Ontologies

Ontologies are descriptions used in creating resource description graphs hosted by providers which state what data and tools they are making available. These descriptions are somewhat analogous to DDL (Data Description Language) used to define tables and columns in SQL. The descriptions for the VPIN platform are written in OWL. It may be useful to use an ontology development tool such as Protege. The description files can be hosted on the providers' website (e.g. TIGR ontologies ) or at another location ( e.g. http://ontologies.ncgr.org ). Either way, sharing ontologies is a great idea since it can cut down on redundant work and can also provide a grassroots standard for commonly used data types and tools.  If you would like to host your ontologies at http://ontologies.ncgr.org  just let us know by attaching your files to a request on the forum under the Ontology Development topic.

The underlying SSWAP platform uses ontologies in an atomic fashion to ensure the ability to access class and property descriptions via a simple http GET command (programmatically, through a browser or from the command line, e.g. WGET). Tools such as Protege produce one encompassing file for all the class and property descriptions created for an ontology. Use this tool on a single owl file to split it into its component parts, create OWL documentation for it and generate a zip file for easy attachment to the forum for hosting in a shared repository.

To validate your ontology graphs against OWL, use this url.

The SSWAP protocol ( the specification for resource description graphs for VPIN ) is itself an ontology hosted at. Its OWL documentation is available here.

OBO to OWL converter tools! 10/27/06
Java code for two conversion strategies, class files, and the output from running both strategies is available for download here.