Icon

ChBEI_​ontology_​explorer

Explore the ChEBI ontology
Explore the ChEBI ontology This workflow shows how to query ontologies in KNIME. Here we concentrate especially on chemistry related topics using the ChEBI (Chemical Entities of Biological Interest) ontology that iscontaining a classification for chemical compounds and their biological, chemical roles and applications. In this example an OWL file was used, alternatively RDF, Turtle and others would be possible (with few adaptations in the workflow).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 differentviews can be used to explore the content of ChEBI. (See more detailed description of those single steps in the workflow description). Step 2* Step 1 Step 3* Step 4* Step 5 Add triples intoa SPARQL endpointRead chebi.owlQuery mol entity classes with rolesQuery all children* of "molecular entity" Memory Endpoint SPARQL Insert Triple File Reader SPARQL Query SPARQL Query Result View String Manipulation Enter SearchOptions Get compounds withselected "role" MoleculeSubstructure Filter Filter TripleFile Store Joining andGrouping View Compounds SharingSelected Roles NetworkVisualization SPARQL queries Explore the ChEBI ontology This workflow shows how to query ontologies in KNIME. Here we concentrate especially on chemistry related topics using the ChEBI (Chemical Entities of Biological Interest) ontology that iscontaining a classification for chemical compounds and their biological, chemical roles and applications. In this example an OWL file was used, alternatively RDF, Turtle and others would be possible (with few adaptations in the workflow).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 differentviews can be used to explore the content of ChEBI. (See more detailed description of those single steps in the workflow description). Step 2* Step 1 Step 3* Step 4* Step 5 Add triples intoa SPARQL endpointRead chebi.owlQuery mol entity classes with rolesQuery all children* of "molecular entity" Memory Endpoint SPARQL Insert Triple File Reader SPARQL Query SPARQL Query Result View String Manipulation Enter SearchOptions Get compounds withselected "role" MoleculeSubstructure Filter Filter TripleFile Store Joining andGrouping View Compounds SharingSelected Roles NetworkVisualization SPARQL queries

Nodes

Extensions

Links

Download

To use this workflow in KNIME, download it from the below URL and open it in KNIME:

Download Workflow
Created by: Martyna
Created at: 2019-04-26
On NodePit since: 2019-11-01
Last update: 2020-03-22
Created with KNIME version: v4.0.2
Tags: owlchebiontologyontologiesSPARQLsubstructure searchSPARQL query

Deploy, schedule, execute, and monitor your KNIME workflows locally, in the cloud or on-premises – with our brand new NodePit Runner.

Try NodePit Runner!