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.
Note : 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
Stores represent the ability store RDF and OWL representations. These tool provide support for larger data sets, and datasets which can be used in a way which will allow for some amount of use within service environments. Although the tools listed below are open source, there are also non-open source tools which provide similar functionality including AlegroGraph and Oracle 11G. These system may also use Jena or Sesame for access.
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 Sails : http://www.openrdf.org/- Sesame provides a way to integrate various representations for access (called SAILS). Sesame sails have been created for in-memory, Relational Database, and a verity of other formats.
db2rq : http://www4.wiwiss.fu-berlin.de/bizer/d2rq/spec/ - Not technically a general purpose store, db2rq provides a semantic reference layer to existing RDBMS environment, allowing for SPARQL and other interactions within a given environment.
Note : These systems can also interact. Specifically Jena can access Sesame through a model factory component and Sesame can access Jena through a SAIL. This does not indicate compatibility, but rather an abstraction. This means that the database tables created by Jena SDF do not match the RDBMS tables generated by Sesame. However, as an example, code written using Jena as an interface, if written correctly, can be independent of the persistence method.
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 : http://www.springsource.org/ - Spring provides a number of components which are designed to either ease the adoption of new technologies, or to provide greater control over certain integrations. The number of Spring components is large, however, some significant components include Spring Framework, Spring Flow, Spring Web Services, and Spring Security. These components are all based on certain core patterns that make components more flexible.
Design
OWL and RDF provide the ability to represent information both as metadata as well as functional components of a system. As a result, individuals may produce RDF or OWL ontologies which will be integrated into the fabric of the system. In addition to the standard tools supported by CBIIT relating to design, the use of good ontology editors will help promote the consistency of representation and functionality. In some senses these are IDEs in the fact that development occurs, however, they can also be considered as PSM design tools because the output becomes a documentable model representation.
Protege 4 : http://protege.stanford.edu/ - Developed and supported at Stanford University, Protege has been used for Ontology development for many years. Protege 4 is an attempt to reach beyond the Frame based roots of Protege and provide a newly envisioned representation of OWL ontologies. Protege 4 utilizes the OwlAPI for accessing owl ontologies and so shares it's limitations. Specifically it does not support persistence to general purpose triple stores, and must be able to load the ontology entirely in memory. However, the use of the OwlAPI in design and editing where it is appropriate, give Protege 4 a performance advantage in the loading of ontologies, and provide unique functionality as it relates to ontology integration. Protege 4 is an Eclipse RCP Application.
TopBraid Composer : - Available in both a community edition as well as a paid license version. TopBraid Composer Community Edition provides an eclipse plugin based approach to ontology editing. This allows for the integration of other tools via the OSGI standard, as well as provides a basis for using other eclipse based tools. TopBraid Composer uses the Jean tool to access ontologies and shares it's limitations. In addition, the community edition is limited to the editing of OWL or RDF files and does not support access of database stores. It does support SPARQL as part of it's functionality, and utilizes the Eclipse approach of projects.
Note : Since there is no open source or community tool for accessing stores other then text files, many developers use Protege 4 or TopBraid Composer, and then create scripted or programed solutions to upload models into those stores. However, there are other significant addition to functionality in the paid versions of TopBraid Composer that are not addressed here.
Rules and Expert Systems
Pellet -
Fact++ -
Hermit -
Jess -
TopBraid SPIN -
Workflow
Open ODE
Bonita
