Icon

06. Integrating External Tools - solution

Integrating External Tools

Solution to "Integrating External Tools" exercise for basic Life Science User Training
- Retrieving data from a web resource via REST
- Converting XML output to a KNIME table




Activity: Use REST nodes to call an external web service- Configure the String Manipulation node so that it creates a new column called resource_url with the following format."https://www.ebi.ac.uk/chembl/api/data/molecule/<ChEMBL ID>.xml"- The new column contains a GET request URL with a coresponding ChEMBL ID.- Access the ChEMBL Rest API with the GET Request node- Use the XPath node to extract standard_inchi and standard_inchi_key- Use RDKit From InChI node to convert the standard_inchi column to RDKit molecules type. - Use Renderer to Image node to convert the RDKit molecules into images.- Display the result in a table viewOptional: Use the R Snippet to filter the standard_inchi and standard_inchi_key. Hint: You can use the Regex column filter template in the snippet with the expression: standard.* Display resultsList of ChEMBL IDsCreate resource urlExtract inchi Table View GET Request Table Creator String Manipulation XPath Renderer to Image R Snippet RDKit From InChI Activity: Use REST nodes to call an external web service- Configure the String Manipulation node so that it creates a new column called resource_url with the following format."https://www.ebi.ac.uk/chembl/api/data/molecule/<ChEMBL ID>.xml"- The new column contains a GET request URL with a coresponding ChEMBL ID.- Access the ChEMBL Rest API with the GET Request node- Use the XPath node to extract standard_inchi and standard_inchi_key- Use RDKit From InChI node to convert the standard_inchi column to RDKit molecules type. - Use Renderer to Image node to convert the RDKit molecules into images.- Display the result in a table viewOptional: Use the R Snippet to filter the standard_inchi and standard_inchi_key. Hint: You can use the Regex column filter template in the snippet with the expression: standard.* Display resultsList of ChEMBL IDsCreate resource urlExtract inchi Table View GET Request Table Creator String Manipulation XPath Renderer to Image R Snippet RDKit From InChI

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: Maarit Laukkanen
Created at: 2018-09-11
On NodePit since: 2024-01-14
Last update: 2024-11-18
Created with KNIME version: v4.6.1
Tags: RESTJSONGET Requestweb serviceeducationlife science

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

Try NodePit Runner!