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
ICR 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/
Please watch for updates to the list of speakers below
Cell Profiler, Mark Bray (The Broad Institute)
Gene Ontology, Judith Blake (The Jackson Laboratory)
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)
BioPAX and GeneMANIA, Gary Bader (U. of Toronto)
I SPY/ Transcend, Sarah Davis (UCSF)
Protein Ontology, Cecilia Neomi Arighi (U. of Delaware)
Data standards and the Cardiovascular DAM at Duke University, Sal Mungal (Duke)
National Center for Biomedical Ontology - BioPortal, Trish Whetzel (Stanford)
The Functional Genomics Data Society (FGED, formerly MGED), Chris Stoeckert (U. of Pennsylvania)]
Life Sciences Domain Analysis Model v2.2.1
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
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.
The meeting Date is hyperlinked to the notes and hyperlinks in the Executive Summary are for specific presentations
John Speakman, NCI CBIIT CPO kicked-off the workspace call with a caBIG Program Update. Mike Smoot, UCSD, is lead developer for Cytoscape. He provided an overview of the Cytoscape software platform for visualizing molecular interactions and pathways and integrating these with annotations and data. His talk also focused on the active Cytoscape community. Sunny Jansen is a researcher at the Mouse Cancer Genetics Program on the Ft. Detrick campus in Maryland. She is doing a mouse GBM study using caBIG tools such as NBIA and caIntegrator with imaging, pre-clinical and genomic data. Ravi Madduri from Argonne National Lab will provide an update on his work with Galaxy. He was recently in the Netherlands at the Galaxy users meeting and presented his work on highthroughput data and identity management in Galaxy.
Mark Bray from the Broad Institute gave a presentation on CellProfiler. It is a tool which integrates various algorithms. It is capable of extracting measurements for every individual cell in an image-based screen, ranging from standard assays (e.g., cell count, size, per-cell protein levels) as well as more complex morphological assays (e.g., cell/organelle shape or subcellular patterns of DNA or protein staining). Judith Blake from the Jackson Laboratory discussed the Gene Ontology (GO). GO provides a standardized representation of gene and gene product attributes and is comprised of a controlled vocabulary, gene product annotation data and tools to access and process the data (GO Browser and OBO ontology editor). GO is maintained by the GO Consortium which is comprised of organism and protein databases and the biological research community.
Rashmi Srinivasa hosted a caArray Users Meeting. She discussed features of the upcoming 2.4.1 release and the plans for the following release. Grace Stafford provided an update on The Jackson Laboratory caBIG Deployment Implementation. This included the impact of next generation sequencing technologies on the computational core tool needs and requirements emerging from new projects. Ravi Madduri provided a demonstration of caBIG workflows run using the Galaxy platform.
The ICR workspace heard reports on the recent BioIT and AACR meetings from Mark Adams (BAH) and Jens Poschet (Sapient) respectively. Jason Hipp of University of Michigan gave a presentation on the use of Laser Capture Microdissection in --omics research.
The ICR participants presented on their assigned projects. Jim McCusker, caIntegrator Community Contribution of Code, discussed his implementation experience and future recommendations. Dennis Thomas , Extending the Use of the NanoParticle Ontology, addressed challenges for using NPO with nano-TAB and caNanoLab NPO for data annotation, semantic integration of data, unambiguous interpretation and data sharing. Mukesh Sharma , HL7 Clinical Genomics WG, discussed “Considering changing mission and charter to reflect changing technology” and “Mission to include bridging semantics between clinical and research domains.” Nathan Baker reviewed the updates and future goals of the Nanotechnology Working Group. In addition, Bob Freimuth , Information Representation Working Group, reviewed the activities and future recommendations for the period.
Alex Kanous from the DSIC Knowledge Center provided a presentation on the electronic Data Use Agreement tool. The tool may be used for generating DUAs for outgoing data based on a catalog of standardized, modular contract clauses, each of which corresponds to one of the E-DSSF’s sensitivity ratings. Joshua Phillips and Ravi Madduri discussed the prototyping activities on workflows for caGrid 2.0. They described use cases and requirements for workflows, defining metadata needed for discovery, composition, and execution of workflows and their consideration of how best to use W3C technologies (e.g. RDF, SPARQL, SA-WSDL, inference). They also provided a demo of a workflow engine prototype based on SADI and Taverna. Ken Quinn spoke about the Roswell Park deployment of caGrid technology and use of caB2B to do federated queries across disparate, decentralized heterogeneous databases and clinical systems to support non-interventional clinical research. He described the process and challenges including: gathering senior leadership support, understanding the myriad research databases, gaining technical expertise, lack of common vocabularies and the excellent collaboration and support provided by the caB2B knowledge center.
Anton Nekrutenko and Daniel Blankenberg and of The Pennsylvania State University gave a presentation on Galaxy, an open-source next generation sequence (NGS) analysis software system. It addresses the need to empower the scientists without access to extensive infrastructure to do the analysis. Galaxy is a free web service, and has a plethora of analysis tools and has workflow generation capabilities
caArray Users Meeting featured upcoming plugin architecture for support the addition of new parsers and data storage mechanisms.
Jenny Kelley, NCI Population Sciences, updated the community on caLIMS v2 new features. She also provided a thorough demonstration of the tool.
The ICR Workspace is hearing reports on activities for the last period.
Looking for older notes? Access ICR Meeting Notes Archive