Skip to content

Latest commit

 

History

History
40 lines (31 loc) · 7.54 KB

README.md

File metadata and controls

40 lines (31 loc) · 7.54 KB
Raw

ROBOT Template For RDFBones Ontology Extensions

This is a ROBOT template for authors of ontology extensions to the RDFBones core ontology. ROBOT is a tool for the development of ontologies that are based on the Resource Description Framework.

To use this template, you need to install ROBOT, following the instructions on their website.

All files required by ROBOT are on the 'robot' branch.

How To Use the Template

Note that within the bash script 'Script-Build_OntologyExtension-Robot.sh comments addressing users are formatted like this:

## This is what you need to do

## ***************************

Create a duplicate of this repository, either by using GitHub's templating mechanism or by cloning. Then take the following steps:

  1. Check out the 'robot' branch.
  2. Open the file 'prefixes.json' in a text editor. Replace the last line, "template" : "http://w3id.org/rdfbones/ext/template/" with a prefix for your own extension. You need to define a prefix (replacing template) and a URI (replacing http://w3id.org/rdfbones/ext/template/).
  3. If your extension has dependencies (i.e. needs other RDFBones ontology extensions to work) other than the RDFBones core ontology, add their repositories as git submodules in the directory dependencies.
  4. Open the bash script 'Script-Build_OntologyExtension-Robot.sh. If your extension has dependencies that need the execution of some script to be built, add the required commands beneath line 128. Use the commands for building the RDFBones core ontology in lines 124 to 128 as an example.
  5. If you have added dependencies, add the required files from the submodules you have created above as additional input to the merge command in line 141.
  6. In the bash script, change the contents of the annotations in lines 6 to 16 to suit your extension. The annotation 'shortname' determines the name of the OWL file the script produces. Several creators or contributors can be specified as arrays. In the output file, each person will have its own statement.
  7. Open the file 'template-category_labels.tsv' in a spreadsheet editor. Lines 1 and 2 contain header information that you need to keep by all means. The following lines contain definitions for some sample entities. Replace these with definitions for your own extension. Use the prefix defined above. If your extension does not contain any categorical labels, just delete the lines with the sample entities.
  8. Open the file 'template-value_specifications.tsv' and process value specifications in your extensions in the same way as explained above for categorical labels.
  9. Open the file 'template-data_items.tsv' and process data items in your extension in the same way as explained above for categorical labels.
  10. Open the file 'template-data_sets.tsv' and process data sets in your extension in the same way as explaihttps://github.com/RDFBones/ExtensionTemplate/blob/robot/Script-Build_OntologyExtension-Robot.shned above for categorical labels.
  11. Open the file 'template-assays.tsv' and process assays in your extension in the same way as explained above for categorical labels.
  12. Open the file 'template-data_transformations.tsv' and process data transformation processes in your extension in the same way as explained above for categorical labels.
  13. Open the file 'template-conclusion_processes.tsv' and process conclusion processes in your extension in the same way as explained above for categorical labels.
  14. Open the file 'template-study_design_executions.tsv' and process study design execution processes in your extension in the same way as explained above for categorical labels.
  15. Open the file 'template-protocols.tsv' and process protocols that your extension is based on in the same way as explained above for categorical labels.
  16. Open the file 'template-study_designs.tsv' and process the study design of your extension in the same way as explained above for categorical labels.
  17. Open the file 'template-planning.tsv' and process the planning process of your extension in the same way as explained above for categorical labels.-
  18. Open the file 'template-investigations.tsv' and process information about the investigation your extension describes in the same way as explained above for categorical labels.
  19. Open the file 'template-roles.tsv' and process information about roles taken by persons and objects in the investigation your extension describes in the same way as explained above for categorical labels.
  20. Open your local instance of the repository in the terminal and execute the bash script: ./Script-Build_OntologyExtension-Robot.sh -u -b -c Type ./Script-Build_OntologyExtension-Robot.sh -h to get a list of all available options. You will find the OWL file of your extension in the ./results/ directory.
  21. To add documentation resources, check out the 'main' branch. In the 'doc' directory, there are templates for concept drawings and network graphics that you can use to create drawings describing your ontology extension. Note that these files work best with the draw.io software.

A good strategy is to delete all dummy data from the ROBOT templates before entering your own content. This gives you the option to run the bash script any time you want to test if a template you have created resolves or throughs some errors. Step-by-step validation helps to spot bugs early and prevents tedious debugging in the end.