Dataset Information

Menoci: lightweight extensible web portal enhancing data management for biomedical research projects

ABSTRACT:

Background

Biomedical research projects deal with data management requirements from multiple sources like funding agencies’ guidelines, publisher policies, discipline best practices, and their own users’ needs. We describe functional and quality requirements based on many years of experience implementing data management for the CRC 1002 and CRC 1190. A fully equipped data management software should improve documentation of experiments and materials, enable data storage and sharing according to the FAIR Guiding Principles while maximizing usability, information security, as well as software sustainability and reusability.

Results

We introduce the modular web portal software menoci for data collection, experiment documentation, data publication, sharing, and preservation in biomedical research projects. Menoci modules are based on the Drupal content management system which enables lightweight deployment and setup, and creates the possibility to combine research data management with a customisable project home page or collaboration platform.

Conclusions

Management of research data and digital research artefacts is transforming from individual researcher or groups best practices towards project- or organisation-wide service infrastructures. To enable and support this structural transformation process, a vital ecosystem of open source software tools is needed. Menoci is a contribution to this ecosystem of research data management tools that is specifically designed to support biomedical research projects.

SUBMITTER: Suhr M

PROVIDER: S-EPMC7745495 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

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Project description:The National Cancer Institute (NCI) Cancer Biomedical Informatics Grid® (caBIG®) program established standards and best practices for biorepository data management by creating an infrastructure to propagate biospecimen resource sharing while maintaining data integrity and security. caTissue Suite, a biospecimen data management software tool, has evolved from this effort. More recently, the caTissue Suite continues to evolve as an open source initiative known as OpenSpecimen. The essential functionality of OpenSpecimen includes the capture and representation of highly granular, hierarchically-structured data for biospecimen processing, quality assurance, tracking, and annotation. Ideal for multi-user and multi-site biorepository environments, OpenSpecimen permits role-based access to specific sets of data operations through a user-interface designed to accommodate varying workflows and unique user needs. The software is interoperable, both syntactically and semantically, with an array of other bioinformatics tools given its integration of standard vocabularies thus enabling research involving biospecimens. End-users are encouraged to share their day-to-day experiences in working with the application, thus providing to the community board insight into the needs and limitations which need be addressed. Users are also requested to review and validate new features through group testing environments and mock screens. Through this user interaction, application flexibility and interoperability have been recognized as necessary developmental focuses essential for accommodating diverse adoption scenarios and biobanking workflows to catalyze advances in biomedical research and operations. Given the diversity of biobanking practices and workforce roles, efforts have been made consistently to maintain robust data granularity while aiding user accessibility, data discoverability, and security within and across applications by providing a lower learning curve in using OpenSpecimen. Iterative development and testing cycles provide continuous maintenance and up-to-date capabilities for this freely available, open-access, web-based software application that is globally-adopted at over 25 institutions.