05_ChEBI_ontology_explorer

Explore the ChEBI Ontology

In this example an ontology in OWL format was used.
After loading the OWL file using the Triple File Reader node, the triples will be stored in a SPARQL Endpoint that allows then to write SPARQL queries to get some usefule data.
When this first step is done, the workflow is containing furthr interaction points where a search query needs to be defined (to search for compounds with a certain substructure and role) and different views can be used to explore the content of ChEBI.

The example workflow can be explored within five steps:

Step 1. Read chebi.owl and insert triples into SPARQL Endpoint
Step 2.* Enter a molecule to search the ontology for chemical compounds containing a certain substructure
- enter a valid SMILES, e.g. N1C2=CC=CC=C2SC2=CC=CC=C12
- enter a role of your interest (e.g. dopaminergic antagonist)
Step 3.* The Tile View shows a list of compounds which match the search query from Step 2. Here only one compound should be selected to go to the next step.
Step 4.* The composite view shows more information about the selected compound. At this point two roles can be selected to go to the next step.
Step 5. Simple Tile View showing results from Step 4.
*User action is needed: Execute + Open Interactive View

Recommendation: increase the memory in your knime.ini as the workflow is loading the whole ontology file into the Memory Endpoint. This will improve the performance of the workflow!

References:
Hastings J, Owen G, Dekker A, Ennis M, Kale N, Muthukrishnan V, Turner S, Swainston N, Mendes P, Steinbeck C. (2016). ChEBI in 2016: Improved services and an expanding collection of metabolites. Nucleic Acids Res.

External resources

• Blog article: Exploring a Chemistry Ontology with KNIME
• ChEBI Ontology