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Sophic

SCan-MarK

SCan-MarK™ Explorer
BioMarker Environment

SCan-MarK Explorer™ was built to support basic research, drug discovery, diagnostic development, clinical research and personalized medicine. The goal was to provide quality scientific intelligence to help researchers and clinicians make sense out of the growing Tsunami of sequence and clinical information.

Sophic’s Cancer Biomarker Knowledge Environment (SCan-MarK) includes a growing manually curated target cancer biomarker database for breast cancer, ovarian cancer, colorectal cancer, non-Hodgkin’s lymphoma and melanoma. Teams of Sophic PhD scientists continue to mine and manually curate full-text clinical research papers rich with patient information including disease state and progression, drug therapies and treatment outcomes, including Kaplan-Meier charts. SCan-MarK’s 3-year development project was funded through a National Cancer Institute (NCI) SBIR award and is designed by scientists for scientists

SCan-MarK’s curated database has been integrated into sophisticated Explorer software, providing end-users with a unique search, discovery and collaboration research system. Sequence-derived mutation information and genomic experimental data from the NCI Cancer Genome Atlas (TCGA) are integrated and enriched with information from over 30 public domain databases which provides a broad, rich and growing foundation of research and clinical information.

Sophic delivers scientific intelligence, a constantly evolving integrated knowledge environment that provides researchers and clinicians with up-to-date, critical, complex cancer information intended to improve decision making, patient treatment outcomes and accelerate the search for cures. SCan-MarK Explorer can be accessed via the web through a user-friendly WIKI portal or installed and integrated with internal research and clinical data sources.

For your convenience,  below please find four buttons that will open documents that provide additional detailed  information on  SCan-MarK Explorer. They include: SCan-MarK Overview and White Paper.   The tabs contain SCan-MarK Explorer screen shots for both the clinical and research use cases.  To make the image larger, click on  the screen image and use the browser back arrow to return to the original size of the screen. Captions explaining the screen shot can be found below each image.  The  last six tabs are Power Point slides that provide additional information on SCan-MarK Explorer.

White PaperWhite PaperIntegrated Knowledge Environment

  • User Console
  • Physician Support
  • Clinical Query Results
  • Kaplan-Meier Curve Genertor
  • Patient Data Heatmap
  • Research Wizard
  • Research Results
  • Knowledge Map
  • SCBO CDE Details
  • SCBO Summary Report
  • SCan-MarK Data Model
  • SCan-MarK Foundation
  • Enrichment Databases
  • Biomarker Pyramid
  • SCan-MarK Version 2
  • Future Plans

The User Console is designed to look, feel and work like a cell phone interface. The “buttons” are organized by research areas of interest, creating a domain specific “Knowledge Environment.” Each “button” is an entry point into the SCan-MarK “Knowledge Environment” and provides access to related information stored in over 30+ databases.

The Physician Support page is the main entry page for physicians to access the system.  There are pull down menus and radio buttons that make it easy for a busy doctor treating patients to enter information specific to an individual patient.  Across the bottom are four queries that are used to search the knowledge environment.  At the top are buttons to access individual support pages for the five disease types in SCan-MarK.

The similar patients from Physician Support are displayed in a table of patient information as well as a pie chart showing the drugs used to treat living patients.  Querying a variety of integrated data sources can be accomplished with tools shown at the top of the table.

Kaplan-Meier curves for groups of patients can be generated on demand from the results of the Physician Support query to show significant differences in patient survival related to treatments and/or biomarkers.

Tables can be “too much data to understand” so SCan-MarK provides a color coded, ranked expression analysis heatmap to display high/low expressed SCBOs at the top or bottom of the map. Genes/proteins at either extreme are potential targets for further bench experiments.

While there is rich information across SCan-MarK Explorer, most scientists want to study their own genes/proteins of interest. The Easy Import Wizard allows scientists to copy, paste, and import their own list of target biomarkers.

The resulting Gene information from using the Import Wizard are displayed in a table with enrichment data from a variety of sources.  In addition, a pie chart showing the common pathways or GO classifications for the genes is displayed at the top. Tool buttons at the top of the table allow for querying a integrated data sources.

This oncology knowledge map shows valid scientific relationships between two breast cancer patients via their up-regulated (red arrow) and down-regulated (green arrow) genes from experimental data.  The genes are further enriched with Gene Ontology (GO) classifications and target drugs. Information in this map is integrated from the most current information in the TCGA, GO, Drug-bank enrichment databases at the time the map is created.

Details from the Critical Data Elements (CDEs) can be displayed for individual SCBOs.  Hyperlinks to GO classification, Sophic Clinical Cohorts, as well as PubMed and NCBI EntrezGene are provided.

This table shows the summary of the information from many sources including Sophic curation, Sophic's Non-redundant COSMIC database, patient data from TCGA, NCBI Biosystems, and The Cancer Gene Index.  Summary results show a snapshot of the information about a SCBO and users can 'drill down' into the details using the hyperlinks in the table or the tools at the top.

Data Model

The data model provides SCan-MarK with connections between valid scientific and semantic element relationships. The networked elements are controlled by standard ontologies that allow SCan-MarK to “speak” and “understand” scientific terms. This combination works like the “GPS” for the software, providing networks of routes, addresses and intersections of scientific elements.

SCan-MarK was developed by expanding on the results of three major previous projects or software products. The backbone of SCan-MarK Explorer is the Biomax BioXM Knowledge management System, the NCI Cancer Gene Index and the Phase I SBIR SCan-MarK prototype. The SCan-MarK curated biomarker repository, Sophic Intelligence and the Explorer functionality all sit on this foundation.

SCBOs and user specific gene/protein lists are all programmatically linked to over 30 enrichment databases. This extensive network allows scientists to “walk around” and study the correlations between clinical, chemical, biological information in the “Knowledge Environment.”

Sophic organizes candidate biomarkers into a pyramid structure based on the type of experiments performed and the evidence provided in each paper. The focus for Sophic’s manual curation are Level 2 biomarkers that have human, bench experimental evidence to support the assertion that the biomarkers are credible candidates.



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