Muhammad Javed Cornell University Nov 20, 2015
- VIVO Ontology extends a number of higher-level ontologies such as BIBO, OBO, FOAF, VCARD, EVENT etc.
- The purpose of this project is to parse the vivo ontology file into its separate ontology modules.
Step 1: Convert .owl (or any other format) ontology file into .nt file.
Step 2: Manually Identify the namespaces you would like to capture and link them to an ontology module. This is done by
- printing out the list of namepsaces first (method: browseNamespaces(Model model)).
- exploring the master .nt file mannually and linking different namespaces to their specific ontology modules. (in java class Namespace.java)
Step 3: Running the process (main class: VivoOntologyParser.java). The ontology modules will be saved in resources/nt or resources/rdf folder (depending upon the selected output format) The unmapped triples will be saved in the resources/unmapped folder.
Step 4: Look at the unmapped triples manually (in file resources/unmapped/unmapped.txt) and add them in their specific ontology modules manually. for example http://purl.org/net/OCRe/study_design.owl http://www.w3.org/2000/01/rdf-schema#label "OCRe study design" . goes to the OCRE_SD.nt ontology module file.
Step 5: If needed, convert .nt files into .rdf using rdf2rdf-1.0.1-2.3.1.jar Run the Java Application RDFModuleGenerator.java in package edu.cornell.vivo.rdfmodulebuilder
Resources Folder's description:
- resources/input: contains the (merged) vivo-isf-1.6 ontology (in owl and nt format)
- resoueces/jar: consists of external jar file used to convert nt files into rdf.
- resources/nt: This is the output folder for .nt format ontology modules. If the output format is selected as nt (VivoOntologyParser.java line 63-66), the application saves the splitted ontology modules in this folder.
- resources/rdf: This is the output folder for .rdf format ontology modules. If the output format is selected as rdf (VivoOntologyParser.java line 63-66), the application saves the splitted ontology modules in this folder.
- resources/unmapped: The unmapped triples of the source (input) file are saved here. A person need to look into them manually in order to decided which ontology modules they belong to.
- resources/final-rdf: This is the output folder for RDFModuleGenerator.java. VivoOntologyParser split the source file into ontology modules in nt format. Once unmapped triples are manually added in their relevant ontology modules, RDFModuleGenerator.java can be used to convert these nt format ontology modules into rdf formats. This converter uses the rdf2rdf-1.0.1-2.3.1.jar jar file saved in the resources/jar folder.