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) v2.1 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.
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.
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.
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.
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).
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.
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.