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05_​DrugBank_​Network_​analysis

DrugBank Network Analysis

The workflow analyses data from DrugBank (http://www.drugbank.ca/) a public available db that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information.
Each drug is described by a drug card with more than 150 data fields of which only some are used in this workflow for demonstration.
All necessary files are available at www.drugbank.ca/downloads

The workflow requieres at least 2GB of main memory during execution (for details see the Requirements annotation)

XML data extraction Text mining of the free form text fields such as description Network creation Basic network analysis and visualization Molecular Fragment Mining DescriptionThe workflow analyses data from DrugBank (http://www.drugbank.ca/) a public available dbthat combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data withcomprehensive drug target (i.e. sequence, structure, and pathway) information. Each drug isdescribed by a drug card with more than 150 data fields of which only some are used in thisworkflow for demonstration. All necessary files are available at www.drugbank.ca/downloads RequirementsTo execute the workflow you need at least 2GB of main memory allocated to KNIME. If youhave asigned only 2 GB please execute the Extract Targets node separately since it consumesmost of the memory during execution time.A description on how to change the memory settings is available in the KNIME FAQ(http://tech.knime.org/faq#q4_2).Features- XML-Processing - Base Chemistry Types & Nodes- Chemistry Add-Ons - Nodes to create KNIME Quick Forms- Network Mining (Labs) - Textprocessing (Labs)- Palladian (Community Contributions) DrugBank Network Analysis The workflow analyses data from DrugBank (http://www.drugbank.ca/) a public available db that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical)data with comprehensive drug target (i.e. sequence, structure, and pathway) information. Each drug is described by a drug card with more than 150 data fields of which only some are used in this workflow for demonstration.All necessary files are available at www.drugbank.ca/downloadsThe workflow requieres at least 2GB of main memory during execution (for details see the Requirements annotation)Required plugins:- XML-Processing- Base Chemistry Types & Nodes- Chemistry Add-Ons- Nodes to create KNIME Quick Forms- Network Mining (Labs)- Textprocessing (Labs)- Palladian (Community Contributions see http://tech.knime.org/community/palladian) categoriesConcatenate alltext columns thatshould be includedin the drug documentgenes etc.drugsonly nounsnode degreehubsfirstobjects per partitionemptynetworkDrugCategoriestargetNamesDrug-DrugDrug-GeneDrug-Termonlyapproveddrugsdrug namesdrugsgenes etc.termseach partitionis representedby a nodefind at least 5 items that have at least 5neighbors in commonand that cooccure in50% of their transactionsneighborhood ofa particular nodeif network is unconnectedfilter edges thatcontain only one nodequasibicliquesThe included xml file contains only the approved drugs. The complete file can be downloaded fromhttp://www.drugbank.ca/system/downloads/current/drugbank.xml.zipPlease do not forget to unzip the file!quasibicliquesthe original file can be download fromhttp://www.drugbank.ca/system/downloads/current/structures/approved.sdf.ziplower caseDrug-FragmentConfigure thenode to changethe size of thestructure imagesin the network vieweraffected oganismsmanufacturermolecule/fragmentstructures & sizeselect onesubgraphsubgraph with molecule andfragment structuresshow onlythe subgraphpartition graphdemonstarting variousvisual propertiesnode size/coloredge widthtargetsATC description from WHO Collaborating Centre for Drug Statistics Methodology http://www.whocc.no/using PalladianATC codethird levelinfo Extract Categories Column Combiner(deprecated) Abner Filter(deprecated) Standard Named EntityFilter (deprecated) POS Filter(deprecated) Network Analyzer Sorter Partition Table Ungroup GroupBy Network Creator Object Inserter Object Inserter Object Inserter Object Inserter Object Inserter Object Inserter Row Filter GroupBy Extract link table Extract link table Extract link table PartitionGraph Creator Node NeighborExtractor Item Set Finder(Borgelt) Subset Matcher SubGraph Extractor Row To Network Network Viewer Extract largestcomponent Edge Degree Filter GroupBy XML Reader GroupBy SDF Reader Case Converter Object Inserter Term Tagging MolecularFragment Mining Extract TextFeatures StandardPreprocessing Multi FeatureInserter Row Filter Network Viewer Filter SubGraph Network Viewer Append ViewProperties Extract Targets Extract ATC codes Object Inserter Extract Drugs XML data extraction Text mining of the free form text fields such as description Network creation Basic network analysis and visualization Molecular Fragment Mining DescriptionThe workflow analyses data from DrugBank (http://www.drugbank.ca/) a public available dbthat combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data withcomprehensive drug target (i.e. sequence, structure, and pathway) information. Each drug isdescribed by a drug card with more than 150 data fields of which only some are used in thisworkflow for demonstration. All necessary files are available at www.drugbank.ca/downloads RequirementsTo execute the workflow you need at least 2GB of main memory allocated to KNIME. If youhave asigned only 2 GB please execute the Extract Targets node separately since it consumesmost of the memory during execution time.A description on how to change the memory settings is available in the KNIME FAQ(http://tech.knime.org/faq#q4_2).Features- XML-Processing - Base Chemistry Types & Nodes- Chemistry Add-Ons - Nodes to create KNIME Quick Forms- Network Mining (Labs) - Textprocessing (Labs)- Palladian (Community Contributions) DrugBank Network Analysis The workflow analyses data from DrugBank (http://www.drugbank.ca/) a public available db that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical)data with comprehensive drug target (i.e. sequence, structure, and pathway) information. Each drug is described by a drug card with more than 150 data fields of which only some are used in this workflow for demonstration.All necessary files are available at www.drugbank.ca/downloadsThe workflow requieres at least 2GB of main memory during execution (for details see the Requirements annotation)Required plugins:- XML-Processing- Base Chemistry Types & Nodes- Chemistry Add-Ons- Nodes to create KNIME Quick Forms- Network Mining (Labs)- Textprocessing (Labs)- Palladian (Community Contributions see http://tech.knime.org/community/palladian) categoriesConcatenate alltext columns thatshould be includedin the drug documentgenes etc.drugsonly nounsnode degreehubsfirstobjects per partitionemptynetworkDrugCategoriestargetNamesDrug-DrugDrug-GeneDrug-Termonlyapproveddrugsdrug namesdrugsgenes etc.termseach partitionis representedby a nodefind at least 5 items that have at least 5neighbors in commonand that cooccure in50% of their transactionsneighborhood ofa particular nodeif network is unconnectedfilter edges thatcontain only one nodequasibicliquesThe included xml file contains only the approved drugs. The complete file can be downloaded fromhttp://www.drugbank.ca/system/downloads/current/drugbank.xml.zipPlease do not forget to unzip the file!quasibicliquesthe original file can be download fromhttp://www.drugbank.ca/system/downloads/current/structures/approved.sdf.ziplower caseDrug-FragmentConfigure thenode to changethe size of thestructure imagesin the network vieweraffected oganismsmanufacturermolecule/fragmentstructures & sizeselect onesubgraphsubgraph with molecule andfragment structuresshow onlythe subgraphpartition graphdemonstarting variousvisual propertiesnode size/coloredge widthtargetsATC description from WHO Collaborating Centre for Drug Statistics Methodology http://www.whocc.no/using PalladianATC codethird levelinfo Extract Categories Column Combiner(deprecated) Abner Filter(deprecated) Standard Named EntityFilter (deprecated) POS Filter(deprecated) Network Analyzer Sorter Partition Table Ungroup GroupBy Network Creator Object Inserter Object Inserter Object Inserter Object Inserter Object Inserter Object Inserter Row Filter GroupBy Extract link table Extract link table Extract link table PartitionGraph Creator Node NeighborExtractor Item Set Finder(Borgelt) Subset Matcher SubGraph Extractor Row To Network Network Viewer Extract largestcomponent Edge Degree Filter GroupBy XML Reader GroupBy SDF Reader Case Converter Object Inserter Term Tagging MolecularFragment Mining Extract TextFeatures StandardPreprocessing Multi FeatureInserter Row Filter Network Viewer Filter SubGraph Network Viewer Append ViewProperties Extract Targets Extract ATC codes Object Inserter Extract Drugs

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

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On NodePit since: 2019-07-12
Last update: 2023-06-07
Created with KNIME version: v3.7.1