README.md

CHEBI slim pipeline

1. You will need to have ROBOT installed on your system.
   • ROBOT can be downloaded from here with installation instructions: http://robot.obolibrary.org/
2. Ensure the latest release of CHEBI is in a new folder named "import" and is in OWL form.
   • This can be downloaded from https://www.ebi.ac.uk/ols/ontologies/chebi
3. Ensure your OBO file containing slim terms is in the "template" directory.
   • By default this is named molecule-tree.obo
     • If this is different please edit the molecule-tree.obo reference in the first command in "run_chebi_slim.sh" to your file name
4. Ensure extract.sparql is in the "sparql" directory.
   • By default, obsolete terms are also extracted into the final slim file.
     • If you do not want obsolete terms, uncomment the last filter statement in the extract.sparql file: #FILTER EXISTS {?s oboInOwl:id ?o}.#
     • If you wish to have a different annotation for your slim terms, this an also be changed in the extract.sparql file
       • Replace "chebi_slim" with your desired annotation. This can be anything relating to your desired slim.
5. Ensure owltools is in the "bin" directory.
   • More information on owltools available here: https://github.com/owlcollab/owltools/wiki
6. Run the following command on the command line: bash run_chebi_slim.sh
   • This will annotate a copy of CHEBI (chebi_annotated.owl) with the slim annotation and also extract the slim.
     • Comment out the last command in the run_chebi_slim.sh file if you do not wish to extract the slim.
   • The contents of this run_chebi_slim.sh file can be run as single commands on the command line if the entire pipeline is not desired such as in the above option

To re-use for other slims/different ontologies

1. Rename "chebi_slim" in the extract.sparql file to the new slim name.
2. Replace the molecule-tree.obo file or edit the molecule-tree.obo reference in the first command in "run_chebi_slim.sh" to your file name.
3. Replace any mention of chebi.owl to your new desired ontology.
4. Ensure any other desired changed to file names are replaced in all commands.