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! - ChEBI ontology can be downloaded here: https://www.ebi.ac.uk/ols/ontologies/chebi 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.
This is a companion discussion topic for the original entry at https://kni.me/w/ksItoNKSSVPzL2Gw