The caBIO 4.3.1 is the minor release with some enhancement in FreeStyleLM Search Summary page and introduction of the Entrez-Gene dataRelease 1.5.3 focuses on 508 compliance, defect fixes and minor enhancements for the web application.

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:

...

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)

Release notes for release 1.5.2 and prior can be found on the GForge project files tab archive.

New Features and Updates

• CANANOLAB-3 - Back button on sample search results
• CANANOLAB-13 - Upgrade for BDA-Lite build script
• CANANOLAB-29 - Include the data submission date in search results
• CANANOLAB-32 - Add URL field to protocol submission
• CANANOLAB-33 - Disable the statistics polling feature on the caNanoLab home page
• CANANOLAB-34 - Add external link disclaimer 
• CANANOLAB-36 - Update protocol search results sorting to be per page only
• CANANOLAB-37 - Updated Protocol File column in Protocol Search Results

Bugs Fixed Since Last Release

• CANANOLAB-5 - Set Column Order functionality on Data Conditions before saving the data matrix
• CANANOLAB-7 - Broken link on home page
• CANANOLAB-8 - Remediate for 508 Compliance
• CANANOLAB-18 - Remediate App Scan vulnerabilities
• CANANOLAB-31 - Update PubMed Link
• CANANOLAB-40 - Advanced Sample Search with OR not working correctly
• CANANOLAB-43 - Publication Submission: Author list disappears after adding Access to Publication

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

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