Dataset Information

E!DAL--a framework to store, share and publish research data.

ABSTRACT: BACKGROUND: The life-science community faces a major challenge in handling "big data", highlighting the need for high quality infrastructures capable of sharing and publishing research data. Data preservation, analysis, and publication are the three pillars in the "big data life cycle". The infrastructures currently available for managing and publishing data are often designed to meet domain-specific or project-specific requirements, resulting in the repeated development of proprietary solutions and lower quality data publication and preservation overall. RESULTS: e!DAL is a lightweight software framework for publishing and sharing research data. Its main features are version tracking, metadata management, information retrieval, registration of persistent identifiers (DOI), an embedded HTTP(S) server for public data access, access as a network file system, and a scalable storage backend. e!DAL is available as an API for local non-shared storage and as a remote API featuring distributed applications. It can be deployed "out-of-the-box" as an on-site repository. CONCLUSIONS: e!DAL was developed based on experiences coming from decades of research data management at the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK). Initially developed as a data publication and documentation infrastructure for the IPK's role as a data center in the DataCite consortium, e!DAL has grown towards being a general data archiving and publication infrastructure. The e!DAL software has been deployed into the Maven Central Repository. Documentation and Software are also available at: http://edal.ipk-gatersleben.de.

SUBMITTER: Arend D

PROVIDER: S-EPMC4080583 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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e!DAL--a framework to store, share and publish research data.

Arend Daniel D Lange Matthias M Chen Jinbo J Colmsee Christian C Flemming Steffen S Hecht Denny D Scholz Uwe U

BMC bioinformatics 20140624

<h4>Background</h4>The life-science community faces a major challenge in handling "big data", highlighting the need for high quality infrastructures capable of sharing and publishing research data. Data preservation, analysis, and publication are the three pillars in the "big data life cycle". The infrastructures currently available for managing and publishing data are often designed to meet domain-specific or project-specific requirements, resulting in the repeated development of proprietary so ...[more]

PMID: 24958009

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Project description:ImportancePatients increasingly demand transparency in and control of how their medical records and biospecimens are shared for research. How much they are willing to share and what factors influence their sharing preferences remain understudied in real settings.ObjectivesTo examine whether and how various presentations of consent forms are associated with differences in electronic health record and biospecimen sharing rates and whether these rates vary according to user interface design, data recipients, data and biospecimen items, and patient characteristics.Design, setting, and participantsFor this survey study, a data and biospecimen sharing preference survey was conducted at 2 academic hospitals from May 1, 2017, to September 31, 2018, after simple randomization of patients to 1 of 4 options with different layout and formats of indicating sharing preferences: opt-in simple, opt-in detailed, opt-out simple, and opt-out detailed.InterventionsAll participants were presented with a list of data and biospecimen items that could be shared for research within the same health care organization or with other nonprofit or for-profit institutions. Participating patients were randomly asked to select the items that they would share (opt-in) or were asked to select items they would not share (opt-out). Patients in these 2 groups were further randomized to select only among 18 categories vs 59 detailed items (simple vs detailed form layout).Main outcomes and measuresThe primary end points were the percentages of patients willing to share data and biospecimen categories or items.ResultsAmong 1800 eligible participants, 1246 (69.2%) who completed their data sharing survey were included in the analysis, and 850 of these patients (mean [SD] age, 51.1 [16.7] years; 507 [59.6%] female; 677 [79.6%] white) responded to the satisfaction survey. A total of 46 participants (3.7%) declined sharing with the home institution, 352 (28.3%) with nonprofit institutions, and 590 (47.4%) with for-profit institutions. A total of 836 (67.1%) indicated that they would share all items with researchers from the home institution. When comparing opt-out with opt-in interfaces, all 59 sharing choice variables (100%) were associated with the sharing decision. When comparing simple with detailed forms, only 14 variables (23.7%) were associated with the sharing decision.Conclusions and relevanceThe findings suggest that most patients are willing to share their data and biospecimens for research. Allowing patients to decide with whom they want to share certain types of data may affect research that involves secondary use of electronic health records and/or biosamples for research.

Project description:BackgroundNatural History science is characterised by a single immense goal (to document, describe and synthesise all facets pertaining to the diversity of life) that can only be addressed through a seemingly infinite series of smaller studies. The discipline's failure to meaningfully connect these small studies with natural history's goal has made it hard to demonstrate the value of natural history to a wider scientific community. Digital technologies provide the means to bridge this gap.ResultsWe describe the system architecture and template design of "Scratchpads", a data-publishing framework for groups of people to create their own social networks supporting natural history science. Scratchpads cater to the particular needs of individual research communities through a common database and system architecture. This is flexible and scalable enough to support multiple networks, each with its own choice of features, visual design, and constituent data. Our data model supports web services on standardised data elements that might be used by related initiatives such as GBIF and the Encyclopedia of Life. A Scratchpad allows users to organise data around user-defined or imported ontologies, including biological classifications. Automated semantic annotation and indexing is applied to all content, allowing users to navigate intuitively and curate diverse biological data, including content drawn from third party resources. A system of archiving citable pages allows stable referencing with unique identifiers and provides credit to contributors through normal citation processes.ConclusionOur framework http://scratchpads.eu/ currently serves more than 1,100 registered users across 100 sites, spanning academic, amateur and citizen-science audiences. These users have generated more than 130,000 nodes of content in the first two years of use. The template of our architecture may serve as a model to other research communities developing data publishing frameworks outside biodiversity research.

Dataset Information

E!DAL--a framework to store, share and publish research data.

Publications

e!DAL--a framework to store, share and publish research data.

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