This is the wiki home page for ICR (Integrative Cancer Research). Here you will find technical information about ICR products and pages for working groups and projects.
ICR products are moving to their own spaces; therefore, more extensive information for some ICR products is found in the spaces named 'ICR - Product Name' on this site. If your team's space is not published, you can see it when you are logged in. The published ICR product spaces are:
Additional information is also found on the Molecular Analysis Knowledge Center site.
We are pleased to announce the release of the caBIG Life Sciences Domain Analysis Model (LS DAM) v2.0. The LS DAM is a shared view of the semantics for Life Sciences, which includes hypothesis driven basic and pre-clinical research as well as discovery 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:
- a consistent level of abstraction and clearer model with traceability to BRIDG by direct inclusion of the relevant BRIDG classes
- LS DAM alignment with the current version of BRIDG (3.0.2)
- The Generic Assay model, developed in collaboration with the HL7 Clinical Genomics Working Group, is included as a core component of the LS DAM. This extensible component of the model represents concepts that are common to life sciences research over multiple technologies.
- For a complete list of modifications and additions to the LS DAM v 2.0 please see the Model Documentation
- For those interested in viewing the LS DAM v2.0 model
- For more information on the LS DAM see the LS DAM Wiki page
The new version of the NanoParticle Ontology (NPO) has been released and uploaded on NCBO BioPortal. To view the NPO, please go to http://purl.bioontology.org/ontology/npo .
The major changes in the new version are:
1. Added new classes: In this version, we have added 35 new classes to the NPO , many of which are related to the description of different types of cores, shells and surfaces found in nanoparticles.
2. Made specific changes to classes from previous version: We fixed some errors, and asserted more relationships between terms from the “quality” branch and those from the “independent continuant” branch of the NPO.
For more information, please view the version release notes that are posted on the NPO project website, http://www.nano-ontology.org/documentation/version-release-notes/2010-10-31 .
Conference call notes are available as separate documents under "Attachments" on this wiki page.
January 12, 2010, 2-4 PM Eastern
The ICR Workspace is hearing reports on activities for the last period.
• Bob Freimuth discussed IRWG work on the LS DAM Updates and additions to the model will appear in the next release. Work on the portion of the model shared with HL7 Clinical Genomics Working Group is extending the generic assay core to include concepts for gene variation.
• Dennis Thomas reported on the processes to integrate the NanoParticle Ontology into the NCI Metathesaurus. This expands NPO accessibility and brings more semantics into the NCImt.
November 10, 2010, 2-4 PM Eastern
Ken Smith from the Molecular Analysis Tools Knowledge Center presented an update on geWorkbench, which is a platform for integrated genomics. A demo involving data from an ovarian cancer study highlighted features from the last two releases including BLAST tools, gene annotation, GO viewer, pathway visualization tools and more.
October 27, 2010, 2-4 PM Eastern
Ulli Wagner presented the website eMICE: electronic Models Information, Communication, and Education. It is a communication tool for the NCI Mouse Models of Human Cancers Consortium (MMHCC). Currently the program has a strong focus on education and the website was constructed to reach the broad spectrum of general audience to researcher. Mukesh Sharma reported in on the recent HL7 Meeting. He gave a review of Clinical Genomics working group activities in the three different tracks. He reported in on the discussion of the generic assay model which was developed as part of a caBIG ICR Information Representation Working Group collaboration with HLy Clinical Genomics Working Group.
October 12, 2010, 2-4 PM Eastern
Rashmi Srinivasa polled the workspace on interest in generic assay management. She provided an update on caArray which included features anticipating handling next generation sequencing data such as: the ability to handle fastq and BAM/SAM files, the ability to move and store large volumes of data. There were also security and technology stack related updated. Rashmi also presented Annotare which provides templates and tools to annotate MAGE-TAB experiments.
Raghu Chintalapati reviewed the SAIF and ECCF Implementation in NCI CBIIT. SAIF is comprised of frameworks to help provide working interoperability. There are four frameworks or grammars (information, behavior, governance, ECCF) and an implementation guide is being written to describe the CBIIT operationalization of SAIF. ECCF is a framework for service specifications and has five viewpoints represented (enterprise, information, computational, engineering and technology). A key component of specifications is modeling a service at different levels of abstraction: conceptual, platform independent, platform specific, implementation.
September 8, 2010, 2-4 PM Eastern
Karen Ketchum provided an overview of caIntegrator, a tool that provides the ability to develop web portal without software skills and allows you to import your data and query it. NCI hosts 5 studies in the caIntegrator platform. Newest features include enhancements to subject annotation interface, list management, upgraded connectivity to the NBIA, external links, expanded microarray platform support and copy number analysis capabilities. The call was closed out with ICR Working Group Reports (LS SMEs, Nano WG, IRWG).
August 25, 2010, 2-4 PM Eastern
Jenny Kelley presented the features and functionalities under development for caLIMS2. The purpose of the caLIMS2 project is to create a Laboratory Information Management System (LIMS) that is interoperable within established caBIG® standards and guidelines and will track a complete laboratory workflow that uses materials from a specimen management service (e.g. caTissue) to generate experimental results for one of the caBIG® data management services (e.g. caArray). Core LIMS functions include the management of personnel, equipment, lab supplies and reagents, samples, laboratory workflow and experimentally derived metadata and data. caLIMS2 will complete the caBIG® bench to bed model by bridging the gap between biospecimen repositories, data repositories and analysis tools. Stephen Goldstein provided the Workspace with a demo on JIRA which is the NCI CBIIT's new issue tracking and project management tool. External users can log into JIRA to create issues and feature requests for specific products. Product teams can use JIRA to manage their development cycles. Testing teams can use JIRA to manage their testing efforts. And the Program team can use JIRA to create reports around issue lifecycles and development progress.
August 11, 2010, 2-4 PM Eastern
Liz Hahn-Dantona of the EVS team demonstrated how to access and use the NCI term browser, NCI thesaurus and NCI Metathesaurus. She described content in various tabs and pointed out features of interest. In preparation for the caBIG® Annual Meeting, Dr. Robert Freimuth created a 508 compliant presentation. He offered many helpful hints and his lively demonstration showed just how easy it is to create compliant presentations using layouts and alt text. Rashmi Srinivasa gave an overview of caArray. The caArray users meeting is now held in the ICR WS calls. Current features and those being added in the next release features were highlighted, including support for next generation sequencing experiments files FASTQ and BAM.
Looking for older notes? Access ICR Meeting Notes Archive
See ISA-TAB-Nano for more information about this public data standard.