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titleUseful Links




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titleICR Active Working Groups
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titlePrevious ICR Working Groups
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The Integrative Cancer Research Workspace is producing modular and interoperable tools and interfaces that provide for integration between biomedical informatics applications and data. This will ultimately enable translational and integrative research by providing for the integration of clinical and basic research data. The Workspace is developing a software-engineered, well-documented and validated biomedical informatics toolset for use throughout the research community.

Additional information is also found on the Molecular Analysis Knowledge Center site.


Open Development and Community Projects Speaker Series

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titleICR WS Teleconference Speakers

The Integrative Cancer Research (ICR) Workspace is hosting a series of speakers on various open development and community driven projects. While the applications may be of greatest interest to ICR, the conversations about success factors for these types of projects is of general interest to the caBIG community.

You are welcome to join us on the 2nd and 4th Wednesdays of each month from 2:00 – 4:00 pm ET. Teleconference information:
800-593-0616 passcode: 2927756.
Adobe connect: http://cbiit.acrobat.com/icrws/

ALL TELECONFERENCE MATERIALS ARE POSTED BELOW.

Please watch for updates to the list of speakers below

May 25
Cell Profiler, Mark Bray (The Broad Institute)
Gene Ontology, Judith Blake (The Jackson Laboratory)

June 8
Cytoscape, Mike Smoot (UCSD)
Use of caBIG tools (caIntegrator, caArray, NBIA) in Mouse GBM Studies, Sunny Jansen (NCI-F)
High-throughput data and identity management in Galaxy, Ravi Madduri (ANL)

June 22
BioPAX and GeneMANIA, Gary Bader (U. of Toronto)
I SPY/ Transcend, Sarah Davis (UCSF)

July 13
Protein Ontology, Cecilia Neomi Arighi (U. of Delaware)
Data standards and the Cardiovascular DAM at Duke University, Sal Mungal (Duke)

July 27
National Center for Biomedical Ontology - BioPortal, Trish Whetzel (Stanford)

August 10
POSTPONED: The Functional Genomics Data Society (FGED, formerly MGED), Chris Stoeckert (U. of Pennsylvania)]


Recent News

The ICR Information Representation Working Group (IRWG) and the LS DAM analyst are focused on developing information models to support the development of interoperable Life Sciences applications.  The LS DAM is a shared view of the semantics for Life Sciences, which includes hypothesis driven and discovery based sciences. It is aligned, where appropriate, with the Clinical Sciences BRIDG model, which covers protocol driven clinical research. The LS DAM is a foundational component for achieving semantic interoperability among the various applications across caBIG® and is bound to the ISO 21090 data type standard.

The major changes in this release are described in the Release Summary and include:

  • Experiment Core Model Implementation Guide
  • Addition of attributes in the Molecular core of the model and linking Experiment to generated Materials
      1. These changes were identified and validated through a survey of multiple public ‘omics databases (200+ potential entities, data types, roles and outcomes likely to result from the study of biologic systems including genetic variation, genomics, and proteomics) and pathology imaging whole slide image scenarios

For a complete list of modifications and additions to the LS DAM v 2.2.1, please see the Release Summary and Model Documentation.  For an exemplar on how to use the Experiment Core of the LS DAM, please see the Experiment Implementation Guide.

The LS DAM v2.2.1 model is available in two formats:

  • An Enterprise Architect file may be downloaded LS DAM v 2.2.1 EA file
  • A web based view of the model is also available using Internet Explorer  LS DAM v2.2.1 HTML
    For more information on the most recent set of activities, see the Information Representation Working Group Report for January 2011- April 2011 Report
    Info
    titleLife Sciences Domain Analysis Model v2caB2B releases v3.2.1

    On behalf of the caBench-to-Bedside (caB2B) development team at Georgetown University and caB2B Knowledge Center at Washington University, I am pleased to announce the availability of the caB2B v3.2.

    In this release caB2B's functionality has been expanded to better support complex queries that involve multiple services from multiple institutions such as caTissue Suite services at Prostate Cancer SPORE sites.

    New features of the caB2B v3.2 include:

    * Support queries that combine data across heterogeneous data services such as caTissue Core and Clinical Annotation Services

    * Ability to group services to allow users to limit data combinations to a services from given institution or organization

    * Ability to support login using NIH/NCI credentials

    * Ability to manually load models using XMI files exported from UML authoring tools or domain model XML files that are available as part of caGrid service metadata

    * Improved user interface navigation

    * Improved default caB2B database with new service models and saved queries

    * Improved server function including error handling, caching, security, and index service updates

    The caB2B Web Application is available for the community's use at the following sites:

    * https://cab2b.georgetown.edu/cab2b  (Georgetown University instance).

    * https://cab2b.wustl.edu/cab2b  (Washington University instance) and

    * https://cab2b.nci.nih.gov/cab2b  (NCI instance).


    Info
    titleNanoParticle Ontology

    We have released a new version of the NanoParticle Ontology(NPO). This version includes new terms that describe “scales of measurement” and nanomaterials. We made some modification to the nanomaterial branch and added new terms based on ISO terminology.

    The NPO is now included in the NCI metathesaurus (NCIm), which can be accessed at NPO IN NCI METATHESAURUS.
    The NCI metathesaurus contains about 3,600,000 terms from over 76 vocabularies, and these terms are mapped to about 1,400,000 biomedical concepts. Terms from multiple vocabularies that are mapped to a single biomedical concept allows the user to choose from the multiple vocabularies to annotate data. Simultaneously, this facilitates discovery of vocabularies unknown to the user. By the inclusion of NPO into the NCI metathesaurus, we expect that NPO accessibility and usage will be extended within the NCIm; NPO will add semantics into the NCIm; and that NCIm users will be able to take advantage of the knowledge provided by NPO.

    The NCI term suggestion application allows for users to suggest terms for NPO. To suggest terms for NPO, you may use the NCI term suggestion application, available at NPO TERM SUGGESTION.

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