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Only hit pathway with pValue equals or below the threshold will be returned","required":false,"schema":{"type":"number","format":"double","default":1.0},"example":1},{"name":"includeDisease","in":"query","description":"set to 'false' to exclude the disease pathways from the result (it does not alter the statistics)","required":false,"schema":{"type":"boolean","default":true},"example":true},{"name":"min","in":"query","description":"minimum number of contained entities per pathway (takes into account the resource)","required":false,"schema":{"type":"integer","format":"int32"}},{"name":"max","in":"query","description":"maximum number of contained entities per pathway (takes into account the resource)","required":false,"schema":{"type":"integer","format":"int32"}},{"name":"importableOnly","in":"query","description":"Filters resources to only includes importable ones","required":false,"schema":{"type":"boolean","default":false}}],"requestBody":{"description":"<b>url</b> A URL pointing to the data to be analysed","content":{"text/plain":{"schema":{"type":"string"}}},"required":true},"responses":{"400":{"description":"Bad request","content":{"application/json":{"schema":{"$ref":"#/components/schemas/AnalysisResult"}}}},"413":{"description":"The file size is larger than the maximum configured size (50MB)","content":{"application/json":{"schema":{"$ref":"#/components/schemas/AnalysisResult"}}}},"415":{"description":"Unsupported Media Type (only 'text/plain')","content":{"application/json":{"schema":{"$ref":"#/components/schemas/AnalysisResult"}}}},"422":{"description":"The provided URL is not processable","content":{"application/json":{"schema":{"$ref":"#/components/schemas/AnalysisResult"}}}}}}},"/import/":{"post":{"tags":["import"],"summary":"Imports the posted json into the service","description":"The accepted format is the same as provided by the method <a href='#/download/downloadResultJSONUsingGET'>/#/download/{token}/result.json</a>.","operationId":"getPostText","requestBody":{"description":"<b>input</b> Identifiers to analyse followed by their expression (when applies)","content":{"application/gzip":{"schema":{"type":"string"}},"application/json":{"schema":{"type":"string"}},"application/zip":{"schema":{"type":"string"}},"text/plain":{"schema":{"type":"string"}}},"required":true},"responses":{"400":{"description":"Bad request. See more details in the response body","content":{"application/json":{"schema":{"$ref":"#/components/schemas/AnalysisSummary"}}}},"415":{"description":"Unsupported Media Type (only 'text/plain' or 'application/json')","content":{"application/json":{"schema":{"$ref":"#/components/schemas/AnalysisSummary"}}}}}}},"/import/form":{"post":{"tags":["import"],"summary":"Imports the posted json file into the service","description":"The accepted format is the same as provided by the method <a href='#/download/downloadResultJSONUsingGET'>/#/download/{token}/result.json</a>. Note: The submitted file can be gzipped.","operationId":"getPostFile","requestBody":{"content":{"multipart/form-data":{"schema":{"type":"object","properties":{"file":{"type":"string","format":"binary","description":"A file with the data to be analysed"}},"required":["file"]}}}},"responses":{"400":{"description":"Bad request. See more details in the response body","content":{"application/json":{"schema":{"$ref":"#/components/schemas/AnalysisSummary"}}}},"413":{"description":"The file size is larger than the maximum configured size (50MB)","content":{"application/json":{"schema":{"$ref":"#/components/schemas/AnalysisSummary"}}}},"415":{"description":"Unsupported Media Type (only 'text/plain' or 'application/json')","content":{"application/json":{"schema":{"$ref":"#/components/schemas/AnalysisSummary"}}}}}}},"/import/url":{"post":{"tags":["import"],"summary":"Imports the json file provided by the posted url into the service","description":"The accepted format is the same as provided by the method <a href='#/download/downloadResultJSONUsingGET'>/#/download/{token}/result.json</a>. 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See more details in the response body","content":{"application/json":{"schema":{"$ref":"#/components/schemas/AnalysisSummary"}}}},"413":{"description":"The file size is larger than the maximum configured size (50MB)","content":{"application/json":{"schema":{"$ref":"#/components/schemas/AnalysisSummary"}}}},"415":{"description":"Unsupported Media Type (only 'text/plain')","content":{"application/json":{"schema":{"$ref":"#/components/schemas/AnalysisSummary"}}}},"422":{"description":"The provided URL is not processable","content":{"application/json":{"schema":{"$ref":"#/components/schemas/AnalysisSummary"}}}}}}},"/mapping/":{"post":{"tags":["mapping"],"description":"Maps the post identifiers over the different species","operationId":"getMapping","parameters":[{"name":"interactors","in":"query","description":"Include interactors","required":false,"schema":{"type":"boolean","default":false},"example":false},{"name":"importableOnly","in":"query","description":"Only include resources which can be later imported","required":false,"schema":{"type":"boolean","default":false},"example":false}],"requestBody":{"description":"<b>input</b> Identifiers to be mapped (if expression values åre submitted these will be omitted in the result)","content":{"text/plain":{"schema":{"type":"string"}}},"required":true},"responses":{" 400":{"description":"Bad request","content":{"application/json":{"schema":{"type":"array","items":{"$ref":"#/components/schemas/MappedEntity"}}}}}}}},"/mapping/form":{"post":{"tags":["mapping"],"description":"Maps the identifiers in the file over the different species","operationId":"getMappingPostFile","parameters":[{"name":"interactors","in":"query","description":"Include interactors","required":false,"schema":{"type":"boolean","default":false},"example":false},{"name":"importableOnly","in":"query","description":"Only include resources which can be later imported","required":false,"schema":{"type":"boolean","default":false},"example":false}],"requestBody":{"content":{"multipart/form-data":{"schema":{"type":"object","properties":{"file":{"type":"string","format":"binary","description":"A file with the data to be mapped"}},"required":["file"]}}}},"responses":{"400":{"description":"Bad request","content":{"application/json":{"schema":{"type":"array","items":{"$ref":"#/components/schemas/MappedEntity"}}}}},"413":{"description":"The file size is larger than the maximum configured size (50MB)","content":{"application/json":{"schema":{"type":"array","items":{"$ref":"#/components/schemas/MappedEntity"}}}}},"415":{"description":"Unsupported Media Type (only 'text/plain')","content":{"application/json":{"schema":{"type":"array","items":{"$ref":"#/components/schemas/MappedEntity"}}}}}}}},"/mapping/form/projection":{"post":{"tags":["mapping"],"summary":"Maps the identifiers in the file over the different species and projects the result to Homo 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(50MB)","content":{"application/json":{"schema":{"type":"array","items":{"$ref":"#/components/schemas/MappedEntity"}}}}},"415":{"description":"Unsupported Media Type (only 'text/plain')","content":{"application/json":{"schema":{"type":"array","items":{"$ref":"#/components/schemas/MappedEntity"}}}}}}}},"/mapping/projection":{"post":{"tags":["mapping"],"summary":"Maps the post identifiers over the different species and projects the result to Homo Sapiens","description":"The projection is calculated by the orthologous slot in the Reactome database.","operationId":"getMappingToHuman","parameters":[{"name":"interactors","in":"query","description":"Include interactors","required":false,"schema":{"type":"boolean","default":false},"example":false},{"name":"importableOnly","in":"query","description":"Only include resources which can be later imported","required":false,"schema":{"type":"boolean","default":false},"example":false}],"requestBody":{"description":"<b>input</b> Identifiers to be mapped (if expression values are submitted these will be omitted in the result)","content":{"text/plain":{"schema":{"type":"string"}}},"required":true},"responses":{"400":{"description":"Bad request","content":{"application/json":{"schema":{"type":"array","items":{"$ref":"#/components/schemas/MappedEntity"}}}}}}}},"/mapping/url":{"post":{"tags":["mapping"],"summary":"Maps the identifiers contained in the provided url over the different species","operationId":"getMappingPostURL","parameters":[{"name":"interactors","in":"query","description":"Include interactors","required":false,"schema":{"type":"boolean","default":false},"example":false},{"name":"importableOnly","in":"query","description":"Only include resources which can be later imported","required":false,"schema":{"type":"boolean","default":false},"example":false}],"requestBody":{"description":"<b>url</b> A URL pointing to the data to be mapped","content":{"text/plain":{"schema":{"type":"string","description":"A URL pointing to the data to be mapped"}}},"required":true},"responses":{"400":{"description":"Bad request","content":{"application/json":{"schema":{"type":"array","items":{"$ref":"#/components/schemas/MappedEntity"}}}}},"413":{"description":"The file size is larger than the maximum configured size (50MB)","content":{"application/json":{"schema":{"type":"array","items":{"$ref":"#/components/schemas/MappedEntity"}}}}},"415":{"description":"Unsupported Media Type (only 'text/plain')","content":{"application/json":{"schema":{"type":"array","items":{"$ref":"#/components/schemas/MappedEntity"}}}}},"422":{"description":"The provided URL is not processable","content":{"application/json":{"schema":{"type":"array","items":{"$ref":"#/components/schemas/MappedEntity"}}}}}}}},"/mapping/url/projection":{"post":{"tags":["mapping"],"summary":"Maps the identifiers contained in the provided url over the different species and projects the result to Homo Sapiens","description":"The projection is calculated by the orthologous slot in the Reactome database.","operationId":"getMappingPostURLToHuman","parameters":[{"name":"interactors","in":"query","description":"Include interactors","required":false,"schema":{"type":"boolean","default":false},"example":false},{"name":"importableOnly","in":"query","description":"Only include resources which can be later imported","required":false,"schema":{"type":"boolean","default":false},"example":false}],"requestBody":{"description":"<b>url</b> A URL pointing to the data to be analysed","content":{"text/plain":{"schema":{"type":"string"}}},"required":true},"responses":{"400":{"description":"Bad request","content":{"application/json":{"schema":{"type":"array","items":{"$ref":"#/components/schemas/MappedEntity"}}}}},"413":{"description":"The file size is larger than the maximum configured size (50MB)","content":{"application/json":{"schema":{"type":"array","items":{"$ref":"#/components/schemas/MappedEntity"}}}}},"415":{"description":"Unsupported Media Type (only 'text/plain')","content":{"application/json":{"schema":{"type":"array","items":{"$ref":"#/components/schemas/MappedEntity"}}}}},"422":{"description":"The provided URL is not processable","content":{"application/json":{"schema":{"type":"array","items":{"$ref":"#/components/schemas/MappedEntity"}}}}}}}},"/report/{token}/{species}/{filename}.pdf":{"get":{"tags":["report"],"summary":"Downloads a report for a given pathway analysis result","description":"This method provides a report for a given pathway analysis result in a PDF document. This document contains data about the analysis itself followed by the pathways overview and the most significant pathways overlaid with the analysis result. Users can download and store this information in a convenient format to be checked in the future when the 'token' is not longer available.","operationId":"generatePdfReport","parameters":[{"name":"token","in":"path","description":"The token associated with the data to query","required":true,"schema":{"type":"string"}},{"name":"species","in":"path","description":"The species for which results will be reported","required":true,"schema":{"type":"string"},"example":"Homo sapiens"},{"name":"filename","in":"path","description":"The name of the file to be downloaded","required":true,"schema":{"type":"string"},"example":"report"},{"name":"number","in":"query","description":"Number of pathways reported (max 50)","required":false,"schema":{"type":"integer","format":"int32","default":25},"example":25},{"name":"resource","in":"query","required":false,"schema":{"type":"string","description":"the resource to sort","example":"TOTAL","enum":["TOTAL","UNIPROT","ENSEMBL","CHEBI","IUPHAR","MIRBASE","NCBI_PROTEIN","EMBL","COMPOUND","PUBCHEM_COMPOUND"]}},{"name":"importableOnly","in":"query","description":"Filters resources to only includes importable ones","required":false,"schema":{"type":"boolean","default":false}},{"name":"diagramProfile","in":"query","required":false,"schema":{"type":"string","description":"Diagram Color Profile","example":"Modern","enum":["Modern","Standard"]}},{"name":"analysisProfile","in":"query","required":false,"schema":{"type":"string","description":"Analysis  Color Profile","example":"Standard","enum":["Standard","Strosobar","Copper Plus"]}},{"name":"fireworksProfile","in":"query","required":false,"schema":{"type":"string","description":"Diagram Color Profile","example":"Barium Lithium","enum":["Cooper","Cooper Plus","Barium Lithium","Calcium Salts"]}}],"responses":{"404":{"description":"No result corresponding to the token was found"},"410":{"description":"Result deleted due to a new data release"}}}},"/species/homoSapiens/{species}":{"get":{"tags":["species"],"summary":"Compares Homo sapiens to the specified species","description":"Use page and pageSize to reduce the amount of data retrieved. Use sortBy and order to sort the result by your preferred option. The resource field will filter the results to show only those corresponding to the preferred molecule type (TOTAL includes all the different molecules type)","operationId":"compareHomoSapiensTo","parameters":[{"name":"species","in":"path","description":"The dbId of the species to compare to","required":true,"schema":{"type":"integer","format":"int64"}},{"name":"pageSize","in":"query","description":"pathways per page","required":false,"schema":{"type":"integer","format":"int32"},"example":20},{"name":"page","in":"query","description":"page number","required":false,"schema":{"type":"integer","format":"int32"},"example":1},{"name":"sortBy","in":"query","required":false,"schema":{"type":"string","description":"how to sort the result","example":"ENTITIES_PVALUE","enum":["NAME","TOTAL_ENTITIES","TOTAL_INTERACTORS","TOTAL_REACTIONS","FOUND_ENTITIES","FOUND_INTERACTORS","FOUND_REACTIONS","ENTITIES_RATIO","ENTITIES_PVALUE","ENTITIES_FDR","REACTIONS_RATIO"]}},{"name":"order","in":"query","required":false,"schema":{"type":"string","description":"specifies the order","example":"ASC","enum":["ASC","DESC"]}},{"name":"resource","in":"query","required":false,"schema":{"type":"string","description":"the resource to sort","example":"TOTAL","enum":["TOTAL","UNIPROT","ENSEMBL","CHEBI","IUPHAR","MIRBASE","NCBI_PROTEIN","EMBL","COMPOUND","PUBCHEM_COMPOUND"]}},{"name":"pValue","in":"query","description":"defines the pValue threshold. Only hit pathway with pValue equals or below the threshold will be returned","required":false,"schema":{"type":"number","format":"double","default":1.0},"example":1},{"name":"min","in":"query","description":"minimum number of contained entities per pathway (takes into account the resource)","required":false,"schema":{"type":"integer","format":"int32"}},{"name":"max","in":"query","description":"maximum number of contained entities per pathway (takes into account the resource)","required":false,"schema":{"type":"integer","format":"int32"}},{"name":"importableOnly","in":"query","description":"Filters resources to only includes importable ones","required":false,"schema":{"type":"boolean","default":false}}],"responses":{"404":{"description":"Species identifier does not match with any of the species in the current data","content":{"application/json":{"schema":{"$ref":"#/components/schemas/AnalysisResult"}}}}}}},"/token/{token}":{"get":{"tags":["token"],"summary":"Returns the result associated with the token","description":"Use page and pageSize to reduce the amount of data retrieved. 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Only hit pathway with pValue equals or below the threshold will be returned","required":false,"schema":{"type":"number","format":"double","default":1.0},"example":1},{"name":"includeDisease","in":"query","description":"set to 'false' to exclude the disease pathways from the result (it does not alter the statistics)","required":false,"schema":{"type":"boolean"}},{"name":"min","in":"query","description":"minimum number of contained entities per pathway (takes into account the resource)","required":false,"schema":{"type":"integer","format":"int32"}},{"name":"max","in":"query","description":"maximum number of contained entities per pathway (takes into account the resource)","required":false,"schema":{"type":"integer","format":"int32"}},{"name":"importableOnly","in":"query","description":"Filters resources to only includes importable ones","required":false,"schema":{"type":"boolean","default":false}}],"responses":{"404":{"description":"No result corresponding to the token was found","content":{"application/json":{"schema":{"$ref":"#/components/schemas/AnalysisResult"}}}},"410":{"description":"Result deleted due to a new data release","content":{"application/json":{"schema":{"$ref":"#/components/schemas/AnalysisResult"}}}}}}},"/token/{token}/filter/pathways":{"post":{"tags":["token"],"summary":"Returns the result for the pathway ids sent by post (when they are present in the original result)","description":"For a given list of pathway identifiers it will retrieve a list containing those that are present in the result (with the results for the indicated molecule type)","operationId":"getTokenFilterPathways","parameters":[{"name":"token","in":"path","description":"The token associated with the data to query","required":true,"schema":{"type":"string"}},{"name":"resource","in":"query","required":false,"schema":{"type":"string","description":"the resource to sort","example":"TOTAL","enum":["TOTAL","UNIPROT","ENSEMBL","CHEBI","IUPHAR","MIRBASE","NCBI_PROTEIN","EMBL","COMPOUND","PUBCHEM_COMPOUND"]}},{"name":"pValue","in":"query","description":"defines the pValue threshold. Only hit pathway with pValue equals or below the threshold will be returned","required":false,"schema":{"type":"number","format":"double","default":1.0},"example":1},{"name":"species","in":"query","description":"list of species to filter the result (accepts taxonomy ids, species names and dbId)","required":false,"schema":{"type":"string"}},{"name":"includeDisease","in":"query","description":"set to 'false' to exclude the disease pathways from the result (it does not alter the statistics)","required":false,"schema":{"type":"boolean"}},{"name":"min","in":"query","description":"minimum number of contained entities per pathway (takes into account the resource)","required":false,"schema":{"type":"integer","format":"int32"}},{"name":"max","in":"query","description":"maximum number of contained entities per pathway (takes into account the resource)","required":false,"schema":{"type":"integer","format":"int32"}},{"name":"importableOnly","in":"query","description":"Filters resources to only includes importable ones","required":false,"schema":{"type":"boolean","default":false}}],"requestBody":{"description":"<b>input</b> A comma separated list with the identifiers of the pathways of interest (NOTE: is plain text, not json)","content":{"text/plain":{"schema":{"type":"string"}}},"required":true},"responses":{"404":{"description":"No result corresponding to the token was found","content":{"application/json":{"schema":{"type":"array","items":{"$ref":"#/components/schemas/PathwaySummary"}}}}},"410":{"description":"Result deleted due to a new data release","content":{"application/json":{"schema":{"type":"array","items":{"$ref":"#/components/schemas/PathwaySummary"}}}}}}}},"/token/{token}/filter/species/{species}":{"get":{"tags":["token"],"summary":"Filters the result by species","operationId":"filterBySpecies","parameters":[{"name":"token","in":"path","description":"The token associated with the data to query","required":true,"schema":{"type":"string"}},{"name":"species","in":"path","description":"The species to filter the result (accepts the taxonomy id, species names and dbId)","required":true,"schema":{"type":"string"}},{"name":"sortBy","in":"query","required":false,"schema":{"type":"string","description":"how to sort the result","example":"ENTITIES_PVALUE","enum":["NAME","TOTAL_ENTITIES","TOTAL_INTERACTORS","TOTAL_REACTIONS","FOUND_ENTITIES","FOUND_INTERACTORS","FOUND_REACTIONS","ENTITIES_RATIO","ENTITIES_PVALUE","ENTITIES_FDR","REACTIONS_RATIO"]}},{"name":"order","in":"query","required":false,"schema":{"type":"string","description":"specifies the order","example":"ASC","enum":["ASC","DESC"]}},{"name":"resource","in":"query","required":false,"schema":{"type":"string","description":"the resource to sort","example":"TOTAL","enum":["TOTAL","UNIPROT","ENSEMBL","CHEBI","IUPHAR","MIRBASE","NCBI_PROTEIN","EMBL","COMPOUND","PUBCHEM_COMPOUND"]}},{"name":"importableOnly","in":"query","description":"Filters resources to only includes importable ones","required":false,"schema":{"type":"boolean","default":false}}],"responses":{"404":{"description":"No result corresponding to the token was found","content":{"application/json":{"schema":{"$ref":"#/components/schemas/SpeciesFilteredResult"}}}},"410":{"description":"Result deleted due to a new data release","content":{"application/json":{"schema":{"$ref":"#/components/schemas/SpeciesFilteredResult"}}}}}}},"/token/{token}/found/all":{"post":{"tags":["token"],"summary":"Returns a summary of the contained identifiers and interactors for each requested pathway and a given token","description":"The identifiers submitted by the user that have a match in Reactome database. 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