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Overview
caBIO is a resource that integrates biomedical data on genes, proteins, clinical protocols, disease ontologies, pharmacological agents, pathways, and other entities with annotations, controlled vocabularies, and metadata models originating from twenty-three data sources, including the Cancer Gene Index, the Pathway Interaction Database, and the University of California, Santa Cruz Distributed Annotation System.
The caBIO APIs allow end users who are familiar with programming interfaces to make calls and pull data directly from caBIO. These APIs expose all of the Cancer Gene Index data, metadata, and annotations. Thus, you can use these APIs to evaluate the evidence from which these associations were extracted and the codes and details that describe these associations. Other annotations, such as sentence status flags, negation indicators, cell line indicators, and organism are information-rich. Additional information is available in the #Using the Cancer Gene Index subsection below.
You may also uncover associations between these data and other information within caBIO (e.g., protein annotations, pathway data, tissue data, or clinical protocols).
Be Careful
To effectively use the caBIO APIs, you should have some understanding of the caBIG® philosophy and a deep understanding of the caBIO object model. If you do not have this knowledge and only wish to explore Cancer Gene Index data, it is highly recommended that you start with the Gene-Disease and Gene-Compound XML. Once you become more comfortable with caBIG® technologies and practices or you would like to take full advantage of caBIO, then begin to use the APIs.
Even with knowledge of caBIO object model, you may still find it difficult to construct more complicated queries. For your convenience, the subset of caBIO classes that are associated with Cancer Gene Index data are shown here.
The caBIO APIs
caBIO 4.3 APIs include, but are not limited to, Java, Python, Perl, .NET, REST, REST with AJAX, and XML-HTTP. For additional information on any of these APIs, please refer to the caBIO wiki.
Sharing Your Code
As you use the caBIO APIs to explore Cancer Gene Index data, you are strongly encouraged to share your code and additional documentation on the Cancer Gene Index Parsed Data and Code wiki page.
