• Molecular Analysis Tools Knowledge Center
  • caArray
  • caIntegrator
  • GenePattern
  • geWorkbench
• Bioconductor
• caB2B
• caBIO
• caLIMS2
• caMOD
• caNanoLab
• Cancer Gene Index
• DWD
• GeneConnect
• gridPIR
• LabKey/CPAS
• TCGA

• Work Products

• Information Representation Working Group (IRWG)
• Nanotechnology Informatics

• Analytical Services Best Practices Working Group
• ICR Interoperability Working Group
• Workflow Working Group

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

For a complete list of modifications and additions to the LS DAM v 2.2, 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 model is available in two formats:

• An Enterprise Architect file may be downloaded LS DAM v 2.2 EA file
• A web based view of the model is also available using Internet Explorer  LS DAM v2.2 HTML

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

• NPO VISUALIZATION

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 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.

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/ NPO TERM SUGGESTION.