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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 API calls and pull data directly from caBIO. These APIs expose all of the Cancer Gene Index data, metadata, and annotations and also allow you to 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 below. Blue classes are core biological entities, whereas green classes are annotations on the core entities. The caBIO 4.3.1 model may be viewed in its entirety on the caBIO gForge page, but modeling tool Enterprise Architect is required to view the file.
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.
