Assessment Report
This section will provide the Assessment Report generated during the prototyping phase.
Existing Tools
The collection of tools and libraries below are not exclusive to support SI functionality, but they have been identified as being able to possibly aid certain aspects of this project and the developed architecture. In general there are supported CBIIT application structures such as the Java platform, Tomcat, JBOSS, Ant, and Maven. This information is available at <<Insert Reference to CBIIT supported standards here >>. The tools listed below have not been formally described as supported by CBIIT at this time, however, they suggest the type of components and architecture that is expected to best satisfy the project requirements.
Triple Store Access
Access tools represent methods for interacting with information represented using RDF and OWL representations of metadata. In addition, these tools may provide additional support for inference engines.
Jena : http://jena.sourceforge.net/ - The Jena Semantic Web Framework is a tool for building semantic web applications. It provides a programmatic environment for RDF, RDFS and OWL as well as a SPARQL engine and rule-based inference. This is a general purpose tool that supports combinations of models in memory as well as support for transactional persistence of triples. Jena works well with ontologies with large numbers of classes and individuals which require read and write functionality.
OwlAPI : http://owlapi.sourceforge.net/- The OWL API is a Java API for reference implementation for creating, manipulating and serializing OWL ontologies. This interface provides a fast, in-memory representation for manipulating OWL ontologies. Provides persistence to OWL in XML format.
Sesame : http://www.openrdf.org/ - Sesame is an open source RDF framework with support for RDF Schema inferencing and querying.
ARQ : http://openjena.org/ARQ/ - Supports the W3C standard for RDF queries. This is packaged with Jena and can be used against Jena models.
Please note that these systems can be used in a combinatorial fashion. For example, OWL files created with OwlAPI can be read by Jena. However, Jena TDB is specific to Jena, and you must use Jena to access it. See below for persistence methods.
Semantic Knowledge Store
Jena TDB : http://openjena.org/TDB/ - This is an integration between the Jena model factory which provides a high speed persistence of RDF triples. Writes to this system are not fully transactional, and so care must be taken to manage transactions externally, were required.
Jena SDB : http://openjena.org/SDB/ - Provides a persistance model using a verity of RDBMS back ends. Utilizing JDBC connections, SDF persists into traditional tables the RDF triple information. This solution is fully transaction, but suffers from insert and query limitations for performance.
Sesame : Sesame provides a way to -
db2rq : -
Data Conversion and Artifact Access
These are tools which aid in the programatic access to artifact sources to aid in transformations and processing.
poi - http://poi.apache.org/ - Poi is a general purpose tool for accessing microsoft documents in the DOC, XLS, and traditional Microsoft proprietary format, in addition Poi also supports the openXML standard including Microsoft DOCX and related formats through the openxml4j api. Information for this standard can be found at http://www.openxml.biz/
OBO-Edit : http://oboedit.org/?page=index - For accessing OBO based ontologies the editor provides an API.
Eclipse EMF : http://www.eclipse.org/modeling/emf/?project=emf - For accessing models in XMI for conversion to other representations. Specifically the ecore component, but other aspects of the Eclipse EMF may be useful.
In addition the standard access tools for accessing RDF and OWL representations see above.
Integration Support
Spring -
Design
Protege 4 -
TopBraid Composer
Rules and Expert Systems
Pellet -
Fact++ -
Hermit -
Jess -
TopBraid SPIN -
Workflow
Open ODE
Bonita
