The CAISIS Research Data System

Fearn, Paul; Sculli, Frank

doi:10.1007/978-1-4419-5714-6_11

Cited by 4 publications

(6 citation statements)

References 9 publications

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“…The Caisis web interface screen for each donor record is divided into two vertical parts (Fearn et al 2007;Fearn and Sculli 2010). On the left appears a running list of all case record items in the database, sorted in chronological order.…”

Section: Methodsmentioning

confidence: 99%

Development of a data entry auditing protocol and quality assurance for a tissue bank database

2011

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Human transcription error is an acknowledged risk when extracting information from paper records for entry into a database. For a tissue bank, it is critical that accurate data are provided to researchers with approved access to tissue bank material. The challenges of tissue bank data collection include manual extraction of data from complex medical reports that are accessed from a number of sources and that differ in style and layout. As a quality assurance measure, the Breast Cancer Tissue Bank (http:\\www.abctb.org.au) has implemented an auditing protocol and in order to efficiently execute the process, has developed an open source database plug-in tool (eAuditor) to assist in auditing of data held in our tissue bank database. Using eAuditor, we have identified that human entry errors range from 0.01% when entering donor's clinical follow-up details, to 0.53% when entering pathological details, highlighting the importance of an audit protocol tool such as eAuditor in a tissue bank database. eAuditor was developed and tested on the Caisis open source clinical-research database; however, it can be integrated in other databases where similar functionality is required.

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Section: Methodsmentioning

confidence: 99%

Development of a data entry auditing protocol and quality assurance for a tissue bank database

2011

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“…All outgoing specimens and patients are flagged by the eBAS Project Key in Caisis, 6,7 and donors and specimens involved in any particular study can be identified using tools built into the customized version of the open-source clinical research database, Caisis, 6 in which all ABCTB clinical and biospecimen information is stored.…”

Section: Project Tracking In Caisismentioning

confidence: 99%

Electronic Biorepository Application System: Web-Based Software to Manage Receipt, Peer Review, and Approval of Researcher Applications to a Biobank

Khushi

Carpenter

Balleine

2012

Biopreservation and Biobanking

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The importance of suitably characterized and preserved biospecimens for research is acknowledged, yet providing information about the availability of biospecimens and associated data, responding to enquiries from researchers, processing applications for material, and seeking independent scientific review of proposed projects are complex and time-consuming processes. Most biorepositories operate as not-for-profit entities; therefore, cost containment is a major consideration. We identified that online systematizing and automation of all of the tasks associated with application management could reduce the administrative workload and therefore reduce costs and improve the efficiency of a biobank. Accordingly, we have developed a Web-based electronic Biorepository Application System (eBAS) that allows researchers to search for suitable material from the biobank database, submit an online expression of interest, and complete all the information required for a full application. Peer review is also managed through eBAS. Implementation of eBAS has streamlined application management and external peer review of researcher applications, and has facilitated automated record storage and management. This approach has potential to reduce the costs and complexities of administering researcher applications. We have also linked eBAS to an open-source clinical research and specimen management database, Caisis.

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“…CAISIS[12] allows the definition of a few of these properties (default values, defined vocabularies and collection requirements) for simple lab and clinical results; however, it provides no support for complex experimental data.…”

Section: Introductionmentioning

confidence: 99%

“…BSI[ 39 ] provides sample requisition support but does not provide for integration of sample and experimental data. CAISIS[ 12 , 13 ] is exceptional in providing both specimen requests and deep support for data integration; however, it only supports simple test results entered through online forms, not complex experimental data types.…”

Section: Introductionmentioning

confidence: 99%

“…Furthermore, no other open source platform known to us provides graphical facilities for defining a broad range of customizable, scientifically-relevant properties for any column of data (such as missing value indicators, regular expression validators, default values and lookup relationships). CAISIS[ 12 ] allows the definition of a few of these properties (default values, defined vocabularies and collection requirements) for simple lab and clinical results; however, it provides no support for complex experimental data.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

LabKey Server: An open source platform for scientific data integration, analysis and collaboration

Nelson¹,

Piehler²,

Eckels³

et al. 2011

BMC Bioinformatics

122

125

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BackgroundBroad-based collaborations are becoming increasingly common among disease researchers. For example, the Global HIV Enterprise has united cross-disciplinary consortia to speed progress towards HIV vaccines through coordinated research across the boundaries of institutions, continents and specialties. New, end-to-end software tools for data and specimen management are necessary to achieve the ambitious goals of such alliances. These tools must enable researchers to organize and integrate heterogeneous data early in the discovery process, standardize processes, gain new insights into pooled data and collaborate securely.ResultsTo meet these needs, we enhanced the LabKey Server platform, formerly known as CPAS. This freely available, open source software is maintained by professional engineers who use commercially proven practices for software development and maintenance. Recent enhancements support: (i) Submitting specimens requests across collaborating organizations (ii) Graphically defining new experimental data types, metadata and wizards for data collection (iii) Transitioning experimental results from a multiplicity of spreadsheets to custom tables in a shared database (iv) Securely organizing, integrating, analyzing, visualizing and sharing diverse data types, from clinical records to specimens to complex assays (v) Interacting dynamically with external data sources (vi) Tracking study participants and cohorts over time (vii) Developing custom interfaces using client libraries (viii) Authoring custom visualizations in a built-in R scripting environment.Diverse research organizations have adopted and adapted LabKey Server, including consortia within the Global HIV Enterprise. Atlas is an installation of LabKey Server that has been tailored to serve these consortia. It is in production use and demonstrates the core capabilities of LabKey Server. Atlas now has over 2,800 active user accounts originating from approximately 36 countries and 350 organizations. It tracks roughly 27,000 assay runs, 860,000 specimen vials and 1,300,000 vial transfers.ConclusionsSharing data, analysis tools and infrastructure can speed the efforts of large research consortia by enhancing efficiency and enabling new insights. The Atlas installation of LabKey Server demonstrates the utility of the LabKey platform for collaborative research. Stable, supported builds of LabKey Server are freely available for download at http://www.labkey.org. Documentation and source code are available under the Apache License 2.0.

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The CAISIS Research Data System

Cited by 4 publications

References 9 publications

Development of a data entry auditing protocol and quality assurance for a tissue bank database

Development of a data entry auditing protocol and quality assurance for a tissue bank database

Electronic Biorepository Application System: Web-Based Software to Manage Receipt, Peer Review, and Approval of Researcher Applications to a Biobank

LabKey Server: An open source platform for scientific data integration, analysis and collaboration

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