive or contextual purposes. The `"codes"` object specifies the source files containing input codes and assigns them to the corresponding concept sets through the `"concept_set"` field. @@ -170,13 +170,21 @@ The `"codes"` object specifies the source files containing input codes and assig ```json { "concept_sets": { - "file":"PHEN_summary_working.csv", - "version":"3.2.10", - "columns":{ - "concept_set_name":"CONCEPT NAME ", - "concept_set_status":"AGREED", - "metadata":["CONCEPT TYPE"] - } + "version": "3.2.10", + "omop": { + "vocabulary_id": "MELDB", + "vocabulary_name": "Multidisciplinary Ecosystem to study Lifecourse Determinants and Prevention of Early-onset Burdensome Multimorbidity", + "vocabulary_reference": "https://www.it-innovation.soton.ac.uk/projects/meldb" + }, + "concept_set": [ + { + "concept_set_name": "ABDO_PAIN", + "concept_set_status": "AGREED", + "metadata": { + "concept_set_description": "Abdominal pain", + } + } + ] }, "codes":[ {