3. ROBOT report

A generic ontology quality control is run on EDAM using the ROBOT report command. ROBOT report is a command line tool calling a customizable list of SPARQL queries that ensure basic requirements for all ontologies following the OBO guidelines (e.g. presence of a licence, no more than one label in a entity) Some of these queries were modified to fit the EDAM properties declaration.

You can check out our custom selection of the robot SPARQL queries in our caseologue repository here.

3.1. Get started

You can access the ROBOT installation documentation here.

Once ROBOT is installed, you can run ROBOT report on EDAM using this command

ROBOT report --input <path to EDAM> --output <output tsv file> --profile report_queries.txt

This tool returns in the output tsv file a table of all the detected errors.

3.2. Test and output documentation

The output of the robot report tool is a tsv file compiling the detected error, warning and info. This tsv file has 5 columns.

  • Level: can be ERROR, WARNING or INFO depending on the settings in the report_queries.txt file.

  • Rule Name: the name of the SPARQL query run. If the SPARQL query is custom made the rule name is the name of the file without the ".rq" extension.

The 3 next columns report the rdf triplet that rose the error:

  • Suject: the URI of the concept that rose the error.

  • Property: the URI of the tested property.

  • Value: the object of the triplet.