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ADR-S

Workflow Entry: ADR-S

Created at: 28/03/11 @ 11:34:18 Last updated: 09/08/11 @ 22:38:12

Version 2 (latest) (of 2)

Version created on: 07/08/11 @ 09:07:21 by: Anna Bauer-Mehren | Revision comments Expand

Last edited on: 09/08/11 @ 22:38:12 by: Anna Bauer-Mehren

Title: ADR-S

Type: Taverna 2

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Description

The ADR-S pathway seeks to establish a connection between the clinical event and the drug through different paths: (i) through proteins in common among the proteins that are drug targets or metabolite targets and proteins associated to the clinical event (ii) through proteins that are drug targets or metabolite targets and proteins associated to the clinical event that participate in a common biological pathway. The workflow proceeds as follows:
First, it checks if there are proteins that are annotated both to the clinical event and to the drug (NESTED WORKFLOW ADR_substantiation_through_proteins).
Second, it looks for connections between the drug and the clinical event through biological pathways. Information about tissue expression of the proteins is used to filter the results Input of the workflow The input of the workflow is a drug-event pair. For the clinical events, the following types are allowed: 1) UMLS CUI concept identifiers (single identifier or a list of identifiers 2) clinical events observed as adverse drug reactions according to the EU-ADR project For the drug, a ATC code (7 digit level) is required. Output of the workflow As result a list of connecting proteins as well as a list of pathways is provided. The results can be visualized as a network using Cytoscape. The network is a multi-partite graph, in which the nodes are the event, the drug and the proteins, and the edges the associations between these nodes. In addition, all the evidences supporting the associations can be explored in the graph representation. The results of the analyisis through biological pathways is summarized in an html file.

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Workflow Components

Authors (8)

Titles (6)

Descriptions (18)

This workflow substantiates drug safety signals composed of a drug and an adverse reaction. In more detail, the workflow tries to find feasible paths connecting the drug and the event. First, it checks if there are proteins that are annotated to a given adverse event and at the same time target of the given drug. (NESTED WORKFLOW ADR_substantiation_through_proteins) Second, it tries to connect drug and event through biological pathways. Here, it checks if there are proteins from drug and event side which are expressed in the same tissue and also annotated to the same biological pathway. As adverse event, the following event types are allowed: 1) events as defined in the EU-ADR project such as UGIB 2) UMLS CUI concept identifiers As drug input 7 digit drug ATC codes are allowed. As result a list of intersecting proteins as well as a list of pathways is provided. If any of the two lists is not empty, the drug-event pair is substantiated as drug safety signal. For the intersecting proteins, a Cytoscape graph is generated for user-friendly visualization. It contains the event, drug and their annotated proteins as well as additional information such as links to publications etc. For the intersecting pathways a html page summarizing the results is generated.

The signal substantiation workflow seeks to establish a connection between the clinical event and the drug through different paths: (i) through proteins in common among the proteins that are drug targets or metabolite targets and proteins associated to the clinical event (ii) through proteins that are drug targets or metabolite targets and proteins associated to the clinical event that participate in a common biological pathway. The workflow proceeds as follows: First, it checks if there are proteins that are annotated both to the clinical event and to the drug (NESTED WORKFLOW ADR_substantiation_through_proteins). Second, it looks for connections between the drug and the clinical event through biological pathways. Information about tissue expression of the proteins is used to filter the results. Input of the workflow: The input of the workflow is a drug-event pair. For the clinical events, the following types are allowed: 1) UMLS concept identifiers (UMLS CUI) 2) clinical events observed as adverse drug reactions according to the EU-ADR project (see http://ibi.imim.es/ADR_Substantiation.html for details) For the drug, a ATC code (5th level, seven digits) is required. NOTE: only one ATC code can be processed at a time Output of the workflow: 1) List of Drug-Event-Liniking proteins: The results can be visualized as a network using Cytoscape. The network is a multi-partite graph, in which the nodes are the event, the drug and the proteins, and the edges the associations between these nodes. In addition, all the evidences supporting the associations can be explored in the graph representation. 2)List of pathways: The results of the analysis through biological pathways is summarized in an html file.

The signal substantiation workflow seeks to establish a connection between the clinical event and the drug through different paths: (i) through proteins in common between the drug-target (ii) through proteins that are drug targets or metabolite targets and proteins associated to the clinical event that participate in a common biological pathway. The workflow proceeds as follows: First, it checks if there are proteins that are annotated both to the clinical event and to the drug (NESTED WORKFLOW ADR_substantiation_through_proteins). Second, it looks for connections between the drug and the clinical event through biological pathways. Information about tissue expression of the proteins is used to filter the results. Input of the workflow: The input of the workflow is a drug-event pair. For the clinical events, the following types are allowed: 1) UMLS concept identifiers (UMLS CUI), a single identifier of a list of identifiers are accepted. 2) clinical events observed as adverse drug reactions according to the EU-ADR project (see http://ibi.imim.es/ADR_Substantiation.html for details) For the drug, a ATC code (5th level, seven digits) is required. NOTE: only one ATC code can be processed at a time. Output of the workflow: 1) List of Drug-Event-Liniking proteins: The results can be visualized as a network using Cytoscape. The network is a multi-partite graph, in which the nodes are the event, the drug and the proteins, and the edges the associations between these nodes. In addition, all the evidences supporting the associations can be explored in the graph representation. 2)List of pathways: The results of the analysis through biological pathways is summarized in an html file.

The signal substantiation workflow seeks to establish a connection between the clinical event and the drug through different paths: (i) through proteins in common among the proteins that are drug targets or metabolite targets and proteins associated to the clinical event (ii) through proteins that are drug targets or metabolite targets and proteins associated to the clinical event that participate in a common biological pathway. The workflow proceeds as follows: First, it checks if there are proteins that are annotated both to the clinical event and to the drug (NESTED WORKFLOW ADR_substantiation_through_proteins). Second, it looks for connections between the drug and the clinical event through biological pathways. Information about tissue expression of the proteins is used to filter the results. Input of the workflow: The input of the workflow is a drug-event pair. For the clinical events, the following types are allowed: 1) UMLS concept identifiers (UMLS CUI), a single identifier of a list of identifiers are accepted. 2) clinical events observed as adverse drug reactions according to the EU-ADR project (see http://ibi.imim.es/ADR_Substantiation.html for details) For the drug, a ATC code (5th level, seven digits) is required. NOTE: only one ATC code can be processed at a time. Output of the workflow: 1) List of Drug-Event-Liniking proteins: The results can be visualized as a network using Cytoscape. The network is a multi-partite graph, in which the nodes are the event, the drug and the proteins, and the edges the associations between these nodes. In addition, all the evidences supporting the associations can be explored in the graph representation. 2)List of pathways: The results of the analysis through biological pathways is summarized in an html file.

The signal substantiation workflow seeks to establish a connection between the clinical event and the drug through different paths: (i) through proteins in common among the proteins that are drug targets or metabolite targets and proteins associated to the clinical event (ii) through proteins that are drug targets or metabolite targets and proteins associated to the clinical event that participate in a common biological pathway. The workflow proceeds as follows: First, it checks if there are proteins that are annotated both to the clinical event and to the drug (NESTED WORKFLOW ADR_substantiation_through_proteins) Second, it looks for connections between the drug and the clinical event through biological pathways. Information about tissue expression of the proteins is used to filter the results Input of the workflow The input of the workflow is a drug-event pair. For the clinical events, the following types are allowed: 1) UMLS CUI concept identifiers (single identifier or a list of identifiers 2) clinical events observed as adverse drug reactions according to the EU-ADR project For the drug, a ATC code (7 digit level) is required Output of the workflow As result a list of connecting proteins as well as a list of pathways is provided. The results can be visualized as a network using Cytoscape. The network is a multi-partite graph, in which the nodes are the event, the drug and the proteins, and the edges the associations between these nodes. In addition, all the evidences supporting the associations can be explored in the graph representation. The results of the analyisis through biological pathways is summarized in an html file.

The signal substantiation workflow seeks to establish a connection between the clinical event and the drug through different paths: (i) through proteins in common among the proteins that are drug targets or metabolite targets and proteins associated to the clinical event (ii) through proteins that are drug targets or metabolite targets and proteins associated to the clinical event that participate in a common biological pathway. The workflow proceeds as follows: First, it checks if there are proteins that are annotated both to the clinical event and to the drug (NESTED WORKFLOW ADR_substantiation_through_proteins). Second, it looks for connections between the drug and the clinical event through biological pathways. Information about tissue expression of the proteins is used to filter the results. Input of the workflow: The input of the workflow is a drug-event pair. For the clinical events, the following types are allowed: 1) UMLS concept identifiers (UMLS CUI) 2) clinical events observed as adverse drug reactions according to the EU-ADR project (see for details) For the drug, a ATC code (5th level, seven digits) is required. NOTE: only one ATC code can be processed at a time Output of the workflow As result a list of connecting proteins as well as a list of pathways is provided. The results can be visualized as a network using Cytoscape. The network is a multi-partite graph, in which the nodes are the event, the drug and the proteins, and the edges the associations between these nodes. In addition, all the evidences supporting the associations can be explored in the graph representation. The results of the analysis through biological pathways is summarized in an html file.

The signal substantiation workflow seeks to establish a connection between the clinical event and the drug through different paths: (i) through proteins in common among the proteins that are drug targets or metabolite targets and proteins associated to the clinical event (ii) through proteins that are drug targets or metabolite targets and proteins associated to the clinical event that participate in a common biological pathway. The workflow proceeds as follows: First, it checks if there are proteins that are annotated both to the clinical event and to the drug (NESTED WORKFLOW ADR_substantiation_through_proteins) Second, it tries to connect drug and event through biological pathways. Here, it checks if there are proteins from drug and event side which are expressed in the same tissue and also annotated to the same biological pathway. As adverse event, the following event types are allowed: 1) events as defined in the EU-ADR project such as UGIB 2) UMLS CUI concept identifiers As drug input 7 digit drug ATC codes are allowed. As result a list of intersecting proteins as well as a list of pathways is provided. If any of the two lists is not empty, the drug-event pair is substantiated as drug safety signal. For the intersecting proteins, a Cytoscape graph is generated for user-friendly visualization. It contains the event, drug and their annotated proteins as well as additional information such as links to publications etc. For the intersecting pathways a html page summarizing the results is generated.

The signal substantiation workflow seeks to establish a connection between the clinical event and the drug through different paths: (i) through proteins in common among the proteins that are drug targets or metabolite targets and proteins associated to the clinical event (ii) through proteins that are drug targets or metabolite targets and proteins associated to the clinical event that participate in a common biological pathway. The workflow proceeds as follows: First, it checks if there are proteins that are annotated both to the clinical event and to the drug (NESTED WORKFLOW ADR_substantiation_through_proteins) Second, it looks for connections between the drug and the clinical event through biological pathways. Information about tissue expression of the proteins is used to filter the results Input of the workflow The input of the workflow is a drug-event pair. For the clinical events, the following types are allowed: 1) UMLS CUI concept identifiers (single identifier or a list of identifiers) 2) clinical events observed as adverse drug reactions according to the EU-ADR project (see "Bauer-Mehren A, van Mullingen E, Carrascosa MC, Lopes P, Oliveira JL, Avillach P, Gayo Diallo, Mestres J, Boyer S, Sanz F, Kors J, Furlong LI. Workflows for the automatic filtering and substantiation of drug safety signals, 2011" for details) For the drug, a ATC code (5th level, seven digits) is required. Output of the workflow As result a list of connecting proteins as well as a list of pathways is provided. The results can be visualized as a network using Cytoscape. The network is a multi-partite graph, in which the nodes are the event, the drug and the proteins, and the edges the associations between these nodes. In addition, all the evidences supporting the associations can be explored in the graph representation. The results of the analyisis through biological pathways is summarized in an html file.

The signal substantiation workflow seeks to establish a connection between the clinical event and the drug through different paths: (i) through proteins in common among the proteins that are drug targets or metabolite targets and proteins associated to the clinical event (ii) through proteins that are drug targets or metabolite targets and proteins associated to the clinical event that participate in a common biological pathway. The workflow proceeds as follows: First, it checks if there are proteins that are annotated both to the clinical event and to the drug (NESTED WORKFLOW ADR_substantiation_through_proteins) Second, it looks for connections between the drug and the clinical event through biological pathways. Information about tissue expression of the proteins is used to filter the results Input of the workflow The input of the workflow is a drug-event pair. For the clinical events, the following types are allowed: 1) UMLS CUI concept identifiers (single identifier or a list of identifiers 2) clinical events observed as adverse drug reactions according to the EU-ADR project For the drug, a ATC code (5th level, seven digits) is required. Output of the workflow As result a list of connecting proteins as well as a list of pathways is provided. The results can be visualized as a network using Cytoscape. The network is a multi-partite graph, in which the nodes are the event, the drug and the proteins, and the edges the associations between these nodes. In addition, all the evidences supporting the associations can be explored in the graph representation. The results of the analyisis through biological pathways is summarized in an html file.

The signal substantiation workflow seeks to establish a connection between the clinical event and the drug through different paths: (i) through proteins in common among the proteins that are drug targets or metabolite targets and proteins associated to the clinical event (ii) through proteins that are drug targets or metabolite targets and proteins associated to the clinical event that participate in a common biological pathway. The workflow proceeds as follows: First, it checks if there are proteins that are annotated both to the clinical event and to the drug (NESTED WORKFLOW ADR_substantiation_through_proteins). Second, it looks for connections between the drug and the clinical event through biological pathways. Information about tissue expression of the proteins is used to filter the results. Input of the workflow: The input of the workflow is a drug-event pair. For the clinical events, the following types are allowed: 1) UMLS concept identifiers (UMLS CUI), a single identifier of a list of identifiers are accepted. 2) clinical events observed as adverse drug reactions according to the EU-ADR project (see http://ibi.imim.es/ADR_Substantiation.html for details) For the drug, a ATC code (5th level, seven digits) is required. NOTE: only one ATC code can be processed at a time. Output of the workflow: 1) List of Drug-Event-Liniking proteins: The results can be visualized as a network using Cytoscape. The network is a multi-partite graph, in which the nodes are the event, the drug and the proteins, and the edges the associations between these nodes. In addition, all the evidences supporting the associations can be explored in the graph representation. 2)List of pathways: The results of the analysis through biological pathways is summarized in an html file.

The signal substantiation workflow seeks to establish a connection between the clinical event and the drug through different paths: (i) through proteins in common among the proteins that are drug targets or metabolite targets and proteins associated to the clinical event (ii) through proteins that are drug targets or metabolite targets and proteins associated to the clinical event that participate in a common biological pathway. The workflow proceeds as follows: First, it checks if there are proteins that are annotated both to the clinical event and to the drug (NESTED WORKFLOW ADR_substantiation_through_proteins) Second, it lootries to connect drug and event through biological pathways. Here, it checks if there are proteins from drug and event side which are expressed in the same tissue and also annotated to the same biological pathway. As adverse event, the following event types are allowed: 1) events as defined in the EU-ADR project such as UGIB 2) UMLS CUI concept identifiers As drug input 7 digit drug ATC codes are allowed. As result a list of intersecting proteins as well as a list of pathways is provided. If any of the two lists is not empty, the drug-event pair is substantiated as drug safety signal. For the intersecting proteins, a Cytoscape graph is generated for user-friendly visualization. It contains the event, drug and their annotated proteins as well as additional information such as links to publications etc. For the intersecting pathways a html page summarizing the results is generated.

The signal substantiation workflow seeks to establish a connection between the clinical event and the drug through different paths: (i) through proteins in common between the drug-target and the event-protein profiles. (ii) assessing if the proteins in the drug-target profile and in the event-protein profile participate in a common biological pathway. The workflow proceeds as follows: First, it checks if there are proteins that are annotated both to the clinical event and to the drug (NESTED WORKFLOW ADR_substantiation_through_proteins). Second, it looks for connections between the drug and the clinical event through biological pathways. Information about tissue expression of the proteins is used to filter the results. Input of the workflow: The input of the workflow is a drug-event pair. For the clinical events, the following types are allowed: 1) UMLS concept identifiers (UMLS CUI), a single identifier of a list of identifiers are accepted. 2) clinical events observed as adverse drug reactions according to the EU-ADR project (see http://ibi.imim.es/ADR_Substantiation.html for details) For the drug, an ATC code (5th level, seven digits) is required. NOTE: only one ATC code can be processed at a time. Output of the workflow: 1) List of Drug-Event-Liniking proteins: The list of proteins that link the drug with the event. The results can be visualized as a network using Cytoscape. The network is a multi-partite graph, in which the nodes are the event, the drug and the proteins, and the edges the associations between these nodes. In addition, all the evidences supporting the associations can be explored in the graph representation. 2)List of pathways: The list of pathways from Reactome that connect the drug and the event. The results of the analysis through biological pathways is summarized in an html file.

The signal substantiation workflow seeks to establish a connection between the clinical event and the drug through different paths: (i) through proteins in common between the drug-target and the event-protein profiles. (ii) assessing if the proteins in the drug-target profile and in the event-protein profile participate in a common biological pathway. The workflow proceeds as follows: First, it checks if there are proteins that are annotated both to the clinical event and to the drug (NESTED WORKFLOW ADR_substantiation_through_proteins). Second, it looks for connections between the drug and the clinical event through biological pathways. Information about tissue expression of the proteins is used to filter the results. Input of the workflow: The input of the workflow is a drug-event pair. For the clinical events, the following types are allowed: 1) UMLS concept identifiers (UMLS CUI), a single identifier of a list of identifiers are accepted. 2) clinical events observed as adverse drug reactions according to the EU-ADR project (see http://ibi.imim.es/ADR_Substantiation.html for details) For the drug, a ATC code (5th level, seven digits) is required. NOTE: only one ATC code can be processed at a time. Output of the workflow: 1) List of Drug-Event-Liniking proteins: The results can be visualized as a network using Cytoscape. The network is a multi-partite graph, in which the nodes are the event, the drug and the proteins, and the edges the associations between these nodes. In addition, all the evidences supporting the associations can be explored in the graph representation. 2)List of pathways: The results of the analysis through biological pathways is summarized in an html file.

This workflow checks if there are proteins that are annotated to a given adverse event and at the same time target of the given drug. (NESTED WORKFLOW EUADR_IBI_CGL_signal_substantiation_through_proteins) Moreover, it tries to connect drug and event through biological pathways. It checks if there are proteins, which are expressed in the same tissue and also annotated to the same pathway. As adverse event, the following event types are allowed: 1) events as defined in the EU-ADR project such as UGIB 2) UMLS CUI concept identifiers As drug input 7 digit drug ATC codes are allowed. As result a list of intersecting proteins as well as a list of intersecting pathways is provided. If any of the two lists is not empty, the drug-event pair is substantiated as signal. For the intersecting proteins, there is a Cytoscape graph is generated for user-friendly visualization. It contains the event, drug and their annotated proteins as well as additional information such as links to publications etc. For the intersecting pathways a html page summarizing the results is generated.

This workflow substantiates drug safety signals composed of a drug and an adverse reaction. In more detail, the workflow tries to find feasible paths connecting the drug and the event. First, it checks if there are proteins that are annotated to a given adverse event and at the same time target of the given drug. (NESTED WORKFLOW ADR_substantiation_through_proteins) Second, it tries to connect drug and event through biological pathways. Here, it checks if there are proteins from drug and event side which are expressed in the same tissue and also annotated to the same biological pathway. As adverse event, the following event types are allowed: 1) events as defined in the EU-ADR project such as UGIB 2) UMLS CUI concept identifiers As drug input 7 digit drug ATC codes are allowed. As result a list of intersecting proteins as well as a list of pathways is provided. If any of the two lists is not empty, the drug-event pair is substantiated as drug safety signal. For the intersecting proteins, a Cytoscape graph is generated for user-friendly visualization. It contains the event, drug and their annotated proteins as well as additional information such as links to publications etc. sFor the intersecting pathways a html page summarizing the results is generated.

The signal substantiation workflow seeks to establish a connection between the clinical event and the drug through different paths: (i) through proteins in common between the drug-target and the event-protein profiles. (ii) through proteins that are drug targets or metabolite targets and proteins associated to the clinical event that participate in a common biological pathway. The workflow proceeds as follows: First, it checks if there are proteins that are annotated both to the clinical event and to the drug (NESTED WORKFLOW ADR_substantiation_through_proteins). Second, it looks for connections between the drug and the clinical event through biological pathways. Information about tissue expression of the proteins is used to filter the results. Input of the workflow: The input of the workflow is a drug-event pair. For the clinical events, the following types are allowed: 1) UMLS concept identifiers (UMLS CUI), a single identifier of a list of identifiers are accepted. 2) clinical events observed as adverse drug reactions according to the EU-ADR project (see http://ibi.imim.es/ADR_Substantiation.html for details) For the drug, a ATC code (5th level, seven digits) is required. NOTE: only one ATC code can be processed at a time. Output of the workflow: 1) List of Drug-Event-Liniking proteins: The results can be visualized as a network using Cytoscape. The network is a multi-partite graph, in which the nodes are the event, the drug and the proteins, and the edges the associations between these nodes. In addition, all the evidences supporting the associations can be explored in the graph representation. 2)List of pathways: The results of the analysis through biological pathways is summarized in an html file.

The signal substantiation workflow seeks to establish a connection between the clinical event and the drug through different paths: (i) through proteins in common among the proteins that are drug targets or metabolite targets and proteins associated to the clinical event (ii) through proteins that are drug targets or metabolite targets and proteins associated to the clinical event that participate in a common biological pathway. The workflow proceeds as follows: First, it checks if there are proteins that are annotated both to the clinical event and to the drug (NESTED WORKFLOW ADR_substantiation_through_proteins) Second, it looks for connections between the drug and the clinical event through biological pathways. Information about tissue expression of the proteins is used to filter the results Input of the workflow The input of the workflow is a drug-event pair. For the clinical events, the following types are allowed: 1) UMLS CUI concept identifiers (single identifier or a list of identifiers) 2) clinical events observed as adverse drug reactions according to the EU-ADR project (see ref. for details) For the drug, a ATC code (5th level, seven digits) is required. NOTE: only one ATC code can be processed at a time Output of the workflow As result a list of connecting proteins as well as a list of pathways is provided. The results can be visualized as a network using Cytoscape. The network is a multi-partite graph, in which the nodes are the event, the drug and the proteins, and the edges the associations between these nodes. In addition, all the evidences supporting the associations can be explored in the graph representation. The results of the analysis through biological pathways is summarized in an html file.

The signal substantiation workflow seeks to establish a connection between the clinical event and the drug through different paths: (i) through proteins in common among the proteins that are drug targets or metabolite targets and proteins associated to the clinical event (ii) through proteins that are drug targets or metabolite targets and proteins associated to the clinical event that participate in a common biological pathway. The workflow proceeds as follows: First, it checks if there are proteins that are annotated both to the clinical event and to the drug (NESTED WORKFLOW ADR_substantiation_through_proteins) Second, it looks for connections between the drug and the clinical event through biological pathways. Information about tissue expression of the proteins is used to filter the results Input of the workflow The input of the workflow is a drug-event pair. For the clinical events, the following types are allowed: 1) UMLS CUI concept identifiers (single identifier or a list of identifiers 2) clinical events observed as adverse drug reactions according to the EU-ADR project For the drug, a ATC code (7 digit level) is required. Output of the workflow As result a list of connecting proteins as well as a list of pathways is provided. The results can be visualized as a network using Cytoscape. The network is a multi-partite graph, in which the nodes are the event, the drug and the proteins, and the edges the associations between these nodes. In addition, all the evidences supporting the associations can be explored in the graph representation. The results of the analyisis through biological pathways is summarized in an html file.

Inputs (5)

Name	Description
atc	Workflow ATC input The 7 digit atc code of a drug The drug input. The ATC code of a drug (5th level, 7 digits) Workflow drug input The ACT code of a drug (5th level, 7 digits) Workflow ATC input
event	Workflow clinical event input Allowed events are: For the clinical events, the following input types are allowed: 1) UMLS CUI concept identifiers (single identifier or a list of identifiers) 2) clinical events observed as adverse drug reactions according to the EU-ADR project (see ref for details) The clinical event input For the clinical events, the following input types are allowed: 1) UMLS: UMLS CUI concept identifiers 2) EUADR_EVENT: clinical events observed as adverse drug reactions according to the EU-ADR project (see ref for details) If you use option 1), insert here a single UMLS CUI identifier or a list of identifiers. If you use option 2), insert here the name of the EUADR_EVENT as defined in ref. Workflow clinical event input Allowed events are: For the clinical events, the following input types are allowed: 1) UMLS: UMLS CUI concept identifiers 2) EUADR_event: clinical events observed as adverse drug reactions according to the EU-ADR project (see ref for details) If you use option 1), insert here a single UMLS CUI identifier or a list of identifiers. If you use option 2), insert here the name of the EUADR_event as defined in ref. The clinical event input For the clinical events, the following input types are allowed: 1) UMLS: UMLS concept identifiers 2) EUADR_EVENT: clinical events observed as adverse drug reactions according to the EU-ADR project (see ref for details) If you use option 1), insert here a single UMLS concept identifier or a list of identifiers. If you use option 2), insert here the name of the EUADR_EVENT as defined in http://ibi.imim.es/ADR_Substantiation.html. The clinical event input For the clinical events, the following input types are allowed: 1) UMLS: UMLS concept identifiers 2) EUADR_EVENT: clinical events observed as adverse drug reactions according to the EU-ADR project (see http://ibi.imim.es/ADR_Substantiation.html for details). If you use option 1), insert here a single UMLS concept identifier or a list of identifiers. If you use option 2), insert here the name of the EUADR_EVENT as defined in http://ibi.imim.es/ADR_Substantiation.html. Workflow event input Allowed events are: 1) events of type EUADR_EVENT as defined in the EUADR project 2) events of type UMLS being a CUI concept identifier The clinical event input For the clinical events, the following input types are allowed: 1) UMLS: UMLS concept identifiers 2) EUADR_EVENT: clinical events observed as adverse drug reactions according to the EU-ADR project (see ref for details) If you use option 1), insert here a single UMLS concept identifier or a list of identifiers. If you use option 2), insert here the name of the EUADR_EVENT as defined in . Workflow clinical event input Allowed events are: 1) events of type EUADR_EVENT as defined in the EUADR project 2) events of type UMLS being a CUI concept identifier The clinical event input For the clinical events, the following input types are allowed: 1) UMLS: UMLS CUI concept identifiers 2) EUADR_event: clinical events observed as adverse drug reactions according to the EU-ADR project (see ref for details) If you use option 1), insert here a single UMLS CUI identifier or a list of identifiers. If you use option 2), insert here the name of the EUADR_event as defined in ref. Name of the event. This is only required for user-friendly visualization of the results. In particular, if the input is a CUI concept identifier. Workflow event input
eventType	Type of the event to be processed. For the clinical events, the following types are allowed: 1) UMLS: if you use UMLS CUI concept identifiers (single identifier or a list of identifiers) 2) EUADR_EVENT: if you use clinical events as defined in the EU-ADR project Type of the event to be processed. Must be either EUADR_EVENT if the event is defined in the EUADR project or UMLS if the event is a list of CUI concept identifiers Type of the event to be processed. Must be either EUADR_EVENT if the event is defined in the EUADR project or UMLS if the event is a list of CUI concept identifiers Type of the event to be processed. For the clinical events, the following types are allowed: 1) UMLS: if you use UMLS CUI concept identifiers (single identifier or a list of identifiers) 2) EUADR_event: if you use clinical events as defined in the EU-ADR project Type of the event to be processed. For the clinical events, the following types are allowed: 1) UMLS: if you use UMLS concept identifiers (single identifier or a list of identifiers) 2) EUADR_EVENT: if you use clinical events as defined in the EU-ADR project (see http://ibi.imim.es/ADR_Substantiation.html)
cytoscape	Insert here the path to your local cytoscape installation. insert here the path to your local cytoscape installation e.g. /home/user/cytoscape-v2.7.0/ insert here the path to your local cytoscape installation e.g. /home/user/cytoscape insert here the path to your local cytoscape installation e.g. /home/user/cytoscape-v2.7.0 Insert here the path to your local cytoscape installation e.g. /home/user/cytoscape-v2.7.0/ Insert here the path to your local Cytoscape installation.
eventName	Name of the event. This is only required for user-friendly visualization of the results. In particular, if the input is a CUI concept identifier. Define a name for the clinical event. This is required for user-friendly visualization of the results. Define a name for the clinical event. This is only required for user-friendly visualization of the results.

Processors (10)

Name	Type	Description
CreateDiseaseProteinList	localworker
generateProteinLists	xmlsplitter
ConvertToHTML	localworker
CheckConnectingPathways	beanshell
XPath_getPathways	localworker
xpath_value	stringconstant
TellResult	localworker
ADR_substantiation_through_proteins	workflow
CreateDrugTargetList	localworker
getPathways	wsdl

Beanshells (2)

Name	Description	Inputs	Outputs
CheckConnectingPathways		intersectionList failDisease failDrug	result
CheckConnectingProteins		intersectionList text fail	result

Outputs (7)

Name	Description
drugTargetsOutput	Full XML output for the get drug targets web service. Full XML output for the getDrugTargets web service. XML output file for the getDrugTargets web service.
drugEventLinkingPathways	List of biological pathways in which both proteins associated to the clinical event and to the drug are present. List of pathways in which at least one event and one drug protein are expressed. List of biological pathways that link the drug with the event. In each pathway contain proteins that are associated to the clinical event and to the drug.
eventProteinsOutput	Full XML output for the get Disease Associated genes web service. Full XML output for the getDiseaseAssociatedProteins web service. XML output file for the getDiseaseAssociatedProteins web service.
drugEventLinkingProteins	List of proteins that link the drug and the event. They represent the intersection between the Drug-Tarhresult from the intersection of the set of proteins annotated to the drug and the set of proteins annotated to the clinical event. List of proteins annotated to both the clinical event and the drug. List of proteins annotated to both, event and drug. List of proteins that link the drug and the event. They represent the intersection between the Drug-Target-Profile and the Event-Protein-Profile. List of proteins that result from the intersection of the set of proteins annotated to the drug and the set of proteins annotated to the clinical event.
CytoscapeResultGraph	Network file that can be visualized in Cytoscape. Simply save this file using the file extension .xgmml and open it in Cytoscape. It contains a multipartite graph in which the nodes are the drug, the clinical event and the proteins and the associations between them. Network file that which can be visualized in Cytoscape. Simply store this file using the file extension .xgmml and open it in Cytoscape. It contains a multipartite graph in which the nodes are the drug, the clinical event and the proteins and the associations between them. Network file that which can be visualized in Cytoscape. Simply save this file using the file extension .xgmml and open it in Cytoscape. It contains a multipartite graph in which the nodes are the drug, the clinical event and the proteins and the associations between them. Cytoscape graph which can be openend in Cytoscape. Simply store this file using the file ending .xgmml and open it in Cytoscape. It contains the drug, event and their annotated proteins as well as supporting information such as link outs to publications etc.
eventProteins	List of proteins annotated to the clinical event. List of all proteins annoated to the event.
drugTargets	List of proteins annotated to the drug.

Datalinks (26)

Source	Sink
ADR_substantiation_through_proteins:diseaseProteins	CreateDiseaseProteinList:string
CreateDiseaseProteinList:concatenated	generateProteinLists:eventProteins
CreateDrugTargetList:concatenated	generateProteinLists:drugProteins
atc	ConvertToHTML:atc
getPathways:intersectingPathways	ConvertToHTML:intersectingPathways
eventName	ConvertToHTML:event
XPath_getPathways:nodelist	CheckConnectingPathways:intersectionList
CreateDiseaseProteinList:fail	CheckConnectingPathways:failDisease
CreateDrugTargetList:fail	CheckConnectingPathways:failDrug
xpath_value:value	XPath_getPathways:xpath
getPathways:intersectingPathways	XPath_getPathways:xml-text
CheckConnectingPathways:result	TellResult:message
atc	ADR_substantiation_through_proteins:atc
eventType	ADR_substantiation_through_proteins:eventType
event	ADR_substantiation_through_proteins:event
eventName	ADR_substantiation_through_proteins:eventName
cytoscape	ADR_substantiation_through_proteins:cytoscape
ADR_substantiation_through_proteins:drugTargets	CreateDrugTargetList:string
generateProteinLists:output	getPathways:proteinLists
ADR_substantiation_through_proteins:drugTargetsOutput	drugTargetsOutput
ConvertToHTML:EUADR_intersectingPathways	drugEventLinkingPathways
ADR_substantiation_through_proteins:diseaseProteinsOutput	eventProteinsOutput
ADR_substantiation_through_proteins:connectingProteins	drugEventLinkingProteins
ADR_substantiation_through_proteins:CytoscapeResultGraph	CytoscapeResultGraph
ADR_substantiation_through_proteins:diseaseProteins	eventProteins
ADR_substantiation_through_proteins:drugTargets	drugTargets