Overview of caBIO
caBIO (cancer Bioinformatics Infrastructure Objects) is a repository of molecular biology data. The entities that concern the Central Dogma of Molecular Biology are the core of the model. Data for the classes come from a variety of sources, including CGAP, Unigene, and the Cancer Gene Index, as well as a number of array manufacturers (for microarray annotations). Given the dynamic nature of this information, the data in caBIO is updated monthly through a series of ETL (Extract, Transform and Load) processes.
The caBIO home page provides access to caBIO data for end users. This simple interface allows users to gain access caBIO data by entering search criteria in the domain class or browser, or by using the Google™-like FreestyleLM search.
Programmatic access to caBIO data is provided by a robust, platform-independent set of data services developed using the caCORE data integration techniques. You can also set up your own caBIO server for data at your site.
Researchers are able to perform innovative analysis on caBIO data via a variety of Application Programming Interfaces (APIs), including Java and HTTP-XML, as well as web services and a service on caGrid. caBIO also provides a number of utilities to search for and manipulate data objects programmatically.
The caBIO download provides licensing information and access to the caBIO source code, web services, Java client.jar files, programming interfaces, use cases and documentation. Please contact NCICB Application Support to obtain the latest caBIO schema, database distribution and instructions for installing the database.
Graphical User Interfaces (GUIs)
- caBIO Home Page - includes a Query-by-Example (QBE)-style interface for browsing the object model
- caBIO Portlet - includes simple and templates searches
Application Programming Interfaces (APIs)
Java API
Java-based clients communicate with caBIO via the Java API which contains the domain objects provided by the caBIO cabioXX-beans.jar file. Developers can download the caBIO client API 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.
Web Services API
Non-Java based applications can communicate with caBIO via web services using the SOAP protocol. Currently, caBIO has a Python API which makes use of the web service.
XML-HTTP API
Also called the REST (Representational State Transfer) API, this interface allows users to query over HTTP and receive objects as XML.
caBIO Home provides 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.
See the page REST API with Ajax for information on using the REST API for quick access to caBIO data from your own web application.
caBIO Utilities APIs
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 an XML representation to share or store.
Manipulating Scalable Vector Graphics (SVG) Diagrams
caBIO provides a utility class called SVGManipulator for manipulating SVG diagrams of pathways. BioCarta and its Proteomic Pathway Project (P3) provide detailed graphical renderings of pathway information. NCI's CMAP website captures pathway information from BioCarta, and transforms the downloaded image data into SVG representations that support interactive manipulation of the online images. An SVG Viewer enables the display of SVG diagrams.
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, and Pathways.
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.
caBIO Grid Service
caBIO data can also be obtained via caBIO Grid Services on caGrid. The current caBIO grid services are found on the caGrid Portal.
Collaboration Opportunities
caBIO enables collaboration opportunities through an open development initiative that allows for the contribution of caBIO expanded capabilities. The following caBIO projects are made available through collaborative development efforts:
If you are interested in participating in collaboration activities, please contact the caBIO Users group.
Using the caBIO Wiki
This is the wiki home page for the caBIO product. caBIO developers may edit this page and any user may add a comment. | 
