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import_​helm_​monomer_​lib_​v0.4

Accessing the HELM Monomer Library
Accessing the HELM monomer library with KNIMEThis workflow retrieves the latest version of the HELM monomer library via the REST API for lib.monomer.org (as a JSON),and exemplifies several concepts:---> Uses the 'GET Request' node to access a JSON string containing the HELM monomoer library via the web(lib.monomer.org)---> Shows how the 'JSON path' and 'JSON to Table' nodes can be used to extract information from JSON-formatted data---> Uses 'Renderer to Image' node for conversion of chemical structure to PNG; enables views in javascript nodes freely, orwhen packaged as metanode/WebPortal views.---> Uses JavaScript tile or table views to display structures and metadata, or generated statistics from the library.---> Guided analytics: Uses CDK community nodes to enable a user-guided substructure search on the monomer library,and JS nodes for visualization of the results. Compute some basic categorization and count stats and views on the HELM monomerlibrary This particular GET request can be structured in a couple ofways: simply by 1) adding the address to the URL free field(top), or 2) by formatting the URL/URI as a column (bottom). Parse information from the JSON using the 'JSON Path' node &'JSON to Table' node Example of substructure searching using CDK nodes, and display of results using the JSTable View node Create a boolean column that captures the embedded Ionisname string from molfile, then delete the Ionis name stringfrom the molfile. (For cleaner visualizations.) Method 1 for library display: This sub-workflow brings in the mol files, and convert them toPNG using the 'Render to Image' node for display in the JS Tile or Table View nodes. json columnonlyconvert the mol stringto mol filelib.monomer.org(via 'URL column')HELM monomerURLlib.monomer.org(via 'URL')convert to CDKformatNode 40basic HELMlibrary stats, visualizationsTabularize all JSONelements ANDnested elementsextract rowsas a list(don't forget to extract as a JSON type)ungroup the list:each monomersub-JSON as a rowclear Ionis metadatafrom mol fileNode 66create Ionis metadataboolean columnrename R-grouplabel & capcolumnsremove extraneouscolumnsNode 83Node 84convert R.group listto stringNode 86sort by Id Column Filter Molecule Type Cast GET Request Table Creator GET Request Molecule to CDK aggregate & prep donut &sunburst views JSON to Table JSON Path Ungroup String Manipulation enter substructure substructuredisplay Renderer to Image String Manipulation Column Rename Column Filter re-engineer R-groupalternateId's Joiner Column Rename Substructure Search Tile View ofall monomers Table View ofall monomers Sorter Accessing the HELM monomer library with KNIMEThis workflow retrieves the latest version of the HELM monomer library via the REST API for lib.monomer.org (as a JSON),and exemplifies several concepts:---> Uses the 'GET Request' node to access a JSON string containing the HELM monomoer library via the web(lib.monomer.org)---> Shows how the 'JSON path' and 'JSON to Table' nodes can be used to extract information from JSON-formatted data---> Uses 'Renderer to Image' node for conversion of chemical structure to PNG; enables views in javascript nodes freely, orwhen packaged as metanode/WebPortal views.---> Uses JavaScript tile or table views to display structures and metadata, or generated statistics from the library.---> Guided analytics: Uses CDK community nodes to enable a user-guided substructure search on the monomer library,and JS nodes for visualization of the results. Compute some basic categorization and count stats and views on the HELM monomerlibrary This particular GET request can be structured in a couple ofways: simply by 1) adding the address to the URL free field(top), or 2) by formatting the URL/URI as a column (bottom). Parse information from the JSON using the 'JSON Path' node &'JSON to Table' node Example of substructure searching using CDK nodes, and display of results using the JSTable View node Create a boolean column that captures the embedded Ionisname string from molfile, then delete the Ionis name stringfrom the molfile. (For cleaner visualizations.) Method 1 for library display: This sub-workflow brings in the mol files, and convert them toPNG using the 'Render to Image' node for display in the JS Tile or Table View nodes. json columnonlyconvert the mol stringto mol filelib.monomer.org(via 'URL column')HELM monomerURLlib.monomer.org(via 'URL')convert to CDKformatNode 40basic HELMlibrary stats, visualizationsTabularize all JSONelements ANDnested elementsextract rowsas a list(don't forget to extract as a JSON type)ungroup the list:each monomersub-JSON as a rowclear Ionis metadatafrom mol fileNode 66create Ionis metadataboolean columnrename R-grouplabel & capcolumnsremove extraneouscolumnsNode 83Node 84convert R.group listto stringNode 86sort by Id Column Filter Molecule Type Cast GET Request Table Creator GET Request Molecule to CDK aggregate & prep donut &sunburst views JSON to Table JSON Path Ungroup String Manipulation enter substructure substructuredisplay Renderer to Image String Manipulation Column Rename Column Filter re-engineer R-groupalternateId's Joiner Column Rename Substructure Search Tile View ofall monomers Table View ofall monomers Sorter

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Created by: KLongo
Created at: 2019-04-04
On NodePit since: 2019-10-03
Last update: 2024-11-17
Created with KNIME version: v4.0.1
Tags: HELMmonomerGuided AnalyticsLife ScienceCDK community nodesREST APIJSONcheminformatics

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