SCCRIP (Sickle Cell Clinical Research and Intervention Program) established a longitudinal cohort at multiple sites with Sickle Cell Disease (SCD) in 2014 managed by St. Jude Clinical Hematology. A new collaborator for SCCRIP has longitudinal data for 600 SCD patients in OMOP CDM format and this effort is to convert OMOP CDM to SCCRIP format.
WHITERABBIT and RABBIT-IN-A-HAT are software tools to help prepare for ETLs of longitudinal healthcare databases into the OMOP CDM. WhiteRabbit scans your data and creates a report containing all the information necessary to begin designing the ETL. WhiteRabbit’s main function is to perform a scan of the source data, providing detailed information on the tables, fields, and values that appear in a field. The source data can be in comma-separated text files, or in a database (MySQL, SQL Server, Oracle, PostgreSQL, Microsoft APS, Microsoft Access, Amazon RedShift). The scan will generate a report that can be used as a reference when designing the ETL, for instance by using it in conjunction with the Rabbit-In-a-Hat tool. WhiteRabbit differs from standard data profiling tools in that it attempts to prevent the display of personally identifiable information (PII) data values in the generated output data file.
The Rabbit-in-a-Hat tools that come with the White Rabbit software are specifically designed to support a team of experts in these areas. In a typical setting, the ETL design team sits together in a room, while Rabbit-in-a-Hat is projected on a screen. In a first round, the table-to-table mappings can be collaboratively decided, after which field-to-field mappings can be designed while defining the logic by which values will be transformed.
Rabbit-In-a-Hat is designed to read and display a White Rabbit scan document. White Rabbit generates information about the source data while Rabbit-In-a-Hat uses that information and through a graphical user interface to allow a user to connect source data to tables and columns within the CDM. Rabbit-In-a-Hat generates documentation for the ETL process, it does not generate code to create an ETL.
Verify Install
Introductory Tutorials
https://ohdsi.org/ohdsi2022-tutorial/
https://ohdsi.org/open-source-tutorials/
Practice with use cases
Discuss OHDSI tool among team with specific relevance to Integrating SCCRIP Data in OMOP format.
From https://ohdsi.org/software-tools/ below
WHITERABBIT and RABBIT-IN-A-HAT are software tools to help prepare for ETLs of longitudinal healthcare databases into the OMOP CDM. WhiteRabbit scans your data and creates a report containing all the information necessary to begin designing the ETL. WhiteRabbit’s main function is to perform a scan of the source data, providing detailed information on the tables, fields, and values that appear in a field. The source data can be in comma-separated text files, or in a database (MySQL, SQL Server, Oracle, PostgreSQL, Microsoft APS, Microsoft Access, Amazon RedShift). The scan will generate a report that can be used as a reference when designing the ETL, for instance by using it in conjunction with the Rabbit-In-a-Hat tool. WhiteRabbit differs from standard data profiling tools in that it attempts to prevent the display of personally identifiable information (PII) data values in the generated output data file.
The Rabbit-in-a-Hat tools that come with the White Rabbit software are specifically designed to support a team of experts in these areas. In a typical setting, the ETL design team sits together in a room, while Rabbit-in-a-Hat is projected on a screen. In a first round, the table-to-table mappings can be collaboratively decided, after which field-to-field mappings can be designed while defining the logic by which values will be transformed.
Rabbit-In-a-Hat is designed to read and display a White Rabbit scan document. White Rabbit generates information about the source data while Rabbit-In-a-Hat uses that information and through a graphical user interface to allow a user to connect source data to tables and columns within the CDM. Rabbit-In-a-Hat generates documentation for the ETL process, it does not generate code to create an ETL.
WHITERABBIT and RABBIT-IN-A-HAT LINKS Documentation: Book of OHDSI – WhiteRabbit and Rabbit-In-A-Hat • Web Sites – WhiteRabbit and Rabbit-In-A-Hat Installation Information: WhiteRabbit and Rabbit-In-A-Hat Source Code: GitHub