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Commit d6a686c1 authored by Jakub Dylag's avatar Jakub Dylag
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Update README

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...@@ -158,10 +158,10 @@ The `"concept_sets"` object defines the structure and rules for grouping input c ...@@ -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. - **`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`**: Defines a list of concept_set objects along with their attributes:
- **`concept_set_name`**: Maps to the column specifying the name of the concept set. - **`concept_set_name`**: Specifies 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! - **`concept_set_status`**: Indicates 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. - **`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. 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 ...@@ -170,13 +170,21 @@ The `"codes"` object specifies the source files containing input codes and assig
```json ```json
{ {
"concept_sets": { "concept_sets": {
"file":"PHEN_summary_working.csv", "version": "3.2.10",
"version":"3.2.10", "omop": {
"columns":{ "vocabulary_id": "MELDB",
"concept_set_name":"CONCEPT NAME ", "vocabulary_name": "Multidisciplinary Ecosystem to study Lifecourse Determinants and Prevention of Early-onset Burdensome Multimorbidity",
"concept_set_status":"AGREED", "vocabulary_reference": "https://www.it-innovation.soton.ac.uk/projects/meldb"
"metadata":["CONCEPT TYPE"] },
} "concept_set": [
{
"concept_set_name": "ABDO_PAIN",
"concept_set_status": "AGREED",
"metadata": {
"concept_set_description": "Abdominal pain",
}
}
]
}, },
"codes":[ "codes":[
{ {
......
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