Lessons Learned from Caisis: An Open Source, Web-Based System for Integrating Clinical Practice and Research

Fearn, Paul; Regan, Kevin; Sculli, Frank; Fajardo, José Luis Crespo; Smith, Brandon; Alli, P.

doi:10.1109/cbms.2007.66

Cited by 10 publications

(10 citation statements)

References 7 publications

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“…However, relatively few[13,74] have explored development guidelines that facilitate adoption of software across biomedical research organizations. We attribute adoption of LabKey Server and Atlas primarily to the use of seven successful development strategies:…”

Section: Discussionmentioning

confidence: 99%

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

Nelson¹,

Piehler²,

Eckels³

et al. 2011

BMC Bioinformatics

121

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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Section: Discussionmentioning

confidence: 99%

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

Nelson¹,

Piehler²,

Eckels³

et al. 2011

BMC Bioinformatics

121

125

View full text Add to dashboard Cite

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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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“…CAISIS (pronounced "keisis") is an open-source, web-based system that was initiated at Memorial Sloan-Kettering Cancer Center (MSKCC) as a Microsoft Access database for retrospective prostate cancer outcomes research in the late 1990s. With contributions from many groups and individuals, it has grown over 10 years and multiple iterations to manage a wide range of clinical research activities across many oncology disease groups, departments, and cancer centers Potters et al 2003;Fearn et al 2004;Fearn et al 2007b). Although CAISIS would probably not be classified as a clinical system (e.g., Electronic Medical Record or Electronic Health Record, see Chap.…”

Section: Availabilitymentioning

confidence: 99%

“…Third, CAISIS should be considered part of an overall IT ecosystem and research data supply chain rather than just a standalone research application for a particular project (Fearn et al 2007c). Manual data entry can be expensive and time consuming, so identifying and implementing a variety of opportunities for data capture from different staff, systems and methods, routing multiple streams of data into CAISIS, and producing useful output in return for data entry (e.g., clinical notes, operational and outcomes reports, research project datasets) can go a long way toward reaping value from the system, gaining stakeholder buy-in, and building a sustainable data supply chain.…”

Section: Suggested Best Practices For Use Of Tool In Research Settingmentioning

confidence: 99%

Biomedical Informatics for Cancer Research

Ochs

Casagrande

Davuluri

2010

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Lessons Learned from Caisis: An Open Source, Web-Based System for Integrating Clinical Practice and Research

Cited by 10 publications

References 7 publications

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

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

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

Biomedical Informatics for Cancer Research

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