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The information and links on this page are no longer being updated and are provided for reference purposes only.

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Release History

Release

Date

4.3.2

September 2012

4.3.1 Data Refresh

September 2010

4.3.1 Data Refresh

May 2010

4.3.1

January 2010

4.3

July 2009

4.2

January 2009

4.1

May 2008, retired June 2012

4.0

December 2007, retired June 2012

Documentation Index

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.

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.setClusterId(new Long(443914)); // SOD1
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)

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.setClusterId(new Long(443914)); // SOD1
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 this link.

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