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CMAP
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Overview
The Cancer Molecular Analysis Project (CMAP) is a prototype system that demonstrates a method
enabling researchers to access and link critical data regarding molecular profiles, molecular
targets, and targeted agents to support advanced clinical research. In addition, the CMAP
approach would provides users with the ability to access clinical trial data for studies
designed to evaluate targeted molecular agents. To further facilitate analysis activities,
clinical trial data are organized by CMAP according to therapeutic agent and cancer type.
The CMAP prototype laid the foundation for many of the translational research projects NCICB
is currently pursuing. It was originally constructed as a prototype informatics effort and
has since been used to try out new functionality. The type of functionality demonstrated by
CMAP would provide researchers with a comprehensive and intuitive way to access, review,
analyze and compare molecular and clinical trial data that is relevant to a particular type
of cancer.
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Product Release
CMAP Public web site
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Objectives
CMAP was designed to facilitate cancer research by providing access to information that is
linked together and displayed based on a specific set of user-defined criteria.
The functionality of CMAP is particularly applicable for researchers operating in distributed
environments as it promotes the sharing of research findings across multiple institutions.
Specifically, CMAP was designed to link cancer research data in the following areas:
- Molecular Profiles – Molecular signatures of various types of cancer. Users can access the
signatures of a specific type of cancer or identify the cancer type that most resembles a
specific signature.
- Molecular Targets – Collections of genes organized by pathways and by ontology. Access to
this data provides researchers with the ability to perform aggregate evaluations of anomalies.
- Molecular Targeted Agents - A collection of agents (drugs and other interventions) targeted
to specific profiles, molecular anomalies, pathways and ontologies.
- Clinical Trials – Data regarding cancer clinical trials designed to evaluate molecular
targeted agents. This data are organized by therapeutic agent and by cancer type.
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CMAP data are organized around six (6) key concepts. These concepts and their associated
definitions form the foundation of the CMAP data structure. They are as follows:
Concept 1. Context – The combination of a specific tissue and disease type. For example,
users might select “Brain” as the tissue type and “Astrocytoma” as the type of disease.
This combination of tissue and disease forms a ‘context.’
Concept 2. Target – A molecule that holds special diagnostic or therapeutic interest for cancer
research. In CMAP, a target is treated as a potential target in any cancer; thus targets are not
specific to contexts. Targets are classified according to function: ontology or pathway.
Concept 3. Anomaly – A deviation in the structure or expression of a target. An anomaly
is associated with one or more kinds of cancer and therefore cannot be filtered by context.
Concept 4. Profile – A set of anomalies that together characterize a type of cancer,
distinguishing it from other types of cancers and from other normal states.
Concept 5. Agent – A drug or other intervention that is effective in the presence of
one or more specific targets.
Concept 6. Trial – A clinical trial is linked to a context and one or more agents.
A trial is not directly linked to any target.
These concepts can be applied to data searches to help refine and link critical research data
across multiple data sources. By utilizing the CMAP functionality, researchers are able to
significantly increase the utility and applicability of data across the spectrum of molecular
cancer research.
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Potential Benefits
The benefits of a fully implemented project based on the CMAP functionality would include:
- Ability to easily access and search information on clinical trials designed to evaluate
Molecular Targeted Agents. Users can query the data using a keyword in the Protocol Title,
based the Phase of the Trial or by the Name of the Agent or Lead Organization.
- Ability to easily access and search Molecular Profile Data and sort the data by chromosome.
Additionally, this information can be displayed in 2-D array format.
- Ability to easily access and search Molecular Target data using ontologies, pathways or genes.
- Ability to easily access and search Molecular Targeted Agents by name, those with CMAP
Targets or those with associated CTEP protocols.
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Detailed Scope
The CMAP project was organized around the primary task of creating new Molecular Pathway
Diagrams and/or extension to existing diagrams. Some ongoing generation of new pathway
diagrams is underway. However there is currently no acquisition of new data or maintenance
of the user interface.
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Integration
Since the CMAP application is a prototype application, it is not integrated as a supporting
technology of the Cancer Bioinformatics Grid (caBIG). However, CMAP is integrated with Cancer
Bioinformatics Infrastructure Objects (caBIO), which is a key component of the Core
Infrastructure developed by the NCI Center for Bioinformatics. caBIO enables CMAP to access
genomic and related data from multiple data sources via a set of standard Java objects.
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