Toward Global Biobank Integration by Implementation of the Minimum Information About BIobank Data Sharing (MIABIS 2.0 Core).

Biobanks are the biological back end of data-driven medicine, but lack standards and generic solutions for interoperability and information harmonization. The move toward a global information infrastructure for biobanking demands semantic interoperability through harmonized services and common ontologies. To tackle this issue, the Minimum Information About BIobank data Sharing (MIABIS) was developed in 2012 by the Biobanking and BioMolecular Resources Research Infrastructure of Sweden (BBMRI.se). The wide acceptance of the first version of MIABIS encouraged evolving it to a more structured and descriptive standard. In 2013 a working group was formed under the largest infrastructure for health in Europe, Biobanking and BioMolecular Resources Research Infrastructure (BBMRI-ERIC), with the remit to continue the development of MIABIS (version 2.0) through a multicountry governance process. MIABIS 2.0 Core has been developed with 22 attributes describing Biobanks, Sample Collections, and Studies according to a modular structure that makes it easier to adhere to and to extend the standard. This integration standard will make a great contribution to the discovery and exploitation of biobank resources and lead to a wider and more efficient use of valuable bioresources, thereby speeding up the research on human diseases. Many within the European Union have accepted MIABIS 2.0 Core as the "de facto" biobank information standard.

The process of moving from a regionally based cervical cytology biobank to a national infrastructure.

This article addresses the important issue of the standardization of the biobank process. It reports on i) the implementation of standard operating procedures for the processing of liquid-based cervical cells, ii) the standardization of storage conditions, and iii) the ultimate establishment of nationwide standardized biorepositories for cervical specimens. Given the differences in the infrastructure and healthcare systems of various county councils in Sweden, these efforts were designed to develop standardized methods of biobanking across the nation. The standardization of cervical sample processing and biobanking is an important and widely acknowledged issue. Efforts to address these concerns will facilitate better patient care and improve research based on retrospective and prospective collections of patient samples and cohorts. The successful nationalization of the Cervical Cytology Biobank in Sweden is based on three vital issues: i) the flexibility of the system to adapt to other regional systems, ii) the development of the system based on national collaboration between the university and the county councils, and iii) stable governmental financing by the provider, the Biobanking and Molecular Resource Infrastructure of Sweden (BBMRI.se). We will share our experiences with biorepository communities to promote understanding of and advances in opportunities to establish a nationalized biobank which covers the healthcare of the entire nation.

Developing a semantically rich ontology for the biobank-administration domain.

BACKGROUND: Biobanks are a critical resource for translational science. Recently, semantic web technologies such as ontologies have been found useful in retrieving research data from biobanks. However, recent research has also shown that there is a lack of data about the administrative aspects of biobanks. These data would be helpful to answer research-relevant questions such as what is the scope of specimens collected in a biobank, what is the curation status of the specimens, and what is the contact information for curators of biobanks. Our use cases include giving researchers the ability to retrieve key administrative data (e.g. contact information, contact's affiliation, etc.) about the biobanks where specific specimens of interest are stored. Thus, our goal is to provide an ontology that represents the administrative entities in biobanking and their relations. We base our ontology development on a set of 53 data attributes called MIABIS, which were in part the result of semantic integration efforts of the European Biobanking and Biomolecular Resources Research Infrastructure (BBMRI). The previous work on MIABIS provided the domain analysis for our ontology. We report on a test of our ontology against competency questions that we derived from the initial BBMRI use cases. Future work includes additional ontology development to answer additional competency questions from these use cases. RESULTS: We created an open-source ontology of biobank administration called Ontologized MIABIS (OMIABIS) coded in OWL 2.0 and developed according to the principles of the OBO Foundry. It re-uses pre-existing ontologies when possible in cooperation with developers of other ontologies in related domains, such as the Ontology of Biomedical Investigation. OMIABIS provides a formalized representation of biobanks and their administration. Using the ontology and a set of Description Logic queries derived from the competency questions that we identified, we were able to retrieve test data with perfect accuracy. In addition, we began development of a mapping from the ontology to pre-existing biobank data structures commonly used in the U.S. CONCLUSIONS: In conclusion, we created OMIABIS, an ontology of biobank administration. We found that basing its development on pre-existing resources to meet the BBMRI use cases resulted in a biobanking ontology that is re-useable in environments other than BBMRI. Our ontology retrieved all true positives and no false positives when queried according to the competency questions we derived from the BBMRI use cases. Mapping OMIABIS to a data structure used for biospecimen collections in a medical center in Little Rock, AR showed adequate coverage of our ontology.

A Minimum Data Set for Sharing Biobank Samples, Information, and Data: MIABIS.

Numerous successful scientific results have emerged from projects using shared biobanked samples and data. In order to facilitate the discovery of underutilized biobank samples, it would be helpful if a global biobank register containing descriptive information about the samples existed. But first, for shared data to be comparable, it needs to be harmonized. In compliance with the aim of BBMRI (Biobanking and Biomolecular Resources Research Infrastructure), to harmonize biobanking across Europe, and the conclusion that the move towards a universal information infrastructure for biobanking is directly connected to the issues of semantic interoperability through standardized message formats and controlled terminologies, we have developed an updated version of the minimum data set for biobanks and studies using human biospecimens. The data set called MIABIS (Minimum Information About BIobank data Sharing) consists of 52 attributes describing a biobank's content. The aim is to facilitate data discovery through harmonization of data elements describing a biobank at the aggregate level. As many biobanks across Europe possess a tremendous amount of samples that are underutilized, this would help pave the way for biobank networking on a national and international level, resulting in time and cost savings and faster emergence of new scientific results.