Oncotrack-eTRIKS data and knowledge management platform, Programming language: Grail, javascript, R, Other requirements: Tomcat7, JDK 7, Postgres 9.3 or higher. Research consortia are attempting ever more ambitious science to better understand disease, by leveraging technologies such as whole genome sequencing, proteomics, patient-derived biological models and computer-based systems biology simulations. It must also cross-check that the data request is consistent with federal and local regulations. PubMed The IRB application will require the researcher to outline the inclusion and exclusion criteria for the study. This approach uses a broad panel of methods such as next generation sequencing, proximity extension assays, reverse phase protein arrays, methylation arrays and mass spectrometry. 2012;3:602–12. web interface, RESTful API). A second data level is generated from the three disease modelling platforms used by OncoTrack: xenograft based in vivo models, 3D cell line based in vitro models (‘biological models’) and cell simulation based in silico models. One collection for data derived directly from patient samples and other collections for data derived from the pre-clinical models.
Informative use cases of such platforms are SHRINE [28] and DARiS [29], where well-defined demands of clinical research projects drove the design and implementation of infrastructure supporting translational medicine. Anthony Rowe is a full time employee and shareholder of Johnson and Johnson.
He is currently head of the Laboratory of Photodynamic Inactivation at the University of Salzburg (PDI-PLUS).
2018;12:1177932218759292. In all these steps, data mapping, linking and preparation are handled automatically by the tranSMART integration platform. 2013 Jun;16(4):461-79. doi: 10.1016/j.jval.2013.04.004. Increasingly, projects are citing the use of specialist knowledge management technologies such as the tranSMART platform [] as used by the IMI UBIOPRED, ABIRISK and OncoTrack projects [2,3,4,5].In reality, however, a knowledge management platform alone is not sufficient to … To date, Dr. Plätzer has published 34 papers in peer-reviewed journals, a book chapter, and regularly serves as conference speaker.
The high dimensional (omics) data from the molecular analyses of the corresponding biological materials were linked to these collections, so that users could browse and analyse these to derive candidate biomarkers. Retrieved 2014-05-31.
We would like to emphasise that this paper is not meant to focus on any specific scientific questions within the OncoTrack project, which have been reported in a separate paper [13], but rather to demonstrate the advantage of the tranSMART platform in solving data integration problems in general.
Primary Data Collection. Many of the problems outlined above are solvable at a strategic level by creating a synergy between research and care improvement teams–both from an infrastructure perspective and an operational perspective. He is an ad hoc reviewer for several journals and member of the Society of Porphyrins and Phthalocyanines. Right panel: easy customized cohort building with drag-and-drop.
Recent reviews have summarized many of the existing computing and analytical software packages designed to ease integrated analysis of ‘omics and/or clinical data [14,15,16]. [11] Since 2009, the field has had specialized journals, the American Journal of Translational Research and Translational Research dedicated to translational research and its findings.
Data Collection .
In line with the above considerations, in the OncoTrack-tranSMART integration, we separated different data levels and data types into separate study-trees to better organise the different categories (clinical data and lab data). This site needs JavaScript to work properly. [19], In U.S., the National Institutes of Health has implemented a major national initiative to leverage existing academic health center infrastructure through the Clinical and Translational Science Awards. As one of the Innovative Medicines Initiative (IMI) oncology projects, it brings together academic and industry scientists from more than twenty partner institutions in a research project to develop and assess novel approaches for identification of new markers for the treatment response of colon cancer.
The problem with collecting data using these tools is that the process creates yet another data silo.
TranSMART is being used by many (> 100) organizations and consortia around the world [2,3,4,5, 16, 38,39,40]. Schütte M, Risch T, Abdavi-Azar N, Boehnke K, Schumacher D, Keil M, Yildiriman R, Jandrasits C, et al. Sharing these innovations and discoveries with other providers helps the healthcare industry as a whole become more effective and improves the health of a global population. For example, while creating a grant proposal, a researcher may need a straightforward count of patients in his system with COPD.
(4) Performing miRNA-ome wide heatmap analysis between the two sub-cohorts (here responder vs. non-responder for a selected drug treatment) using SmartR workflows.
Researchers often must rely on Excel spreadsheets and Access databases to enter study-specific data that may not be found in the medical record.
Bioinformatics.
Wierling C, Kühn A, Hache H, Daskalaki A, Maschke-Dutz E, Peycheva S, Li J, Herwig R, Lehrach H. Prediction in the face of uncertainty: a Monte Carlo-based approach for systems biology of cancer treatment. His work in immunology has earned recognition from the Weizmann Institute, the National MS Society, the National Institutes of Health, Nature Biotechnology, and the Harvard Catalyst. 3 (2)) that will automatically handle the many-to-one relationship across the different data layers. Whenever data leaves the medical center for research purposes, the medical center must ensure the transfer is secure. The systems biology model of the cancer cell incorporates the combined results of genome, transcriptome, methylome and proteome analyses [6]. AMIA Annu Symp Proc.
In all these steps, data mapping, linking and preparation are handled automatically by the OncoTrack-tranSMART integration platform. Xenografts, DNA_Methylation, etc. It is important to note that RWD will never replace the more traditional and more robust RCT data; however, the emerging trend is to incorporate data that are more generalizable. 2015;8:18.
The webinar will last approximately 60 minutes. 2018 Aug 3;15(8):1644. doi: 10.3390/ijerph15081644. A consortium that provides a data coordination capability accelerates the work of the specialist data scientist who can access the raw data from a single location for specialist analysis. Among the above-mentioned solutions, tranSMART stands out as a community-driven, rapidly growing, web-based data and visual-analytics platform for clinical and translational research [1, 16]. Some well-known examples are EuPathDB (a eukaryotic pathogen genomics database resource, [30]), the DNA Microarray Inter-omics Analysis Platform [31], Mayday SeaSight (combined analysis of deep sequencing and microarray data, [32]), GeneTrail2 (multi-omics enrichment analysis, [33]), OmicsAnalyzer (a Cytoscape plug-in suite for modeling ‘omics data, [34]), PathVisioRPC (visualise and analyse data on pathways, [35]), 3Omics (analysis, integration and visualization of human transcriptomic, proteomic and metabolomic data, [36]) and PaintOmics (joint visualization of transcriptomics and metabolomics data, [37]). Kuo TC, Tian TF, Tseng YJ. 115234 (OncoTrack) and 115446 (eTRIKS), resources of which are composed of financial contributions from the European Union’s Seventh Framework Programme (FP7/2007–2013) and The European Federation of Pharmaceutical Industries and Associations (EFPIA) companies’ in-kind contributions (www.imi.europa.eu). These features ensure high data quality by providing all clinical sites with identical case report forms and by flagging data entry errors so they can be rapidly fixed. This is achieved by the use of flexible user interfaces, combined with analytical and visualization tools that can be used by all stakeholders in the consortium and not just those with the specialist data handling skills such as bioinformaticians and statisticians. BMC Bioinformatics Using the COPD example from above, the researcher may request information from the health system on patients with chronic coughs, wheezing, or a COPD diagnosis.
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