State-of-the-Art and Future Challenges in the Integration of Biobank Catalogues

Use case driven evaluation of open databases for pediatric cancer research

BACKGROUND

A plethora of Web resources are available offering information on clinical, pre-clinical, genomic and theoretical aspects of cancer, including not only the comprehensive cancer projects as ICGC and TCGA, but also less-known and more specialized projects on pediatric diseases such as PCGP. However, in case of data on childhood cancer there is very little information openly available. Several web-based resources and tools offer general biomedical data which are not purpose-built, for neither pediatric nor cancer analysis. Additionally, many Web resources on cancer focus on incidence data and statistical social characteristics as well as self-regulating communities.

METHODS

We summarize those resources which are open and are considered to support scientific fundamental research, while we address our comparison to 11 identified pediatric cancer-specific resources (5 tools, 6 databases). The evaluation consists of 5 use cases on the example of brain tumor research and covers user-defined search scenarios as well as data mining tasks, also examining interactive visual analysis features.

RESULTS

Web resources differ in terms of information quantity and presentation. Pedican lists an abundance of entries with few selection features. PeCan and PedcBioPortal include visual analysis tools while the latter integrates published and new consortia-based data. UCSC Xena Browser offers an in-depth analysis of genomic data. ICGC data portal provides various features for data analysis and an option to submit own data. Its focus lies on adult Pan-Cancer projects. Pediatric Pan-Cancer datasets are being integrated into PeCan and PedcBioPortal. Comparing information on prominent mutations within glioma discloses well-known, unknown, possible, as well as inapplicable biomarkers. This summary further emphasizes the varying data allocation. Tested tools show advantages and disadvantages, depending on the respective use case scenario, providing inhomogeneous data quantity and information specifics.

CONCLUSIONS

Web resources on specific pediatric cancers are less abundant and less-known compared to those offering adult cancer research data. Meanwhile, current efforts of ongoing pediatric data collection and Pan-Cancer projects indicate future opportunities for childhood cancer research, that is greatly needed for both fundamental as well as clinical research.

BioSCOOP - Biobank Sample Communication Protocol. New approach for the transfer of information between biobanks

Dynamic development of biobanking industry (both business and science) resulted in an increased number of IT systems for samples and data management. The most difficult and complicated case for the biobanking community was cooperation between institutions, equipped with different IT systems, in the field of scientific research, mainly data interchange and information flow. Tools available on the market relate mainly to the biobank or collection level. Efficient and universal protocols including the detailed information about the donor and the sample are still very limited. Here, we have developed BioSCOOP, a communication protocol in the form of a well documented JSON API. The main aim of this study was to harmonize and standardize the rules of communication between biobanks on the level of information about the donor together with information about the sample. The purpose was to create a communication protocol for two applications: to transfer the information between different biobanks and to allow the searching and presentation of the sample and data sets.

A systematic review on the use of best practices for publishing linked data

Purpose

Data providers have been increasingly publishing content as linked data (LD) on the Web. This process includes guidelines (i.e. good practices) to publish, share, and connect data on the Web. Several people in different areas, for instance, sciences, medicine, governments and so on, use these practices to publish data. The LD community has been proposing many practices to aid the publication of data on the Web. However, discovering these practices is a costly and time-consuming task, considering the practices that are produced by the literature. Moreover, the community still lacks a comprehensive understanding of how these practices are used for publishing LD. Thus, the purpose of this paper is to investigate and better understand how best practices support the publication of LD as well as identifying to what extent they have been applied to this field.

Design/methodology/approach

The authors conducted a systematic literature review to identify the primary studies that propose best practices to address the publication of LD, following a predefined review protocol. The authors then identified the motivations for recommending best practices for publishing LD and looked for evidence of the benefits of using such practices. The authors also examined the data formats and areas addressed by the studies as well as the institutions that have been publishing LD.

Findings

In summary, the main findings of this work are: there is empirical evidence of the benefits of using best practices for publishing LD, especially for defining standard practices, integrability and uniformity of LD; most of the studies used RDF as data format; there are many areas interested in dissemination data in a connected way; and there is a great variety of institutions that have published data on the Web.

Originality/value

The results presented in this systematic review can be very useful to the semantic web and LD community, since it gathers pieces of evidence from the primary studies included in the review, forming a body of knowledge regarding the use best practices for publishing LD pointing out interesting opportunities for future research.

Conception and Implementation of an Austrian Biobank Directory Integration Framework

INTRODUCTION

Sample collections and data are hosted within different biobanks at diverse institutions across Europe. Our data integration framework aims at incorporating data about sample collections from different biobanks into a common research infrastructure, facilitating researchers' abilities to obtain high-quality samples to conduct their research. The resulting information must be locally gathered and distributed to searchable higher level information biobank directories to maximize the visibility on the national and European levels. Therefore, biobanks and sample collections must be clearly described and unambiguously identified. We describe how to tackle the challenges of integrating biobank-related data between biobank directories using heterogeneous data schemas and different technical environments.

METHODS

To establish a data exchange infrastructure between all biobank directories involved, we propose the following steps: (A) identification of core entities, terminology, and semantic relationships, (B) harmonization of heterogeneous data schemas of different Biobanking and Biomolecular Resources Research Infrastructure (BBMRI) directories, and (C) formulation of technical core principles for biobank data exchange between directories.

RESULTS

(A) We identified the major core elements to describe biobanks in biobank directories. Since all directory data models were partially based on Minimum Information About BIobank Data Sharing (MIABIS) 2.0, the MIABIS 2.0 core model was used for compatibility. (B) Different projection scenarios were elaborated in collaboration with all BBMRI.at partners. A minimum set of mandatory and optional core entities and data items was defined for mapping across all directory levels. (C) Major core data exchange principles were formulated and data interfaces implemented by all biobank directories involved.

DISCUSSION

We agreed on a MIABIS 2.0-based core set of harmonized biobank attributes and established a list of data exchange core principles for integrating biobank directories on different levels. This generic approach and the data exchange core principles proposed herein can also be applied in related tasks like integration and harmonization of biobank data on the individual sample and patient levels.