Journal Article

DKFZ-2022-01984

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png On-The-Fly Query Translation Between i2b2 and Samply in the German Biobank Node (GBN) Prototypes.

Mate, S. ; Vormstein, P. D.DKFZ* ; Kadioglu, D. ; Majeed, R. W. ; Lablans, M.DKFZ* ; Prokosch, H.-U. ; Storf, H.DKFZ*

2017
IOS Press Amsterdam

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Abstract: Information retrieval is a major challenge in medical informatics. Various research projects have worked on this task in recent years on an institutional level by developing tools to integrate and retrieve information. However, when it comes down to querying such data across institutions, the challenge persists due to the high heterogeneity of data and differences in software systems. The German Biobank Node (GBN) project faced this challenge when trying to interconnect four biobanks to enable distributed queries for biospecimens. All biobanks had already established integrated data repositories, and some of them were already part of research networks. Instead of developing another software platform, GBN decided to form a bridge between these. This paper describes and discusses a core component from the GBN project, the OmniQuery library, which was implemented to enable on-the-fly query translation between heterogeneous research infrastructures.

Keyword(s): Biological Specimen Banks (MeSH) ; Information Storage and Retrieval (MeSH) ; Software (MeSH) ; Data harmonization ; biobanking ; federated search ; interoperability

Note: POF Topic: 317

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Contributing Institute(s):

1. DKTK Frankfurt (L501)
2. Medizinische Informatik in der Translationalen Onkologie (G230)

Research Program(s):

1. 317 - Translational cancer research (POF3-317) (POF3-317)

Appears in the scientific report 2017

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Database coverage:
; NCBI Molecular Biology Database ; SCOPUS

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