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Explore the ChEBI Ontology

Owl Chebi Ontology Ontologies SPARQL
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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

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

Used extensions & nodes

Created with KNIME Analytics Platform version 4.1.2
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    KNIME Base Chemistry Types & Nodes Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.1.1

    KNIME profile image
    knime
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    KNIME Core Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.1.2

    KNIME profile image
    knime
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    KNIME Expressions Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.1.0

    KNIME profile image
    knime
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    KNIME JavaScript Views Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.1.2

    KNIME profile image
    knime
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    KNIME Network Mining Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.1.0

    KNIME profile image
    knime
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    KNIME Quick Forms Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.1.2

    KNIME profile image
    knime
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    KNIME Semantic Web Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.1.0

    KNIME profile image
    knime
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    KNIME SVG Support Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.1.0

    KNIME profile image
    knime
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    RDKit KNIME integration Trusted extension

    NIBR

    Version 4.0.1

    manuelschwarze
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