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03.2 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, connect the result to the Molecule Type Cast node- 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 withthe expression: standard.* Display resultsList of ChEMBL IDsCreate resource urlExtract inchiTable View GET Request Table Creator String Manipulation XPath Molecule Type Cast 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, connect the result to the Molecule Type Cast node- 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 withthe expression: standard.* Display resultsList of ChEMBL IDsCreate resource urlExtract inchiTable View GET Request Table Creator String Manipulation XPath Molecule Type Cast 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:

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Created by: Maarit Laukkanen
Created at: 2018-09-11
On NodePit since: 2024-03-15
Last update: 2024-11-23
Created with KNIME version: v4.1.3
Tags: RESTJSONGET Requestweb serviceeducation

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