QL4MDR: a GraphQL query language for ISO 11179-based metadata repositories.

BACKGROUND: Heterogeneous healthcare instance data can hardly be integrated without harmonizing its schema-level metadata. Many medical research projects and organizations use metadata repositories to edit, store and reuse data elements. However, existing metadata repositories differ regarding software implementation and have shortcomings when it comes to exchanging metadata. This work aims to define a uniform interface with a technical interlingua between the different MDR implementations in order to enable and facilitate the exchange of metadata, to query over distributed systems and to promote cooperation. To design a unified interface for multiple existing MDRs, a standardized data model must be agreed on. The ISO 11179 is an international standard for the representation of metadata, and since most MDR systems claim to be at least partially compliant, it is suitable for defining an interface thereupon. Therefore, each repository must be able to define which parts can be served and the interface must be able to handle highly linked data. GraphQL is a data access layer and defines query techniques designed to navigate easily through complex data structures. RESULTS: We propose QL4MDR, an ISO 11179-3 compatible GraphQL query language. The GraphQL schema for QL4MDR is derived from the ISO 11179 standard and defines objects, fields, queries and mutation types. Entry points within the schema define the path through the graph to enable search functionalities, but also the exchange is promoted by mutation types, which allow creating, updating and deleting of metadata. QL4MDR is the foundation for the uniform interface, which is implemented in a modern web-based interface prototype. CONCLUSIONS: We have introduced a uniform query interface for metadata repositories combining the ISO 11179 standard for metadata repositories and the GraphQL query language. A reference implementation based on the existing Samply.MDR was implemented. The interface facilitates access to metadata, enables better interaction with metadata as well as a basis for connecting existing repositories. We invite other ISO 11179-based metadata repositories to take this approach into account.

[Requirements for a cross-location biobank IT infrastructure : Survey of stakeholder input on the establishment of a biobank network of the German Biobank Alliance (GBA)]. / Anforderungen an eine standortübergreifende Biobanken-IT-Infrastruktur : Erhebung des Stakeholderinputs zum Aufbau eines Biobankennetzwerks der German Biobank Alliance (GBA).

BACKGROUND: The large number of biobanks within Germany results in a high degree of heterogeneity with regard to the IT components used at the respective locations. Within the German Biobank Alliance (GBA), 13 biobanks implement harmonized processes for the provision of biomaterial and accompanying data. OBJECTIVES: The networking of the individual biobanks and the associated harmonisation of the IT infrastructure should facilitate access to biomaterial and related clinical data. METHODS: For this purpose, the relevant target groups were first identified in order to determine their requirements for IT solutions to be developed in a workshop. RESULTS: Of the seven identified interest groups, three were initially invited to a first round of discussions. The stakeholder input expressed resulted in a catalogue of requirements with regard to IT support for (i) a sample and data request, (ii) the handling of patient consent and inclusion, and (iii) the subsequent evaluation of the sample and data request. CONCLUSIONS: The next step is to design the IT solutions as prototypes based on these requirements. In parallel, further user groups are being surveyed in order to be able to further concretise the specifications for development.

[The regional network ADAPTHERA : Rheumatology care through coordinated cooperation: comprehensive, trans-sectoral, covering all health insurance. Initial results]. / Das landesweite Netzwerk ADAPTHERA : Erste Ergebnisse einer flächendeckenden, krankenkassenübergreifenden und transsektoralen rheumatologischen Versorgung.

The aim of the rheumatology network ADAPTHERA ("risk-adapted rheumatology therapy") is to achieve a comprehensive improvement in rheumatology care by coordinating treatment in a regional, trans-sectoral network. Accompanying biomedical research projects, training concepts, and the construction of a rheumatology register (gathering data and biomaterials) should furthermore ensure the stable and sustainable optimisation of care. In the pilot phase (2012-2015) the focus of the ADAPTHERA network, required as a "regional key project" within the framework of the Initiative on Health Economy of Rheinland-Palatinate (RL-P), Germany, was placed on the optimisation of the early diagnosis of rheumatoid arthritis, where it is well-known that there is a significant care deficit.Through the intensive, stable, and coordinated cooperation of all health care partners in the field of rheumatology (registered general practitioners and orthopaedic specialists, registered core rheumatologists as well as the Association of Rheumatology of RL-P) a unique regional, comprehensive offer with verifiable care optimisation has been established in RL-P. The network is supported by outstanding collaboration with the Association of Statutory Health Insurance Physicians and the self-help organisation Rheumatology League.The aims that were established at the start of the project will be achieved by the end of the pilot phase:- significant improvement in the early diagnosis of rheumatoid arthritis (an average of 23.7 days until diagnosis by rheumatologists)- access covering all health insurance (regardless of the particular scheme the patients belong to)- comprehensive (verifiable participation of general practitioners from all over RL-P)- data and biomaterials collection, established as a basis for biomarker research, and a rheumatology register for RL-P.

A Generic Method and Implementation to Evaluate and Improve Data Quality in Distributed Research Networks.

BACKGROUND: With the increasing personalization of clinical therapies, translational research is evermore dependent on multisite research cooperations to obtain sufficient data and biomaterial. Distributed research networks rely on the availability of high-quality data stored in local databases operated by their member institutions. However, reusing data documented by independent health providers for the purpose of care, rather than research ("secondary use"), reveal a high variability in terms of data formats, as well as poor data quality, across network sites. OBJECTIVES: The aim of this work is the provision of a process for the assessment of data quality with regard to completeness and syntactic accuracy across independently operated data warehouses using common definitions stored in a central (network-wide) metadata repository (MDR). METHODS: For assessment of data quality across multiple sites, we employ a framework of so-called bridgeheads. These are federated data warehouses, which allow the sites to participate in a research network. A central MDR is used to store the definitions of the commonly agreed data elements and their permissible values. RESULTS: We present the design for a generator of quality reports within a bridgehead, allowing the validation of data in the local data warehouse against a research network's central MDR. A standardized quality report can be produced at each network site, providing a means to compare data quality across sites, as well as to channel feedback to the local data source systems, and local documentation personnel. A reference implementation for this concept has been successfully utilized at 10 sites across the German Cancer Consortium. CONCLUSIONS: We have shown that comparable data quality assessment across different partners of a distributed research network is feasible when a central metadata repository is combined with locally installed assessment processes. To achieve this, we designed a quality report and the process for generating such a report. The final step was the implementation in a German research network.

One Step Away from Technology but One Step Towards Domain Experts-MDRBridge: A Template-Based ISO 11179-Compliant Metadata Processing Pipeline.

BACKGROUND: Secondary use of routine medical data relies on a shared understanding of given information. This understanding is achieved through metadata and their interconnections, which can be stored in metadata repositories (MDRs). The necessity of an MDR is well understood, but the local work on metadata is a time-consuming and challenging process for domain experts. OBJECTIVE: To support the identification, collection, and provision of metadata in a predefined structured manner to foster consolidation. A particular focus is placed on user acceptance. METHODS: We propose a software pipeline MDRBridge as a practical intermediary for metadata capture and processing, based on MDRSheet, an ISO 11179-3 compliant template using popular spreadsheet software. It serves as a practical mediator for metadata acquisition and processing in a broader pipeline. Due to the different origins of the metadata, both manual entry and automatic extractions from application systems are supported. To enable the export of collected metadata into external MDRs, a mapping of ISO 11179 to Clinical Data Interchange Standards Consortium (CDISC) Operational Data Model (ODM) was developed. RESULTS: MDRSheet is embedded in the processing pipeline MDRBridge and delivers metadata in the CDISC ODM format for further use in MDRs. This approach is used to interactively unify core datasets, import existing standard datasets, and automatically extract all defined data elements from source systems. The involvement of clinical domain experts improved significantly due to minimal changes within their usual work routine. CONCLUSION: A high degree of acceptance was achieved by adapting the working methods of clinical domain experts. The designed process is capable of transforming all relevant data elements according to the ISO 11179-3 format. MDRSheet is used as an intermediate format to present the information at a glance and to allow editing or supplementing by domain experts.

Exploiting Distributed, Heterogeneous and Sensitive Data Stocks while Maintaining the Owner's Data Sovereignty.

BACKGROUND: To achieve statistical significance in medical research, biological or data samples from several bio- or databanks often need to be complemented by those of other institutions. For that purpose, IT-based search services have been established to locate datasets matching a given set of criteria in databases distributed across several institutions. However, previous approaches require data owners to disclose information about their samples, raising a barrier for their participation in the network. OBJECTIVE: To devise a method to search distributed databases for datasets matching a given set of criteria while fully maintaining their owner's data sovereignty. METHODS: As a modification to traditional federated search services, we propose the decentral search, which allows the data owner a high degree of control. Relevant data are loaded into local bridgeheads, each under their owner's sovereignty. Researchers can formulate criteria sets along with a project proposal using a central search broker, which then notifies the bridgeheads. The criteria are, however, treated as an inquiry rather than a query: Instead of responding with results, bridgeheads notify their owner and wait for his/her decision regarding whether and what to answer based on the criteria set, the matching datasets and the specific project proposal. Without the owner's explicit consent, no data leaves his/her institution. RESULTS: The decentral search has been deployed in one of the six German Centers for Health Research, comprised of eleven university hospitals. In the process, compliance with German data protection regulations has been confirmed. The decentral search also marks the centerpiece of an open source registry software toolbox aiming to build a national registry of rare diseases in Germany. CONCLUSIONS: While the sacrifice of real-time answers impairs some use-cases, it leads to several beneficial side effects: improved data protection due to data parsimony, tolerance for incomplete data schema mappings and flexibility with regard to patient consent. Most importantly, as no datasets ever leave their institution, owners can reject projects without facing potential peer pressure. By its lower barrier for participation, a decentral search service is likely to attract a larger number of partners and to bring a researcher into contact with the right potential partners.