gms | German Medical Science

GMDS 2014: 59. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie e. V. (GMDS)

Deutsche Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie

07. - 10.09.2014, Göttingen

A lightweight solution for biomaterial metadata documentation

Meeting Abstract

Suche in Medline nach

  • M. Kaspar - Comprehensive Heart Failure Center Würzburg, Würzburg
  • M. Neumann - Interdisciplinary Bank of Biomaterials and Data Würzburg, Würzburg
  • A. Nätscher - Comprehensive Heart Failure Center Würzburg, Würzburg; Interdisciplinary Bank of Biomaterials and Data Würzburg, Würzburg
  • S. Störk - Comprehensive Heart Failure Center Würzburg, Würzburg; University Hospital Würzburg, Department of Internal Medicine I, Würzburg

GMDS 2014. 59. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie e.V. (GMDS). Göttingen, 07.-10.09.2014. Düsseldorf: German Medical Science GMS Publishing House; 2014. DocAbstr. 250

doi: 10.3205/14gmds086, urn:nbn:de:0183-14gmds0865

Veröffentlicht: 4. September 2014

© 2014 Kaspar et al.
Dieser Artikel ist ein Open Access-Artikel und steht unter den Creative Commons Lizenzbedingungen (http://creativecommons.org/licenses/by-nc-nd/3.0/deed.de). Er darf vervielfältigt, verbreitet und öffentlich zugänglich gemacht werden, vorausgesetzt dass Autor und Quelle genannt werden.


Gliederung

Text

Background: The collection of biomaterials and associated clinical data within the scope of clinical trials is not new, but requires more advanced technology with increasing clinical trial populations in order to provide high quality biomaterial and data for medical research.

Our clinical trial center runs a multitude of clinical trials (e.g. the Extended INH study [1]), each acquiring a variety of biomaterials taken at different points in time, ranging from a single time during the first patient visit up to multiple times after years of the first visit. Since the center's first clinical trial initiation, the number of -80°C biomaterial freezers necessary to store all of our biomaterials grew from one to nine. During this time, the material's metadata was documented in two different databases, including a documentation of material type, aliquots, and clinical trial and patient references. However, this documentation was only done once at the time of material taking.

Our current task was to provide an up-to-date inventory of each material's location, to document any further material withdrawals and storage and to be compatible with the Interdisciplinary Bank of Biomaterials and Data Würzburg (ibdw) [2], which is currently under development.

Methods: In order to solve this task, we developed a Microsoft Visual C++ application according to the ibdw’s software development concepts. This application was continuously adapted to current needs during its usage within the last 12 month. Each release was verified via black box testing before its practical application. Additionally to the application, we also implemented a biomaterial submission paper form in collaboration with the ibdw to allow a specific documentation according to SPREC criteria [3]. This system was then used to improve the biomaterial documentation of all of our clinical trials.

System design: The resulting system architecture consists of three basic parts: the identifier database, the transaction documentation, and the inventory overview.

The identifier database is the basis of the whole system. It contains identifier/value lists of all concepts, required for our documentation. The most important of these concept lists are the clinical trial, clinical trial visit, material type, vial type, cryobox type, task type, task reason, and the locations, hierarchically subdivided by freezer, shelf, and slider.

The transaction documentation is a graphical user interface (GUI) used to document every modification done to the biomaterials as separate transactions. It consists of several dialogs that show, as required, the lists defined in the identifier database, text fields to scan barcodes, and few text fields for unstructured text. Additionally, it includes modules to load the lists from the database and to write the data given by the GUI as separate XML files per transaction.

The inventory overview is a command line tool that parses the transaction XML files and accumulates its data in a relational database. This tool contains a module to parse single XML files or complete directories (including sub-directories) of XML files and a module to write its data into the database, which is linked to the identifier database.

Results: The system usage starts by asking for the operator's identification, the specific task to be performed (currently supported are: register or aliquot vials, register or move cryoboxes and sliders, export vials into a new cryobox, withdraw a cryobox) and a task reason (e.g. export material to be analyzed for a specific clinical trial analysis, freezer re-organization). The application then shows a task-specific dialog to scan cryobox and vial barcodes or to select entries in list fields as described above. In order to integrate our previous databases, their data was exported and converted into the new XML file format so that it could simply be handled like all other XML transaction files.

The creation of the inventory is done by starting the command line tool with parameters of the database location and the XML file directory. This process can be started on an empty database, but also iteratively with XML files that are new since its last execution.

Today we are using the application and the biomaterial submission paper form in our standard biomaterial processing workflow and document the location of any earlier integrated cryobox. Since the location of the vials within these boxes was previously documented inconsistently and was not reliable anymore, we also re-scanned the vial's position of a large part of our cryoboxes. This inventory was then used for any specific query that was necessary to provide metrics for active clinical trials and to collect specific vials for a clinical trial specific analysis.

Discussion: The new application allows us to provide a homogeneous documentation and presentation of the most important data of our clinical trial biomaterials. The re-scanning of vials of a large amount of our cryboxes required an extensive time investment of our technical staff, but in return yields a consistent documentation of new biomaterial analyses and a much faster vial extraction from the freezer. The application helps us to document the collection, processing, and storage of biomaterial within clinical trials in a consistent way providing higher quality data than before. It also bridges the time gap until the ibdw will be fully functioning and all biomaterials will be collected, processed, and stored utilizing the ibdw biobanking services.


References

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Angermann CE, Störk S, Gelbrich G, et al. Mode of action and effects of standardized collaborative disease management on mortality and morbidity in patients with systolic heart failure: the Interdisciplinary Network for Heart Failure (INH) study. Circulation. 2012;5(1):25-35.
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Jahns R, Neumann M, Geiger J, Kößler J, Störk S, Walter U. Banks of biomaterials: Potential and challenges for laboratory medicine. (Biomaterialbanken, Potential und Herausforderung für die klinischeLaboratoriumsmedizin). Bayer Ärzteblatt. 2011;6:54-9.
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Betsou F, Lehmann S, Ashton G, Barnes M, Benson EE, Coppola D, DeSouza Y, Eliason J, Glazer B, Guadagni F, Harding K, Horsfall DJ, Kleeberger C, Nanni U, Prasad A, Shea K, Skubitz A, Somiari S, Gunter E; International Society for Biological and Environmental Repositories (ISBER) Working Group on Biospecimen Science. Standard preanalytical coding for biospecimens: defining the sample PREanalytical code, Cancer Epidemiol Biomarkers Prev. 2010 Apr;19(4):1004-11.