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Disease_​related_​protein_​classification_​and_​PPI_​networks

Single_disease_ChEMBL_TTD_OpenTargets_String_PPI

This workflow allows the user to select a disease from ChEMBL DB and perform a search of every target (single protein or protein complex) that has reports of (experimental or annotations) compounds or drugs related to the disease. Those targets are classified based on the phase of development of their compounds or drugs. Also a protein-protein interaction network is constructed via STRING API.
The results are two networks, full network and filtered by Open Targets Platform disease associated targets; and two lists of targets containing all targets and filtered by Open targets Platform with a score based in the types of target classification.

Disease related protein classification and PPI networks 2. Disease selection 3. Identify disease related targets onChEMBL and TTDdatabases. 4. Target clasification 5. Protein-proteininteractions (PPI) 6. Target scoring 1. Databases, input files and output folder 7. Write network andlist of targets files - Download ChEMBL database for mysql(https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/) .- Load the database on your local mysql server.- Configure the node with your mysql credentialsand select the corresponding chembl_Xdatabase.- Download files "Target to disease mappingwithICD identifiers" and "Drug to diseasemapping with ICD identifiers" from TTD (http://db.idrblab.net/ttd/full-data-download).- Configure the node by selecting thecorresponding files. - Search a disease on Open Targets Platform(https://platform.opentargets.org/) anddownload the assosiated targets table as TSVfile.- Configure the node by selecting the TSV file. From a user defined disease, this workflow searches on multiple databases(ChEMBL, Therapeutic Target Database, Uniprot, Open Target Platformand STRING) for disease related targets, classify them based on thedevelopment phase of their compunds or drugs and builds protein-proteininteractions networks. To run this workflow follow these steps:1. Configure red box nodes.2. Execute orange box node.3. Configure the yellow box node.4. Configure and execute green box nodes.5. Execute all executable nodes (SHIFT + F7). On "Disease list" node the disease listis extracted from ChEMBL DB and thenis possible to select the disease on the" Disease Selector" node. The" Disease list" node has to be alreadysuccessfully excecuted to properlyconfigure "Disease selector" node. Ifthere is no list on "Disease selector" node, reset and run "Disease list" node before configure "Diseaseselector" node. Targets are selectedfrom ChEMBL and TTDDBs if their aremodulated by anymolecule or drugindicated for theselected disease.The information of thetargets found on TTD isfilled with the localChEMBL DB and Uniprot API. - Select a folder (not a file) where the workflow willwrite the result files. The targets are classifiedby the development phasefor the indicated diseaseof the compounds anddrugs capable of modulatetheir activities. For each target the best 20interacting proteins areobtained via STRING API.The information for thesenew proteins is filled withthe local ChEMBL DB andUniprot API. These newproteins are classified astargets T4.The output tables include:- PPI-network.- PPI-network filtered byOpen Targets Platform.- List of targets. - List of targets filtered byOpen Target Platform. The following resuls filesare written:- PPI-network.- PPI-network filtered byOpen Targets Platform.-PPI-network targetsattributes.- List of targets sorted bytarget scores.- List of targets filtered byOpen Targets Platformsorted by target scores. A score is assigned to thetargets based on theirtarget classification, asfollows:- T1 = 1.0- T2 = 0.7- T3 = 0.4- T4 = 0.1These scores are summed ,normalized by target. Theminimum target score is0.1, when is T4 only and themaximum target score is2.2 when it has all targetclassifications, T1 T2 T3and T4 at the same time. LocalChEMBL DBTTD targets and drugs filesrelated to diseasesDisease Associated targets TSV filefrom Open Targets PlatformDirectory towrite result filesMySQL Connector Disease selector Disease list ChEMBL TherapeuticTarget Database TTD T1 T2 T3 targetclassification Open TargetsPlatform PPI String and OpenTarget Platform filter Target groupscoring Folder towrite results Write Result files Disease related protein classification and PPI networks 2. Disease selection 3. Identify disease related targets onChEMBL and TTDdatabases. 4. Target clasification 5. Protein-proteininteractions (PPI) 6. Target scoring 1. Databases, input files and output folder 7. Write network andlist of targets files - Download ChEMBL database for mysql(https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/) .- Load the database on your local mysql server.- Configure the node with your mysql credentialsand select the corresponding chembl_Xdatabase.- Download files "Target to disease mappingwithICD identifiers" and "Drug to diseasemapping with ICD identifiers" from TTD (http://db.idrblab.net/ttd/full-data-download).- Configure the node by selecting thecorresponding files. - Search a disease on Open Targets Platform(https://platform.opentargets.org/) anddownload the assosiated targets table as TSVfile.- Configure the node by selecting the TSV file. From a user defined disease, this workflow searches on multiple databases(ChEMBL, Therapeutic Target Database, Uniprot, Open Target Platformand STRING) for disease related targets, classify them based on thedevelopment phase of their compunds or drugs and builds protein-proteininteractions networks. To run this workflow follow these steps:1. Configure red box nodes.2. Execute orange box node.3. Configure the yellow box node.4. Configure and execute green box nodes.5. Execute all executable nodes (SHIFT + F7). On "Disease list" node the disease listis extracted from ChEMBL DB and thenis possible to select the disease on the" Disease Selector" node. The" Disease list" node has to be alreadysuccessfully excecuted to properlyconfigure "Disease selector" node. Ifthere is no list on "Disease selector" node, reset and run "Disease list" node before configure "Diseaseselector" node. Targets are selectedfrom ChEMBL and TTDDBs if their aremodulated by anymolecule or drugindicated for theselected disease.The information of thetargets found on TTD isfilled with the localChEMBL DB and Uniprot API. - Select a folder (not a file) where the workflow willwrite the result files. The targets are classifiedby the development phasefor the indicated diseaseof the compounds anddrugs capable of modulatetheir activities. For each target the best 20interacting proteins areobtained via STRING API.The information for thesenew proteins is filled withthe local ChEMBL DB andUniprot API. These newproteins are classified astargets T4.The output tables include:- PPI-network.- PPI-network filtered byOpen Targets Platform.- List of targets. - List of targets filtered byOpen Target Platform. The following resuls filesare written:- PPI-network.- PPI-network filtered byOpen Targets Platform.-PPI-network targetsattributes.- List of targets sorted bytarget scores.- List of targets filtered byOpen Targets Platformsorted by target scores. A score is assigned to thetargets based on theirtarget classification, asfollows:- T1 = 1.0- T2 = 0.7- T3 = 0.4- T4 = 0.1These scores are summed ,normalized by target. Theminimum target score is0.1, when is T4 only and themaximum target score is2.2 when it has all targetclassifications, T1 T2 T3and T4 at the same time. LocalChEMBL DBTTD targets and drugs filesrelated to diseasesDisease Associated targets TSV filefrom Open Targets PlatformDirectory towrite result filesMySQL Connector Disease selector Disease list ChEMBL TherapeuticTarget Database TTD T1 T2 T3 targetclassification Open TargetsPlatform PPI String and OpenTarget Platform filter Target groupscoring Folder towrite results Write Result files

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Created by: cpena
Created at: 2022-09-05
On NodePit since: 2022-10-25
Last update: 2024-09-16
Created with KNIME version: v4.6.3
Tags: DiseaseTargetsDrugsCompoundsChEMBLUniprotOpen Targets PlatformSTRINGTherapeutics Target Database

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