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caBIO End User Scenarios

caBIO provides the research community with access to a variety of integrated biomedical data to address molecular annotation needs. An example follows of a high-level user scenario demonstrating potential uses of caBIO.

A researcher studying the "CHEK2" gene for links to breast cancer needs a complete list of known SNPs located on this gene. caBIO can be leveraged to retrieve SNPs for a given gene symbol “CHEK2”.

caBIO End User Access

The caBIO Home Page, portlet, and iPhone App provide access to caBIO data for end users.

  • caBIO Home Page – The caBIO Home Page is the entry point for browsing and querying caBIO data from caBIO search criteria. The caBIO Home Page also provides a full text search capability facilitating a keyword search.
  • caBIO Portlet– The caBIO Portlet is a user interface component that operates within the caGrid® Portal as a community service. The caBIO Portlet provides a simple search for performing keyword queries and a templated-based search allowing users to execute pre-defined queries. Currently, the caBIO Portlet provides support for the following templated searches:
    • Genome Range Queries – Absolute range queries by Taxon or Chromosome
    • Microarray Annotations – Reporter lookup by Gene, SNP, or Reporter Name
    • Genomic Annotations – Gene lookup by Gene symbol or HUGO symbol and Gene Ontology Lookup by Protein.
    • Pathways – Pathway search by Pathway name, Pathway by Source/Provider, Pathway by Protein, or Gene symbol
    • Cancer Gene Index – Search for Diseases or Agents associated with a Gene
  • caBIO iPhone App – The caBIO iPhone App allows researchers to query for genomic annotations (genes, chromosomes, pathways, diseases, agents, etc.) from the Apple iPhone. For example, leveraging the caBIO iPhone App, a researcher can query for information on BRCA1, a gene associated with breast and ovarian cancers, and retrieve information on the gene and its location on the chromosome, a list and visualization of cellular pathways in which the gene participates in, a list of diseases associated with BRCA1 with supporting evidence information, and agents (drugs and other therapies) used to target the gene. Having access to this information via a mobile device enables on-the-spot hypothesis testing and fosters scientific collaboration through “tele” research.
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