Contributors: Igor Engel, Thomas Ganslandt
TODO TG: content
Relevance & Approach
Large collections of biosamples e.g. from tumors or "remainder" material from routine clinical laboratories play an increasing role in translational research. The intuitive query capabilities of i2b2 make it an ideal platform for querying combined data from clinical or study records, biosamples, and analysis data gained from biomaterial. Importing biosample data into i2b2, however, has so far required individually coded ETL pathways.
Unlike the CDISC ODM format for clinical trial data, there currently exists no established standard format for biomaterial data. Therefore, the IDRT biomaterial extractor takes the approach of a "generic concept hierarchy" that contains data elements typically used for sample collection, and combines it with a "system-specific driver" that can be adapted to the actual source system to be connected.
The data elements of the generic biomaterial concept hierarchy are:
- specimen basic information: sample ID, material type
- storage hierarchy and sample location
- SPREC (Standard PREanalytical Code) describing sample preparation and storage conditions (see Betsou et al. 2010)
- individually defined metadata elements
In the IDRT project, a driver was developed to import biosample data from the Starlims Biorepository® by Abbott Informatics (tested with version 10.5 and 10.7).
Implementation
In this section, the specific implementation for the Starlims® driver is described. The driver was implementation on the Talend Open Studio platform in order to integrate with the other components of the IDRT toolkit. The driver creates CSV files for the full ontology and fact data generated from the source system, which is then imported using the standard IDRT CSV extractor. A driver for a different biosample management system only needs to implement the extration and preparation of ontology and fact CSV files.
Staging
All required raw data tables are copied from the source system into a staging area. Read-access to the database of the production system or a database copy is required. The following tables are copied:
Context |
Table |
Description |
|---|---|---|
Sample core data |
INVENTORY |
Biosample inventory objects (e.g. samples, aliquots, containers), including relevant core attributes (e.g. sample ID, material type) |
|
INVENTORY_TRANSACTIONS |
Actions taken with samples (e.g. splitting into aliquots, moving) including links to parent samples of aliquots |
|
MATERIALS |
material types |
|
RASPROJECT_INVENTORY |
links between samples and projects |
Sample metadata |
METADATA |
metadata content for samples |
|
METADATA_TEMPLATE_FIELDS |
field definitions for flexible sample metadata |
Storage hierarchy |
DEPARTMENTS |
top level of storage hierarchy |
|
BUILDINGS |
buildings inside of departments |
|
ROOMS |
rooms inside of buildings |
|
LOCATIONS |
recursive storage structure inside of a room (e.g. a freezer subdivided into slots, racks and rack positions) |
