The cancer Bioinformatics Infrastructure Objects (caBIO) model and architecture was the first model-driven information system built
using caCORE, a synthesis of software, vocabulary, and metadata models for cancer research.
Each of the caBIO domain objects represents an entity found in biomedical research such as Gene,
Chromosome, Sequence, SNP, Library, Clone, and Pathway. Examining the relationships between these objects can reveal
biomedical knowledge that was previously buried in the various
primary data sources.
caBIO data can be accessed via a robust, platform-independent set of data services developed using the caCORE
data integration techniques.
Researchers are able to perform innovative analysis on caBIO data via a variety of APIs, web services, and html interfaces.
Consistent with other caCORE software products, caBIO data services are an open source project built upon
open source technologies and standards such as Java,
SOAP, SVG, XML, and UML.
Users can access caBIO in a variety of methods. Java-based clients communicate with caBIO via the Java API
which contains the domain objects provided by the caBIO client.jar file. Developers can download the caBIO
client.jar file and directly use its packages in their programs. Each Java bean object class in the caBIO
domain packages acts as its own search criteria object and provides methods for the retrieval of attributes and
related domain objects. Non-Java based applications can communicate via SOAP services or by using the
caBIO HTTP API and receive objects as XML. The caBIO Home Page
is a convenient way to search and retrieve data via HTTP queries. By default, it returns HTML objects,
but the generated query can be edited to return the XML object by simply changing the
"...//GetHTML?query=..." to "...//GetXML?query=..." in caBIO Home Page results. All caBIO objects can be
transformed into XML, and XSL/XSLT is used to present data in documents, web pages or other interfaces.
caBIO provides the following utility APIs:
- XML Utility
caBIO includes a utility class that provides the capability of converting caBIO domain objects between native Java objects and XML serializations. This allows applications using the caBIO API to quickly persist any caBIO domain object as XML representation to share or store.
- Manipulating Scalable Vector Graphics (SVG) Diagrams
 caBIO provides a utility class called SVGManipulator for manipulating pathway SVG diagrams. BioCarta and its Proteomic Pathway Project (P3) provide detailed graphical renderings of pathway information. NCI's CMAP web site captures pathway information from BioCarta, and transforms the downloaded image data into SVG representations that support interactive manipulation of the online images.
- Utilities for Text Search Manipulation
The caBIO API provides a full text search (Google™-like search) capability known as the FreestyleLM (Freestyle Lexical Mine). The FreestyleLM search component consists of interfaces and APIs for conducting horizontal searches across caBIO domain objects. For example, when searching for “brca1”, the FreestyleLM search capability will return any object that makes mention of the “brca1” gene in its attributes, such as Genes, Proteins, Pathways, etc.
- Genome Range Queries
The Range Query API provides an alternative way to search for
genomic features on a chromosome, based on the physical locations. The API is capable of
performing arbitrary range searches on any given chromosome (absolute search), or
range searches around a feature of interest (relative search).
- Array Annotation API
This client-side convenience API is intended for users of the
Microarray annotations in caBIO. The API simplifies access to bulk microarray annotations such as reporters, genes, and SNPs.
The caBIO 4.x+ software code, object model, use cases, and user documentation are
available for use under an open-source license.
Please visit the
caBIO area of our Downloads Center for access to the relevant files and
licensing information. The caBIO 4.x+ release involved a separation of
caBIO from the caCORE infrastructure to allow for continued and
frequent enhancements to caBIO genomic annotations. As such,
caBIO 4.x provides support for the caBIO API only. Access to the caCORE 3.2
release, which contains caBIO, the caDSR, and EVS APIs is available for download
on the caBIO download site in the archives section of the page. The caBIO 4.x
licensing agreement applies.
For information on obtaining the caBIO schema, data, and instructions for installing the caCORE database, please contact the NCICB Help Desk.
NCICB maintains the following mailing lists as discussion forums with caBIO users and developers:
- caBIO GForge - Project site for users and developers of caBIO. Includes documentation, source code, and feature requests.
The ODI is a way to contribute to caBIO and expand its capabilities. The following projects are currently available under the ODI:
NCICB encourages you to submit questions and bug reports via NCICB Application Support .
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