The Biobank Access Framework – p-BioSPRE
A Biobank Access Framework called p-BioSPRE has been developed within the p-medicine platform to enable and simplify access to existing biobanks but also to offer own biomaterial collections to research communities and manage biobank specimens over the ObTiMA Trial Biomaterial Manager.
The main component of the framework is p-BioSPRE, the p-medicine Biomaterial Search and Project Request Engine, which is a metabiobank to share biomaterial for research purposes. Furthermore, the framework comprises the p-Biobank Wrappers, which are tools to support biobank owners to offer their biomaterial and related data, (regardless which biobank information system they are running on-site), in p-BioSPRE and manage associated requests. In order to enable users of the p-medicine trial management system ObTiMA to integrate biomaterial data in clinical trials and offer it in p-BioSPRE a Trial Biomaterial Manager is provided.
In the following the functionality of the different key components is described.
p-BioSPRE - The p-medicine Biomaterial Search and Project Request Engine
p-BioSPRE is a metabiobank that provides to researchers the possibility to search for and request biomaterial that fits their research purposes.
p-BioSPRE provides a search interface that enables authorized users to search for biomaterial. After authentication, users access an interactive search tool (Fig. 1 a)) where they can search for different search parameters (e.g. Fig. 1.b)).
As a first-step search result, users will retrieve the number of cases/specimens matching their request, enabling them to decide whether a further query makes sense. If the user wants to find further information on the retrieved material and data, he may enter a Project Request on-line.
Biomaterial data is uploaded to p-BioSPRE from so called p-Biobank Wrappers which enable a biobank to share their biomaterial and related data in p-BioSPRE within an open or closed research community. Technically, a p-Biobank Wrapper is based on the IDB, a local server installed at the site of the biomaterial owner and configured to link one or more of their biobank management systems. As a precondition to link a biobank information management system (BIMS) to a p-Biobank Wrapper, the system needs to implement an export interface that allows exporting pseudonymized biomaterial data to the IDB.
Upon import into the IDB, pseudonymized data is harmonized and de-identified further, e.g. by converting a patient’s exact age into full years.
Before export to the p-BioSPRE metabiobank, the IDB software will strip off any pseudonyms thus generating anonymized data for on-line queries.
In addition to performing project requests, the IDB allows the biobank owner to select the imported data that he wants to share with certain research communities, anonymize, and upload the data to p-BioSPRE.
ObTiMA Trial Biomaterial Manager
The Trial Biomaterial Manager is developed as a component of the web based trial management system of the p-medicine infrastructure ObTiMA. It enables management of biobanks and associated specimen data in clinical trials and sharing selected specimen data.
For this purpose a predefined biobanking specimen CRF is provided that can be adjusted to the user’s needs. This CRF is stored in the ObTiMA CRF repository.
An interface is provided to get an overview of the available biomaterial. Furthermore, it is possible to link clinical data and biomaterial data within clinical trials.
It is also possible to select the biomaterial data that the biobank wants to share, and upload the data to p-BioSPRE.