“Integration, Annotation and Analysis Services for Biomedical Data”
To share and fully utilize biomedical data, it needs to be integrated with other data and annotated with metadata using standard terminologies and methods. Similarly biological objects such as genes, proteins, pathways, drug interactions, and treatments need to be culled from the literature and organized by their functions and interactions - even the best-automated methods need quality training sets. Only organized data informs.
- The Clinical Proteomics Tumor Analysis Consortium (CPTAC) – Data Center
- The CPTAC Assay Portal
- Clinical Genome Resource (ClinGen)
Publications resulting from work in this research platform
McGarvey, P.N., A. Luo, J. Huang, H. Martin, M.J. Wu, C. UniProt, C., UniProt Genomic Mapping for Deciphering Functional Effects of Missense Variants. Human Mutation, 2018. (Submitted).
Madhavan, S., Ritter, D., Micheel, C., Rao, S., Roy, A., Sonkin, D., Sidiropoulos, N., McCoy, M., Griffith, O., Griffith, M., Mcgarvey, P., Kulkarni, S. On Behalf of The Clingen Somatic Working Group, Clingen Somatic Working Group – Standardizing And Democratizing Access To Cancer Molecular Diagnostic Data To Drive Translational Research. Pacific Symposium on Biocomputing, 2018.
Boca, S.M., Panagiotou, O. A., Rao, S., McGarvey, P. B., Madhavan, S., Future of Evidence Synthesis in Precision Oncology: Between Systematic Reviews and Biocuration. JCO Precision Oncology, 2018. 2: p. 1-9.
Gusev, Y.M., P. H Haddad, B. R. Demystifying Biomedical Big Data: A User’s Guide. 2017. Available from: https://www.edx.org/course/demystifying-biomedical-big-data-users-georgetownx-biox-201-01x .
Edwards, N.J., et al., The CPTAC Data Portal: A Resource for Cancer Proteomics Research. J Proteome Res, 2015. 14(6): p. 2707-13.
Edwards, N.J, Oberti M, Thangudu R, Cai S, McGarvey P, Jacob S, Madhavan S, and Ketchum K. 2015. The CPTAC Data Portal: A Resource for Cancer Proteomics Research, J Proteome Res, 2015. 14(6): p. 2707-13.
McGarvey. P.B., Dharia, S., Oberti, M., Dragomir A, Hedlund, E., Tanenbaum, D., Suzek, B., and Madhavan S. 2012. Informatics and Data Quality at Collaborative Multicenter Breast and Colon Cancer Family Registries, J Am Med Inform Assoc. Feb 9. PMC3392863