The Libre Biobank Management System: Toward an Extensible, Free and Open Source Web-Based Biobank Management System

Keiron Teilo O'Shea, Robert Alexander Bolton, Luis Mur, Chuan Lu, Priyadharshini Sai-Giridhar

Research output: Contribution to conferenceAbstractpeer-review

Abstract

Statement of the problem: Through the provision of large, well-annotated repositories of biospecimens, biobanks are now among the main facilitators of data-driven medicine. The core function of these biobanks is producing a huge amount of big data, leading many facilities to employ the use of Biobank Management Systems (BIMS). Whilst there exists a plethora of proprietary or open source BIMS solutions, it remains a great challenge to manage the metadata associated to common biobanking elements such as samples, donors, sample collection and processing.

Moreover, commercial BIMS vendors often require users to “license” their software, putting facilities into positions where data is often held by the service provider with arbitrary barriers placed to make it difficult to retrieve and reuse biobank data once the license has expired - often locking their licensees in unfairly or asking for additional “support” fees to allow access to said features.

Proposed solution: The Libre Biobank Management System
(LimBuS) is a feature-rich, open source, highly extensible,
standards compliant, platform-independent biobank management system that enhances the collation, dissemination,
and querying of a digital database of biospecimens through
a highly accessible web-based interface. Through our highly
accessible user interface, we are able to advocate the use of
standard control vocabularies and ontologies for capturing
essential metadata - which may provide a fully contextualised
source of information that can be exploited for scientific
research and candidate selection for clinical trials. To support and supplement new or existing tooling, we have broken out most of the functionality present within the webbased interface out to a number of Application Programming Interface (API) endpoints. These end points allow programmatic access to the database, and allows authenticated users to delete, modify, query and view information stored within the BIMS.

Conclusions: We envisage that our highly extensible platform twinned with a determined focus on community participation and feedback will be fruitful in both extending our system with new features and identifying and fixing bugs ensuring that each release will better reflect the requirements of the biobanking community at large.

LimBuS is licensed under the terms of the GPLv3 or later, and
is freely available to download at https://www.github.com/
AberystwythSystemsBiology/limbus.
Original languageEnglish
Publication statusPublished - 2020
EventInternational Society for Biological and Environmental Repositories Symposium 2020 -
Duration: 22 Oct 202023 Oct 2020
https://www.isber.org/page/events

Conference

ConferenceInternational Society for Biological and Environmental Repositories Symposium 2020
Abbreviated titleISBER 2020
Period22 Oct 202023 Oct 2020
Internet address

Keywords

  • Biobankling,
  • information management systems,
  • BIMS,
  • open source software

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