The caBIO 4.3.1 is the minor release with some enhancement in FreeStyleLM Search Summary page and introduction of the Entrez-Gene data.caNanoLab is a data sharing portal designed to facilitate information sharing in the biomedical nanotechnology research community to expedite and validate the use of nanotechnology in biomedicine. caNanoLab provides support for the annotation of nanomaterials with characterizations resulting from physico-chemical and in vitro assays and the sharing of these characterizations and associated nanotechnology protocols in a secure fashion. 

Release History

New Features and Updates

1. Enhanced Display of FreestyleLM Search Results
To allow users to more readily find data of interest, the results for a FreestyleLM search from the Home Page are now organized into categories based on domain objects.

2. Inclusion of all Entrez Genes
caBIO now provides all human and mouse genes from Entrez Gene. For details, please see the caBIO Data Release Notes.

Documentation Index

• caBIO 4.3.1 Data Refresh Release Notes(September 2010)
• caBIO 4.3.1 Data Refresh Release Notes(May 2010)
• caBIO 4.3.1 Release Notes
• caBIO Javadocs Online (Download)
• caBIO 4.3.1 Technical Guide
• caBIO Object Model in HTML (Download EA model)
• caBIO Data Sources

caBIO Code Examples using Entrez As a Base Gene Model

The new Entrez Gene data will be available through the existing caBIO APIs. Below are coding examples demonstrating the query of gene information using DatabaseCrossReference.

1.     Querying for a Entrez Gene (BRCA1) and Get Pathways

...

DatabaseCrossReference dbRef = new DatabaseCrossReference();
dbRef.setDataSourceName("Entrez"); // Entrez
dbRef.setCrossReferenceId("672"); // Entrez Gene Id for BRCA1
List<DatabaseCrossReference> refList = new ArrayList<DatabaseCrossReference>();
refList.add(dbRef);
Gene gene = new Gene();
gene.setDatabaseCrossReferenceCollection(refList);
try
{
   List<Gene> resultList = appService.search(Gene.class, gene);
   for (Gene g : resultList) {
       System.out.println("Symbol: " + g.getSymbol());
       System.out.println("Name: " + g.getFullName());
       System.out.println("Taxon: " + g.getTaxon().getScientificName());
       Collection<Pathway> pathways = g.getPathwayCollection();
       for(Pathway p : pathways)
       {
            System.out.println(" Pathway: " 18 + p.getName()+" ("+p.getSource()+")");
       }
    }
} catch {}

The following is the output:

...

New Features and Updates

Old Archive Releases

For caNanoLab

...

Symbol: BRCA1
Name: Breast cancer 1, early onset
Taxon: Hs
  Pathway: h_atmPathway (BioCarta)
  Pathway: h_atrbrcaPathway (BioCarta)
  Pathway: h_bard1Pathway (BioCarta)
  Pathway: h_carm-erPathway (BioCarta)
  Pathway: h_g2Pathway (BioCarta)
  Pathway: h_ATM_mediated_phosphorylation_of_repair_proteins (Reactome)
Pathway: h_Recruitment_of_repair_and_signaling_proteins_to_double_strand_breaks (Reactome)

2.     Querying for a Unigene Gene (BRCA1) and Get Pathways

...

DatabaseCrossReference dbRef = new DatabaseCrossReference();
dbRef.setDataSourceName("Unigene"); // Unigene
dbRef.setCrossReferenceId("Hs.194143");  // Unigene Cluster Id for BRCA1
List<DatabaseCrossReference> refList = new ArrayList<DatabaseCrossReference>();
refList.add(dbRef);
Gene gene = new Gene();
gene.setDatabaseCrossReferenceCollection(refList);
try
{
    List<Gene> resultList = appService.search(Gene.class, gene);
    for (Gene g : resultList) {
       System.out.println("Symbol: " + g.getSymbol());
       System.out.println("Name: " + g.getFullName());
       System.out.println("Taxon: " + g.getTaxon().getScientificName());
       Collection<Pathway> pathways = g.getPathwayCollection();
       for(Pathway p : pathways) {
           System.out.println("  Pathway: " + p.getName()+" ("+p.getSource()+")");
       }
    }
} catch {}

The output is same as in example 1) above.

Old Archive Releases

For caBIO Archive Releases, please follow the link here.