org.mmisw.ont - The MMI Ont service Carlos Rueda - carueda@mbari.org $Id$

org.mmisw.ont is a Web service that supports programmatic interaction with a BioPortal repository instance as well as ontology and term URI dereferencing for users and clients in general.

= Using the service =

The following description assumes http://example.net as the base address of the involved services. In particular, the Ont service address would be http://example.net/ont. However, note that the code is written in a way that is independent of the actual server and root components in the URI.

A central functionality is that any URI that starts with "http://example.net/ont/" is resolved by this service, for example: "http://example.net/ont/mmi/someVocab". Resolution means that the given URI is used to search for the corresponding ontology in the database. If found, the contents of the ontology is returned to the client in the appropriate format according to content negotiation or explicit file extension or "form" parameter if given.

= Requirements =

== BioPortal back-end ==

The Ont service requires a running instance of the BioPortal back-end in the same machine. Please see ReadMe-BioPortal.txt for instructions to build and deploy the BioPortal back-end so it can be used by the Ont service.

== AllegroGraph triple store server ==

Although the Ont service can operate with various triple store implementations, the most robust option at the moment is AllegroGraph (http://www.franz.com/agraph). Please have an AllegroGraph server running somewhere in your network.

Here are some quick instructions:

• Download the package for your environment from http://www.franz.com/agraph/downloads/
• Extract the contents into /some/directory/ of your choice
• cd /some/directory/
• sudo ./AllegroGraphServer The server continues running in the background. The log file is /some/directory/agraph.log. You can of course instruct your OS to launch this server at boot time. It is highly recommended that you install the most recent stable version of AllegroGraph.

= Building and deploying the Ont service =

Using latest code image from trunk in the SVN repository: cd SOME_DIRECTORY svn checkout http://mmisw.googlecode.com/svn/trunk/org.mmisw.ont cd org.mmisw.ont cp sample.build.properties build.properties

Edit build.properties and complete/adjust the following as appropriate, for example: appserver.home = /usr/local/tomcat appserver.host = http://example.net aquaportal.resource.directory = /mmiorr_workspace/bioportal/resources aquaportal.voc2rdf.dir = /mmiorr_workspace/mmiregistry/preuploads/voc2rdf/ aquaportal.jdbc.url = jdbc:mysql://localhost:3306/bioportal aquaportal.jdbc.password = THE_ACTUAL_PASSWORD aquaportal.rest.url = http://example.net/bioportal/rest agraph.host = localhost agraph.ts.dir = /mmiorr_workspace/mmiregistry/agraph/ts portal.service.url = http://example.net/orr ont.internal.dir = /mmiorr_workspace/mmiregistry/internal ga.uanumber = UA-00000000-0 ga.domainName = example.com ga.dir = /mmiorr_workspace/mmiregistry/ga More details in build.properties.

Some of the mentioned working directories need to exist so: mkdir -p /mmiorr_workspace/mmiregistry/agraph/ts mkdir -p /mmiorr_workspace/bioportal/resources mkdir -p /mmiorr_workspace/mmiregistry/preuploads/voc2rdf mkdir -p /mmiorr_workspace/mmiregistry/internal mkdir -p /mmiorr_workspace/mmiregistry/ga

We're ready to build Ont, but the following is needed so the MySQL JDBC driver is found at runtime: the driver library should be located under Tomcat's lib/ directory. If not already there, make a copy (for example, using the library coming with BioPortal, mysql-connector-java-5.1.6-bin.jar) and restart Tomcat.

Now: ant war ant deploy-war # you may need to run this as 'root' (eg., with sudo)

Inspect the ont.log and catalina.out logs (under /usr/local/tomcat/logs/) to verify the installation.

= Change log =

See ChangeLog.txt