 |
| Delve deeper into
"caCORE"
|
|
|
|
|
|
|
caCORE is open source software and services developed by the NCICB Core Infrastructure Group.
Providing a data management and application development framework
caCORE-based systems include the semantic underpinning for interoperable data and
analytical services. Two key components of caCORE are the Enterprise Vocabulary Services (EVS) and the
Cancer Data Standards Repository (caDSR). The caCORE Product Line includes the Software
Developer's Toolkit (SDK), Semantic Integration Workbench (SIW) and UML Loader,
caAdapter, CSM and CLM - products that when used
together simplify development of caCORE-like systems including deployment on caGrid.
The application source code and programming interfaces are available on
the NCICB Download Center.
(see below for latest release information for each product).
"caCORE-Like" Systems are those with information models
whose meaning is linked to EVS vocabularies; are registered in caDSR; are object oriented;
have open/public APIs
and web services for accessing the data. The caBIO data service is
an example of a caCORE-like system and was
developed using caCORE products.
caCORE product support includes an
NCICB GForge Project page for each project,
technical and programming guides, a description of the overall process
and role each product fulfills
in developing caCORE-like systems.
caCORE 4.0 product releases usher in a new generation of independently released products
and services,
as opposed to simultaneous "caCORE" releases, thus enabling product developers to be more
responsive to end user needs. See the links below for information about
caCORE products and related releases.
Major Enhancements in caCORE current releases include:
EVS 4.x:
EVS
is the first of the standalone caCORE services to be released under the new 4.0 architecture.
EVS has adopted a version of the open source
BioPortal
as the NCI EVS terminology browser
for use with EVS/caCORE4.x.
BioPortal was developed by the National Center for Biomedical Ontology (NCBO).
Effective with the 4.0 release, EVS offered a new LexBIG API as well as providing methods to
enable compatibility with applications developed using the older caCORE 3.2 EVS API.
Because adoption of the LexBIG terminology server
is a major change for EVS users, we continue to support
caCORE 3.2 servers. caDSR 3.2.X.X Releases:
The post caCORE 3.2 caDSR product releases provides performance and feature enhancements
including CDE and UML Model Browser navigation tree performance,
the ability to annotated inherited attributes in UML models using SIW
and a variety of features specific to each product.
See "Post 3.2 Incremental Release Notes" page for individual
caDSR product release notes.
caAdapter:
caAdapter now supports a web service to generate HL7 v3 messages. Applications can send source data to the web service and receive HL7 v3 messages in return. The latest version of caAdapter also has three new components including an object model to data model mapping service in support of caCORE SDK, a Regulatory Date Sets (RDS) mapping and transformation service, and an HL7 v2 to v3 conversion service.
caCORE SDK 4.0:
includes support for connecting multiple remote services from the same Java API client and
in addition to Enterprise Architect, there is now support for generating systems from
the open source UML tool ArgoUML. See
caCORE SDK
page for details! Common Security Module (CSM)/Common Logging Module (CLM) 4.0
CSM/CLM 4.0 release includes High Performance Instance Level Security, Attribute Level Security,
Support for Digital Certificate as credentials, Integration with caCORE SDK 4.0, 21 CFR Part 11 Readiness and
other features described on the
CSM and
CLM
pages. caBIO:
The caBIO domain objects are an example of a caCORE-like system.
See the caBIO product page for details!
 |
 |
Cancer Bioinformatics Infrastructure Objects (caBIO)
We create UML models of biomedical objects to facilitate data integration and consistent representation. These UML models are then implemented in Java as middleware that is connected to various cancer research databases. Java, WebService, and HTTP-XML programming interfaces to the NCICB-hosted data are available. You can also set up your own caBIO server for data at your own site. More...
|
 |
|
Cancer Data Standards Repository (caDSR)
Common Data Elements (CDEs) based on EVS thesauri and standard vocabularies are
developed by various NCI-sponsored organizations, including
caBIG™
 ,
and centrally stored and managed at NCICB in the Cancer Data Standards Repository.
caDSR leverages the ISO/IEC 11179 Information Technologies: Metadata Registries (MDR)
standard to harmonize, register and integrate user defined UML information models with existing
and new caDSR content. caDSR is comprised of a suite of tools for creating, sharing and deploying
CDEs including a public CDE Browser
that lets you search for data elements, create forms and download CDEs.
caCORE provide web services to access caDSR content programmatically.
The UML Model Browser
, now in its first full release, is specifically designed for
browsing registered UML information models.
The caDSR, based on open source standards, is freely available for use by other government agencies and for download and use by interested parties. More...
|
 |
|
Enterprise Vocabulary Services (EVS)
At the foundation of the caCORE "standards stack" is controlled vocabulary. The NCI Enterprise Vocabulary Services, a collaborative effort of the NCI Center for Bioinformatics and the NCI Office of Communications, develops the NCI Thesaurus and the NCI Metathesaurus , two broadly used vocabulary sources for cancer research. EVS also hosts and contributes to other standards, and works with vendors to create and improve tools for vocabulary development, curation and deployment. More...
|
 |
|
Common Security Module (CSM)
The NCICB Common Security Module (CSM) provides a flexible solution for application security and access control. CSM is intended to be used as a common starting point for any development team that has security requirements, and thus helps to avoid duplication of effort and inconsistent security implementations. CSM has three main functions: Authentication to validate and verify a user's credentials; Authorization to grant or deny access to data, methods, and objects; and User Authorization Provisioning to allow an administrator to create and assign authorization roles and privileges.
CSM offers an additional solution that works with the caCORE Software Development Kit (SDK). CSM-SDK Adapter, provides the ability to integrate CSM security, session management, and writeable APIs into SDK generated software. More...
|
 |
|
Common Logging Module (CLM)
The NCICB Common Logging Module (CLM) was chartered to provide a comprehensive solution to Audit and Logging objectives and also to prevent the duplication of the effort and time involved in developing a logging solution. CLM is flexible enough to allow application developers to integrate audit logging into almost any code design with minimal coding effort. This phase of the Common Logging Module brings the NCICB team one step closer to the goal of CFR 21 / part 11 (FDA) compliance. The CLM features include Event Logging, Object State Logging, Asynchronous Logging to database, Query API's and a web based Log Locator Tool.
More...
|
 |
|
caAdapter
caAdapter is an open source tool set that provides model mapping services in support of caCORE components and facilitates data mapping and transformation among different kinds of data sources including HL7 v2 messages, HL7 v3 messages, and Regulatory Data Sets.
caAdapter has a component-based architecture to support message development and reporting using standard data formats. It also integrates with other clinical trials applications such as caXchange. caAdapter provides web service access and APIs for easy application integration.
More...
|
- Java API -- caCORE offers direct access to the domain objects through the Java API. Developers can download the client.jar file and directly use its packages in their programs. Each java bean object class in the caCORE domain packages acts as its own search criteria object and provides methods for the retrieval of attributes and related domain objects.
- caCOREService. The caCOREService web service has a single endpoint (caCOREService) which provides SOAP based inter-application communication using the Apache Axis standard.
- HTTP-XML Interface -- Using the HTTP-XML interface, a user can submit a query to caBIO as a URL from a browser and retrieve the results of the query in XML. The HTTP interface leverages the GetXML service, which allows researchers to perform an operation and pass in the associated search criteria as parameters embedded in the URL. An XML document that contains the results of the query is returned. For example, a researcher can obtain an XML document containing information on the PTEN gene via http://cabioapi.nci.nih.gov/cabio40/GetHTML?query=Gene&Gene[@symbol=NAT2] (where 'query' indicates which domain object is requested, 'Gene[@symbol=NAT2]'is the search criterion. One or more search criterion-value pairs can be included.
NCICB provides access to the caCORE interfaces on its public servers. The underlying software code, object model, use cases, and user documentation are available for use under an open-source license. Please visit our the caCORE area of our Downloads Center for access the relevant files and licensing information.
Most of the caCORE components are available under an open source licensing mechanism -- and open source technologies are used wherever practical. caCORE is powered by a number of projects, including: HTTP Server , Tomcat , JBoss , Ant , JUnit , Struts , OJB , Hibernate , Xalan , Xerces , XML-RPC , Axis , Jakarta Commons , and POI . We use ZOPE and Plone for web site management.
|
