Cancer Bioinformatics Infrastructure Objects (caBIO)
By Himanso Sahni
Sr.Software Engineer, NCI/SAIC
Building common infrastructure components to facilitate data integration amongst a variety of scientific disciplines is an essential element in today's biological research. To provide a multi-disciplinary approach to data integration, the National Cancer Institute Center for Bioinformatics (NCICB) established the cancer Bioinformatics Infrastructure Objects (caBIO) project. The caBIO project provides a robust platform independent infrastructure that illustrates data integration techniques that allow researchers to perform innovative analysis via a variety of APIs and web services. The initiative employs industry-standard software engineering methodologies to develop objects, data models, middleware, vocabularies and ontologies for biomedical research.
caBIO is the primary programming interface to caCORE, a synthesis of software, vocabulary, and metadata models for cancer research. caBIO objects are implemented using Java and Java Bean technology, and represent biological and laboratory entities such as genes, chromosomes, sequences, SNPs, libraries, clones, pathways, and ontologies. caBIO provides uniform API access to a variety of genomic, biological, and clinical data sources including Unigene, LocusLink, Homologene, Biocarta, Golden Path, DAS servers, CGAP, NCI Enterprise Vocabulary Services, and clinical trials protocols. 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.jar file. Non-Java based applications can communicate via SOAP services or by using the caBIO HTTP API and receive objects as XML. All caBIO objects can be transformed into XML, and XSL/XSLT is used to present data in documents, web pages or other interfaces. Since caBIO provides a web services interface, making caBIO available via universal registries such as bioMOBY or UDDI is planned for the future.
caBIO is an open source project build upon open source technologies such as Java, SOAP, Apache, Jakarta Tomcat, SVG, XML and UML. Users can download caBIO version 1.0 and learn about its open source license at http://ncicb.nci.nih.gov.