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.
caBIG® Life Sciences Domain Analysis Model (LS DAM) v2.0 has been released. 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:
For those interested in viewing the LS DAM v2.1 model
For more information on the LS DAM see the LS DAM Wiki page.
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.
NPO RELEASE DOCUMENTS: To view the new release documents, please go to http://www.nano-ontology.org/documentation/version-release-notes/2011-02-12 .
NPO VISUALIZATION: To browse and visualize the NPO, please go to http://purl.bioontology.org/ontology/npo .
NPO INCLUDED IN NCI METATHESAURUS: The NPO is now included in the NCI metathesaurus (NCIm), which can be accessed at http://ncimeta.nci.nih.gov/ .
NPO TERM SUGGESTION: 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: http://ncitermform.nci.nih.gov/
The meeting Date is hyperlinked to the notes and hyperlinks in the Executive Summary are for specific presentations
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.