Info

Biosample Data

Objective: Establish a common standard for biobanking summary data, create catalog solution for biospecimen data and develop a generic workflow for biospecimen request and ordering.

Rationale

Biobanks are extremely valuable resources for (bio)medical and epidemiological research. The term biobank refers to any collection of materials of patients or participants in a cohort study, e.g. blood, tissue, tumor or urine. Biobanks range from long-term population studies, e.g. LifeLines, to small collections of patient biomaterials that are stored by individual research groups in multi-site clinical studies.

Because most of these biobanks are individually organized and managed, it is almost impossible for researchers to survey which collections and data are available at other centers. TraIT WP3 aims to facilitate researchers looking for data as well as biobank managers looking for ways to increase usage (and thus: relevance) of their collections by building a catalogue of biobanking data, defining a common standard for biobanking (meta)data, which facilitates exchange between researchers in multi-site clinical studies, and developing a workflow that enables researchers to request and retrieve samples and data.

The Biobanking work package in TraIT aims to provide scientist with tools and services that address ICT challenges around collecting, storing, exchanging, combining and analyzing bio-specimens as well as their related data. Turnkey solutions that help scientist to focus on their core business: Research.

 

Target groups

- Researchers in (bio)medicine, epidemiology

- Biobank managers / coordinators

- Biobank/UMC ICT-staff

 

Approach

In line with other national biobanks (e.g. Parelsnoer), and based on a stakeholder analysis and inventory of wishes and needs among researchers associated with CTMM projects and coordinators/managers of biobanks, a minimal dataset from the USA Common Biorepository Model (CBM) has been adapted to Dutch standards. The CBM builds on a commonly defined standard for data and metadata. This standard also allows (meta)data to be populated and analyzed using tranSMART.

A number of use cases have been selected based on the inventory, which generate tangible objectives for the ICT-staff of biobanks to start actual implementation of the new standard at their respective locations. This includes, a generic workflow for requesting sample and data retrieval and a bio-specimen catalogue of all biobanking data associated with CTMM and/or translational biomedical research projects.

The development of these services and tools were the results of joined efforts with BBMRI-NL, the Parelsnoer Institute, Mondriaan and UMC Groningen, and international collaboration with BBMRI-EU, tranSMART, BioSHaRE, and BioMedBridges.

 

Status

- A standard information model and data format for bio-specimens

- A generic electronic workflow to monitor bio-specimen collection and distribution

- The bio-specimen catalogue (based on the CBM model) is available for all users.

- A benchmark on Biobank Information Management Systems (BIMS) has been performed.

 

More information

Work Package leader: David van Enckevort (UMC Groningen)

david.van.enckevort <at> umcg.nl