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.
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
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)
National Center for Biomedical Ontology - BioPortal, Trish Whetzel (Stanford)
August 10 The Functional Genomics Data Society (FGED, formerly MGED), Chris Stoeckert (U. of Pennsylvania)]
Life Sciences Domain Analysis Model
We are pleased to announce the release of the caBIG® Life Sciences Domain Analysis Model (LS DAM) v2.2. The LS DAM provides a shared view of the semantics for the Life Sciences domain, which includes hypothesis driven basic and pre-clinical research as well as discovery sciences. It is aligned with the BRIDG model, (which supports protocol-driven clinical research) and is bound to the ISO 21090 data type standard. The LS DAM is a tool that will aid software developers in achieving semantic interoperability across information systems.
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
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.