{ "opencollection": "1.0.0", "info": { "name": "Pathway Analysis Service database exporter API", "version": "2.0" }, "items": [ { "info": { "name": "exporter", "type": "folder" }, "items": [ { "info": { "name": "Exports a given pathway diagram to the specified image format (png, jpg, jpeg, svg, gif)", "type": "http" }, "http": { "method": "GET", "url": "/AnalysisService/exporter/diagram/:identifier.:ext", "params": [ { "name": "identifier", "value": "R-HSA-177929", "type": "path", "description": "Event identifier (it can be a pathway with diagram, a subpathway or a reaction)" }, { "name": "ext", "value": "png", "type": "path", "description": "File extension (defines the image format)" }, { "name": "quality", "value": "5", "type": "query", "description": "Result image quality between [1 - 10]. It defines the quality of the final image (Default 5)" }, { "name": "flg", "value": "", "type": "query", "description": "Gene name, protein or chemical identifier or Reactome identifier used to flag elements in the diagram" }, { "name": "flgInteractors", "value": "", "type": "query", "description": "Defines whether to take into account interactors for the flagging" }, { "name": "sel", "value": "", "type": "query", "description": "Highlight element(s) selection in the diagram. CSV line." }, { "name": "title", "value": "true", "type": "query", "description": "Sets whether the name of the pathway is shown below" }, { "name": "margin", "value": "15", "type": "query", "description": "Defines the image margin between [0 - 20] (Default 15)" }, { "name": "ehld", "value": "true", "type": "query", "description": "Defines whether textbook-like illustration are taken into account" }, { "name": "diagramProfile", "value": "Modern", "type": "query", "description": "Diagram Color Profile" }, { "name": "token", "value": "", "type": "query", "description": "The analysis token with the results to be overlaid on top of the given diagram" }, { "name": "resource", "value": "", "type": "query", "description": "The analysis resource for which the results will be overlaid on top of the given pathways overview" }, { "name": "analysisProfile", "value": "Standard", "type": "query", "description": "Analysis Color Profile" }, { "name": "expColumn", "value": "", "type": "query", "description": "Expression column. When the token is associated to an expression analysis, this parameter allows specifying the expression column for the overlay" }, { "name": "view", "value": "", "type": "query", "description": "Global parameter - Customise the view to be more concise and/or aggregate relationships" }, { "name": "includeRef", "value": "", "type": "query", "description": "Global parameter - If true, replace element ref to dbId by standard JSOG object {@ref}" } ] }, "docs": "This method accepts identifiers for Event class instances.
When a diagrammed pathway is provided, the diagram is exported to the specified format.
When a subpathway is provided, the diagram for the parent is exported and the events that are part of the subpathways are selected.
When a reaction is provided, the diagram containing the reaction is exported and the reaction is selected.

Find out more about this method analysis token with the results to be overlaid on top of the given diagram" }, { "name": "resource", "value": "", "type": "query", "description": "The analysis resource for which the results will be overlaid on top of the given pathways overview" }, { "name": "importableOnly", "value": "", "type": "query", "description": "Filters resources to only includes importable ones" }, { "name": "expColumn", "value": "", "type": "query", "description": "Expression column. When the token is associated to an expression analysis, this parameter allows specifying the expression column for the overlay" }, { "name": "analysisProfile", "value": "Standard", "type": "query", "description": "Analysis Color Profile" }, { "name": "view", "value": "", "type": "query", "description": "Global parameter - Customise the view to be more concise and/or aggregate relationships" }, { "name": "includeRef", "value": "", "type": "query", "description": "Global parameter - If true, replace element ref to dbId by standard JSOG object {@ref}" } ] }, "docs": "This method accepts identifiers for Event class instances.
The generated document contains the details for the given event and, optionally, its children (see level parameter). These details include:
- A diagram image
- Summation
- Literature references
- Edit history
- Other details: type, location, compartments, diseases

Documents can also be overlaid with pathway an" }, { "info": { "name": "Exports a given pathway or reaction to SBGN", "type": "http" }, "http": { "method": "GET", "url": "/AnalysisService/exporter/event/:identifier.sbgn", "params": [ { "name": "identifier", "value": "R-HSA-5205682", "type": "path", "description": "DbId or StId of the requested pathway or reaction" }, { "name": "view", "value": "", "type": "query", "description": "Global parameter - Customise the view to be more concise and/or aggregate relationships" }, { "name": "includeRef", "value": "", "type": "query", "description": "Global parameter - If true, replace element ref to dbId by standard JSOG object {@ref}" } ] }, "docs": "Exports a given pathway or reaction to SBGN" }, { "info": { "name": "Exports a given pathway or reaction to SBML", "type": "http" }, "http": { "method": "GET", "url": "/AnalysisService/exporter/event/:identifier.sbml", "params": [ { "name": "identifier", "value": "R-HSA-68616", "type": "path", "description": "DbId or StId of the requested pathway or reaction" }, { "name": "view", "value": "", "type": "query", "description": "Global parameter - Customise the view to be more concise and/or aggregate relationships" }, { "name": "includeRef", "value": "", "type": "query", "description": "Global parameter - If true, replace element ref to dbId by standard JSOG object {@ref}" } ] }, "docs": "Exports a given pathway or reaction to SBML" }, { "info": { "name": "Exports a given pathway overview to the specified image format (png, jpg, jpeg, svg, gif)", "type": "http" }, "http": { "method": "GET", "url": "/AnalysisService/exporter/fireworks/:species.:ext", "params": [ { "name": "species", "value": "9606", "type": "path", "description": "Species identifier (it can be the taxonomy id, species name or dbId)" }, { "name": "ext", "value": "svg", "type": "path", "description": "File extension (defines the image format)" }, { "name": "quality", "value": "5", "type": "query", "description": "Result image quality between [1 - 10]. It defines the quality of the final image (Default 5)" }, { "name": "flg", "value": "", "type": "query", "description": "Gene name, protein or chemical identifier or Reactome identifier used to flag elements in the diagram" }, { "name": "flgInteractors", "value": "", "type": "query", "description": "Defines whether to take into account interactors for the flagging" }, { "name": "sel", "value": "", "type": "query", "description": "Highlight element(s) selection in the diagram. CSV line." }, { "name": "title", "value": "true", "type": "query", "description": "Sets whether the name of the pathway is shown below" }, { "name": "margin", "value": "15", "type": "query", "description": "Defines the image margin between [0 - 20] (Default 15)" }, { "name": "diagramProfile", "value": "Copper", "type": "query", "description": "Diagram Color Profile" }, { "name": "token", "value": "", "type": "query", "description": "The analysis token with the results to be overlaid on top of the given pathways overview" }, { "name": "resource", "value": "", "type": "query", "description": "The analysis resource for which the results will be overlaid on top of the given pathways overview" }, { "name": "expColumn", "value": "", "type": "query", "description": "Expression column. When the token is associated to an expression analysis, this parameter allows specifying the expression column for the overlay" }, { "name": "coverage", "value": "", "type": "query", "description": "Set to 'true' to overlay analysis coverage values" }, { "name": "view", "value": "", "type": "query", "description": "Global parameter - Customise the view to be more concise and/or aggregate relationships" }, { "name": "includeRef", "value": "", "type": "query", "description": "Global parameter - If true, replace element ref to dbId by standard JSOG object {@ref}" } ] }, "docs": "Exports a given pathway overview to the specified image format (png, jpg, jpeg, svg, gif)" }, { "info": { "name": "Exports a given reaction to the specified image format (png, jpg, jpeg, svg, gif)", "type": "http" }, "http": { "method": "GET", "url": "/AnalysisService/exporter/reaction/:identifier.:ext", "params": [ { "name": "identifier", "value": "R-HSA-6787403", "type": "path", "description": "Reaction identifier" }, { "name": "ext", "value": "png", "type": "path", "description": "File extension (defines the image format)" }, { "name": "quality", "value": "5", "type": "query", "description": "Result image quality between [1 - 10]. It defines the quality of the final image (Default 5)" }, { "name": "flg", "value": "", "type": "query", "description": "Gene name, protein or chemical identifier or Reactome identifier used to flag elements in the diagram" }, { "name": "flgInteractors", "value": "", "type": "query", "description": "Defines whether to take into account interactors for the flagging" }, { "name": "sel", "value": "", "type": "query", "description": "Highlight element selection in the diagram." }, { "name": "title", "value": "true", "type": "query", "description": "Sets whether the name of the reaction is shown below" }, { "name": "margin", "value": "15", "type": "query", "description": "Defines the image margin between [0 - 20] (Default 15)" }, { "name": "diagramProfile", "value": "Modern", "type": "query", "description": "Diagram Color Profile" }, { "name": "token", "value": "", "type": "query", "description": "The analysis token with the results to be overlaid on top of the given reaction" }, { "name": "analysisProfile", "value": "Standard", "type": "query", "description": "Analysis Color Profile" }, { "name": "resource", "value": "", "type": "query", "description": "The analysis resource for which the results will be overlaid on top of the given pathways overview" }, { "name": "expColumn", "value": "", "type": "query", "description": "Expression column. When the token is associated to an expression analysis, this parameter allows specifying the expression column for the overlay" }, { "name": "view", "value": "", "type": "query", "description": "Global parameter - Customise the view to be more concise and/or aggregate relationships" }, { "name": "includeRef", "value": "", "type": "query", "description": "Global parameter - If true, replace element ref to dbId by standard JSOG object {@ref}" } ] }, "docs": "This method accepts identifiers for ReactionLikeEvent class instances." } ] } ], "bundled": true }