An RDFBones ontology extension modelling the acquisition routine for pathological data developed by the Phaleron Bioarchaeological Project. Besides the RDFBones core ontology, it also depends on the standards-patho ontology extension.
We are using the ROBOT tool for developing the first version of the ontology extension. The relevant files are in the robot branch of this repository.
Specifications of ontology elements are in a series of template files in the tab-separated value format (.tsv). From these, the web ontology language (.owl) file is compiled using the script Script_PhaleronPatho-Robot.sh. To execute, navigate to the directory containing the file and run the scipt as
./Script_PhaleronPatho-Robot.sh -b -c -u
The output will appear in a newly created directory 'results' and consist of the single file 'phaleron-patho.owl'.
The scipt generates a series of intermediate files during the compilation process. To obtain these in the 'results' folder, drop the '-c' ('clean-up') option when executing the script.
Compilation relies on the standards-patho ontology extension which is included in a submodule (./dependencies/StandardsPatho/) within this repository. The script automatically updates the submodule as long as the '-u' (update) option is set. Through the submodule, version 0.2 of the RDFBones core ontology is also made available.
The '-b' (build) option causes the script to compile the output file. Use the script without this option to update the submodule or clean up a previously compiled output.