Common Service IT

What are we aiming to achieve?

1. Ensure the findability of biobanking and biomolecular resources (-> Directory, Locator)
2. Facilitate access to biobanks (-> Access Policy, Negotiator)
3. Stimulate the biobanking infrastructure to effective behaviour (-> KPIs)
4. Help biobanks in providing quality-defined samples & datasets (-> ISO TC276 works – quality standards, provenance information management, SAS tool, Directory)
5. Support biobanks in implementing missing IT components (-> BIBBOX)
6. Support legal and ethical compliance (-> developing a GDPR Code of Conduct for use of health data for research)

The above points (except 5) constitute components of FAIR-Health principles.

How are we doing it?

• Defining neutral interfaces and data models for components
• Providing reference open-source implementations of those components
• We encourage the BBMRI-ERIC community to contribute to the open-source development
• We encourage companies to implement interfaces and data models

A brief summary of selected components

Services and Tools

Directory

The Directory is a metadata and public data information service with aggregated information about biobanks, their sample and data collections, as well as additional services offered by the biobanks. The BBMRI-ERIC National Nodes are responsible for providing and curating the data in the Directory for the respective country. The Directory 3.3 contains more than 520 biobanks hosting 1405 sample and data collections, with an estimated 100,000,000+ samples. The Directory uses MIABIS 2.0 Core as a data model and provides a documented REST API for accessing and manipulating the data (authentication is required for editing data).

The source code is available here.

Negotiator

Implementing the BBMRI-ERIC Access Policy, the BBMRI-ERIC Negotiator is a communication platform between researchers requesting samples/data and biobanks indicating that they have material and data suitable for the outlined research project. It allows a requesting researcher to communicate effectively with multiple biobanks at the same time, while it also allows biobanks to provide sample/data availability information confidentially to the researcher. The Negotiator is currently linked to the BBMRI-ERIC Directory: the researcher searches for candidate biobanks and collections in the Directory and then proceeds to the Negotiator. Once the BBMRI-ERIC Locator has been released, the Negotiator will be accessible through both the Directory and Locator. Access to the Negotiator requires authentication and the requesting researcher needs to have a research project in order to allow biobanks to assess compliance with the available informed consent and secondary use of data permits.

The source code is available here.

Locator

The BBMRI-ERIC Locator is a distributed search tool that allows querying preliminary sample availability statistics. In a typical scenario, biobanks will run a connector (either using reference open-source implementation provided by BBMRI-ERIC or implementing the Connector API in their own systems), which will communicate with the Locator about new queries. In its responses, the connector will provide numbers of samples fulfilling the search criteria – thus eliminating the need for biobanks to transfer their data to any central database. Replies will be anonymised on the level of the central connector, something that will also be possible on the level of individual connectors. Access to the Locator will require authentication and acceptance of the terms and conditions of using BBMRI-ERIC IT services, but no project is needed for initial querying; hence the Locator is suitable for research hypothesis generation and for the formulation of new research projects. However, a project description is required in case the Negotiator is used to contact biobanks for access to samples and data. A first version of the Locator is expected to be released during the second half of 2018.

BIBBOX

BIBBOX is an open-source toolbox of reference IT tools for biobanks: ranging from biobank information management systems (BIMS), laboratory information management systems (LIMS), phenotyping tools, data integration platform, to bioinformatics data analysis tools. Based on the integration of existing open-source tools, BIBBOX provides an all-in-one solution for operating newly established biobanks on an open-source platform, while also allowing the use of individual components in case biobanks already have their systems and are only looking for some additional components. The tools are available as Docker images so that they can be easily deployed within biobanks with relatively low IT support. Once the Locator is released, BIBBOX will also include the reference open-source implementation of the connector to be run by the biobanks. BIBBOX is not designed for biobanks with larger collections of biomaterials or with comprehensive data associated with the biomaterials.

The source code is available here.

Data harmonisation tools

Data harmonisation tools are a set of middleware services that provide ontology registries and translation tools to be used by other BBMRI-ERIC IT services and possibly also external services in the future. These tools are the response to the heterogeneity of standards in medical informatics (e.g., various clinical ontologies such as ICD-10 and SNOMED CT) used across Europe and beyond.

Self-Assessment Surveys (SAS)

Biobankers and researchers based in BBMRI-ERIC Member/Observer States can request the BBMRI-ERIC Self-Assessment Surveys online and submit them after completion, including a compliance statement signed by the biobank manager. BBMRI-ERIC then reviews the surveys and awards quality grades. If a biobank/sample collection meets the quality criteria according to CEN/TS, it will be flagged in the BBMRI-ERIC Directory, increasing their visibility. Using the Self-Assessment Survey, biobankers and researchers are encouraged to meet certain quality standards on the one hand, while getting valuable feedback on their quality management procedures on the other hand. The SAS tool has been developed by the quality services of BBMRI-ERIC in collaboration with 106 quality experts from all over Europe.

Interoperability & Data Models

MIABIS

MIABIS 2.0 represents the minimum information required to initiate collaborations between biobanks and to enable the exchange of biological samples and data. The aim is to facilitate the reuse of bio-resources and associated data by harmonising biobanking and biomedical research.

Defined APIs of IT services

BBMRI-ERIC publishes APIs of its services, such as the Directory and Connector, in order to enable interoperability.

Data provenance standardisation

BBMRI-ERIC drives an activity to standardise a common sample and data provenance information model within ISO TC276 (Biotechnology) WG5. Provenance information describes the history of objects and data and its interoperable and machine-readable implementation is a cornerstone of quality automation, i.e., the ability to at least partially automatically assess the fitness of data or samples for the given research purpose.

Mapping of selected services onto the BBMRI-ERIC access pipeline

What do biobanks and BBMRI-ERIC Nodes need in order to participate?

National Nodes

The critical role of the BBMRI-ERIC National Nodes is in acting as a link between the respective national biobanks and the BBMRI-ERIC central level. The necessary duties include:

• Implementing data collection procedures for the Directory (either by deploying a national directory and then pushing the data into the BBMRI-ERIC Directory or by maintaining the data directly in the Directory);
• Supporting biobanks in data mapping/harmonisation activities to connect to BBMRI-ERIC services (Directory, Locator, Negotiator, data harmonisation repository);
• Supporting biobanks in deploying their IT infrastructure if necessary.

Biobanks

• [Local] Compiling samples and associated data. Providing data for federated queries at sample level and to feed the Directory with aggregated data.
• [Toward BBMRI-ERIC] Supporting a two-step query procedure for researchers:
  • (i) Responding to queries for data and biomaterials with an estimated number of cases fulfilling the search criteria (Locator-Connector);
  • (ii) Negotiating with the requestor for further refinement of the sample/data request with the aim of providing the material and data for the defined research project.
• It is highly desirable that the researchers provide feedback to biobanks regarding the suitability of the samples and data for their research purpose and regarding the type of analysis performed with the samples. This helps to enrich the annotation of the samples and potentially avoids unnecessary reuse.