VICC is the Variant Interpretation for Cancer Consortium. One of the aims of this consortium is to create a harmonized meta-knowledgebase from various actual knowledgebases (see paper).
This module imports the data that has been generated as part of this paper, and in addition does the following:
- For each feature, determines the event type as defined by the SERVE datamodel.
- Provides classification mapping to map all VICC entries onto SERVE actionable events.
- Loads up the database into a MySQL database
In order to load the VICC database into a MySQL database, one needs to:
- Create the database using create_vicc_database.sql script from the VICC importer resources.
- Run ViccJsonSQLImporter (default class in the vicc-importer jar) with the following arguments:
| Argument | Description |
|---|---|
| vicc_json | Required: Path to the VICC json file containing the VICC data. |
| db_url | Required: The URL of the database in which to ingest the data. |
| db_user | Required: The DB user which has access to the the URL specified |
| db_pass | Required: The password needed for the DB user to authenticate on the URL. |