Sophic Papers and Publications

Cancer Journal

"Toward an Integrated Knowledge Environment to Support Modern Oncology."
Blake PM,* Decker DA,† Glennon TM,* Liang YM,* Losko S,§ Navin N,//** Suh KS.¶

Source from the *Sophic Alliance Inc, East Falmouth, MA; †Florida Hospital Cancer Institute, ‡University of Central Florida, Orlando, FL; §Biomax Informatics AG, Planegg, Germany; ¶The John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ; //**MD Anderson Cancer Center, **Department of Genetics and Department of Bioinformatics and Computational Biology, Houston, TX.

Around the world, teams of researchers continue to develop a wide range of systems to capture, store, and analyze data including treatment, patient outcomes, tumor registries, next-generation sequencing, single-nucleotide polymorphism, copy number, gene expression, drug chemistry, drug safety, and toxicity. Scientists mine, curate, and manually annotate growing mountains of data to produce high-quality databases, while clinical information is aggregated in distant systems. Databases are currently scattered, and relationships between variables coded in disparate datasets are frequently invisible. The challenge is to evolve oncology informatics from a "systems" orientation of standalone platforms and silos into an "integrated knowledge environments" that will connect "knowable" research data with patient clinical information. The aim of this article is to review progress toward an integrated knowledge environment to support modern oncology with a focus on supporting scientific discovery and improving cancer care.
PMID: 21799334 [PubMed - in process]

Click here to Purchase The Cancer Journal or "Toward an Integrated Knowledge Environment to Support Modern Oncology"

pdf2015 Informatics for Clinical Decision Support - HUMC - Suh.pdf

pdf2013 Tissue Banking-Bioinformatics-EMRs

pdf2011 Abstract: Toward an integrated knowledge environment to support modern oncology

pdf2011 Abstract: Sophic to release SCan-Mark (Sophic Cancer Biomarker Database)

pdf2010 Ovarian cancer biomarkers for molecular biosensors and translational medicine, Expert Review, Sophic co-authored Dr. Stephen Suh's paper.

pdf2010 Inferring tumor progression from genomic heterogeneity – Wigler, et al., Cold Spring Harbor Labs – Sophic provided annotated cancer genes from the Cancer Gene Index Project.

pdf2010 Cancer Letters - Expression profiling identifies epoxy anthraquinone derivative as a DNA topoisomerase inhibitor, Khan, et al. , NCI – Sophic developed and provided the integrated cMAP configuration of BioXM.

pdf2009 First Complete Compendium of Cancer Genes – The Cancer Gene Index Project – Presented at 2009 caBIG Conference.

pdf2008 CCR/NCI Integrated and Collaborative Knowledge Environment – Presented at the 2008 CCR Principle Investigator’s Retreat.

pdf2007 Progress Toward a Comprehensive Catalogue of Cancer Genes Based on gene- disease and gene-drug relationships identified – Presented at the 2007 National Cancer Institute Science Fair.

pdf2007 CCR/NCI Integrated and Collaborative Knowledge Environment – Presented at the 2007 National Institute of Health Science Fair.

Software Products

pdfBioXM Knowledge Integration Suite Whitepaper

pdfBioXM Knowledge Management Environment

pdfBioRS Data Integration and Retrieval System

pdfBioLT Linguistics Tool

Sophic White Papers

The Cancer Gene Index

The Cancer Genome ATLAS

The Common Knowledge Environment

The Sophic Druggble Genome


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