openapi-directory/api/wikipathways.org.json

Building & bundling https://github.com/APIs-guru/openapi-directory for easy use from JS

{"openapi":"3.0.0","servers":[{"url":"https://webservice.wikipathways.org"}],"info":{"title":"WikiPathways Webservices","version":"1.0","x-origin":[{"format":"swagger","url":"http://webservice.wikipathways.org/index.php?swagger","version":"2.0"}],"x-providerName":"wikipathways.org"},"paths":{"/createPathway":{"post":{"description":"createPathwayCreate a new pathway on the wiki with the given GPML code.<br>Note: To create/modify pathways via the web service, you need to have an account with web service write permissions. Please contact us to request write access for the web service.","parameters":[{"description":"The GPML code for the new pathway","in":"query","name":"gpml","required":true,"schema":{"type":"string"}},{"description":"The authentication info","in":"query","name":"auth","required":true,"schema":{"type":"string"}},{"description":"The user name","in":"query","name":"username","required":true,"schema":{"type":"string"}},{"in":"query","name":"format","required":false,"schema":{"default":"xml","enum":["json","xml","html","dump","jpg","pdf"],"type":"string"}}],"responses":{"200":{"description":"everything ok"}},"tags":["All functions","Write (create/update/delete)"]}},"/findInteractions":{"get":{"description":"findInteractionsFind interactions defined in WikiPathways pathways.","parameters":[{"description":"The name of an entity to find interactions for (e.g. 'P53')","in":"query","name":"query","required":true,"schema":{"type":"string"}},{"in":"query","name":"format","required":false,"schema":{"default":"xml","enum":["json","xml","html","dump","jpg","pdf"],"type":"string"}}],"responses":{"200":{"description":"everything ok"}},"tags":["Search","All functions"]}},"/findPathwaysByLiterature":{"get":{"description":"findPathwaysByLiterature","parameters":[{"description":"The query, can be a pubmed id, author name or title keyword.","in":"query","name":"query","required":true,"schema":{"type":"string"}},{"in":"query","name":"format","required":false,"schema":{"default":"xml","enum":["json","xml","html","dump","jpg","pdf"],"type":"string"}}],"responses":{"200":{"description":"everything ok"}},"tags":["Search","All functions"]}},"/findPathwaysByText":{"get":{"description":"findPathwaysByText","parameters":[{"description":"The query, e.g. 'apoptosis'","in":"query","name":"query","required":true,"schema":{"type":"string"}},{"description":"Optional, limit the query by species. Leave","in":"query","name":"species","required":false,"schema":{"type":"string"}},{"in":"query","name":"format","required":false,"schema":{"default":"xml","enum":["json","xml","html","dump","jpg","pdf"],"type":"string"}}],"responses":{"200":{"description":"everything ok"}},"tags":["All functions","Search"]}},"/findPathwaysByXref":{"get":{"description":"findPathwaysByXref","parameters":[{"description":"string","explode":false,"in":"query","name":"ids","required":true,"schema":{"items":{},"type":"array"},"style":"form"},{"description":"string","explode":false,"in":"query","name":"codes","required":false,"schema":{"items":{},"type":"array"},"style":"form"},{"in":"query","name":"format","required":false,"schema":{"default":"xml","enum":["json","xml","html","dump","jpg","pdf"],"type":"string"}}],"responses":{"200":{"description":"everything ok"}},"tags":["All functions","Search"]}},"/getColoredPathway":{"get":{"description":"getColoredPathwayGet a colored image version of the pathway.","parameters":[{"description":"The pathway identifier","in":"query","name":"pwId","required":true,"schema":{"type":"string"}},{"description":"The revision of the pathway (use '0' for most recent)","in":"query","name":"revision","required":true,"schema":{"type":"string"}},{"description":"string","explode":false,"in":"query","name":"graphId","required":true,"schema":{"items":{},"type":"array"},"style":"form"},{"description":"string","explode":false,"in":"query","name":"color","required":true,"schema":{"items":{},"type":"array"},"style":"form"},{"description":"The image type (One of 'svg', 'pdf' or 'png').","in":"query","name":"fileType","required":true,"schema":{"type":"string"}},{"in":"query","name":"format","required":false,"schema":{"default":"xml","enum":["json","xml","html","dump","jpg","pdf"],"type":"string"}}],"responses":{"200":{"description":"everything ok"}},"tags":["All functions","Download"]}},"/getCurationTagHistory":{"get":{"description":"getCurationTagHistory","parameters":[{"description":"The pathway identifier","in":"query","name":"pwId","required":true,"schema":{"type":"string"}},{"description":"Only include history from after the given date","in":"query","name":"timestamp","required":false,"schema":{"type":"string"}},{"in":"query","name":"format","required":false,"schema":{"default":"xml","enum":["json","xml","html","dump","jpg","pdf"],"type":"string"}}],"responses":{"200":{"description":"everything ok"}},"tags":["All functions","History","Curation tags"]}},"/getCurationTags":{"get":{"description":"getCurationTagsGet all curation tags for the given tag name. Use this method if you want to find all pathways that are tagged with a specific curation tag.","parameters":[{"description":"The pathway identifier","in":"query","name":"pwId","required":true,"schema":{"type":"string"}},{"in":"query","name":"format","required":false,"schema":{"default":"xml","enum":["json","xml","html","dump","jpg","pdf"],"type":"string"}}],"responses":{"200":{"description":"everything ok"}},"tags":["All functions","Pathway information","Curation tags"]}},"/getCurationTagsByName":{"get":{"description":"getCurationTagsByNameGet all curation tags for the given tag name. Use this method if you want to find all pathways that are tagged with a specific curation tag.","parameters":[{"description":"The tag name","in":"query","name":"tagName","required":true,"schema":{"type":"string"}},{"in":"query","name":"format","required":false,"schema":{"default":"xml","enum":["json","xml","html","dump","jpg","pdf"],"type":"string"}}],"responses":{"200":{"description":"everything ok"}},"tags":["All functions","Pathway list","Curation tags"]}},"/getOntologyTermsByPathway":{"get":{"description":"getOntologyTermsByPathway","parameters":[{"description":"The pathway identifier","in":"query","name":"pwId","required":true,"schema":{"type":"string"}},{"in":"query","name":"format","required":false,"schema":{"default":"xml","enum":["json","xml","html","dump","jpg","pdf"],"type":"string"}}],"responses":{"200":{"description":"everything ok"}},"tags":["Pathway information","Curation tags","All functions"]}},"/getPathway":{"get":{"description":"getPathway","parameters":[{"description":"The pathway identifier","in":"query","name":"pwId","required":true,"schema":{"type":"string"}},{"description":"The revision number of the pathway (use 0 for most recent)","in":"query","name":"revision","required":false,"schema":{"type":"integer"}},{"in":"query","name":"format","required":false,"schema":{"default":"xml","enum":["json","xml","html","dump","jpg","pdf"],"type":"string"}}],"responses":{"200":{"description":"everything ok"}},"tags":["Pathway information","All functions"]}},"/getPathwayAs":{"get":{"description":"getPathwayAsDownload a pathway in the specified file format.","parameters":[{"description":"The file type to convert to, e.g.","in":"query","name":"fileType","required":true,"schema":{"type":"string"}},{"description":"The pathway identifier","in":"query","name":"pwId","required":true,"schema":{"type":"string"}},{"description":"The revision number of the pathway (use 0 for most recent)","in":"query","name":"revision","required":false,"schema":{"type":"integer"}},{"in":"query","name":"format","required":false,"schema":{"default":"xml","enum":["json","xml","html","dump","jpg","pdf"],"type":"string"}}],"responses":{"200":{"description":"everything ok"}},"tags":["Download","All functions"]}},"/getPathwayHistory":{"get":{"description":"getPathwayHistoryGet the revision history of a pathway.","parameters":[{"description":"The pathway identifier","in":"query","name":"pwId","required":true,"schema":{"type":"string"}},{"description":"Limit by time, only history items after the given","in":"query","name":"timestamp","required":true,"schema":{"type":"string"}},{"in":"query","name":"format","required":false,"schema":{"default":"xml","enum":["json","xml","html","dump","jpg","pdf"],"type":"string"}}],"responses":{"200":{"description":"everything ok"}},"tags":["History","All functions"]}},"/getPathwayInfo":{"get":{"description":"getPathwayInfoGet some general info about the pathway, such as the name, species, without downloading the GPML.","parameters":[{"description":"The pathway identifier","in":"query","name":"pwId","required":true,"schema":{"type":"string"}},{"in":"query","name":"format","required":false,"schema":{"default":"xml","enum":["json","xml","html","dump","jpg","pdf"],"type":"string"}}],"responses":{"200":{"description":"everything ok"}},"tags":["Pathway information","All functions"]}},"/getPathwaysByOntologyTerm":{"get":{"description":"getPathwaysByOntologyTerm","parameters":[{"description":"The Ontology term","in":"query","name":"term","required":true,"schema":{"type":"string"}},{"in":"query","name":"format","required":false,"schema":{"default":"xml","enum":["json","xml","html","dump","jpg","pdf"],"type":"string"}}],"responses":{"200":{"description":"everything ok"}},"tags":["Pathway list","Ontology tags","All functions"]}},"/getPathwaysByParentOntologyTerm":{"get":{"description":"getPathwaysByParentOntologyTerm","parameters":[{"description":"The Ontology term","in":"query","name":"term","required":true,"schema":{"type":"string"}},{"in":"query","name":"format","required":false,"schema":{"default":"xml","enum":["json","xml","html","dump","jpg","pdf"],"type":"string"}}],"responses":{"200":{"description":"everything ok"}},"tags":["Pathway list","Ontology tags","All functions"]}},"/getRecentChanges":{"get":{"description":"getRecentChangesGet the recently changed pathways.<br>Note: the recent changes table only retains items for a limited time (2 months), so there is no guarantee that you will get all changes when the timestamp points to a date that is more than 2 months in the past.","parameters":[{"description":"Get the changes after this time","in":"query","name":"timestamp","required":true,"schema":{"type":"string"}},{"in":"query","name":"format","required":false,"schema":{"default":"xml","enum":["json","xml","html","dump","jpg","pdf"],"type":"string"}}],"responses":{"200":{"description":"everything ok"}},"tags":["History","All functions"]}},"/getUserByOrcid":{"get":{"description":"getUserByOrcid","parameters":[{"description":"string","in":"query","name":"orcid","required":true,"schema":{"type":"string"}},{"in":"query","name":"format","required":false,"schema":{"default":"xml","enum":["json","xml","html","dump","jpg","pdf"],"type":"string"}}],"responses":{"200":{"description":"everything ok"}},"tags":["User management","All functions"]}},"/getXrefList":{"get":{"description":"getXrefList","parameters":[{"description":"The pathway identifier.","in":"query","name":"pwId","required":true,"schema":{"type":"string"}},{"description":"The database code to translate to (e.g. 'S' for UniProt).","in":"query","name":"code","required":true,"schema":{"type":"string"}},{"in":"query","name":"format","required":false,"schema":{"default":"xml","enum":["json","xml","html","dump","jpg","pdf"],"type":"string"}}],"responses":{"200":{"description":"everything ok"}},"tags":["Download","All functions"]}},"/listOrganisms":{"get":{"description":"listOrganisms","parameters":[{"in":"query","name":"format","required":false,"schema":{"default":"xml","enum":["json","xml","html","dump","jpg","pdf"],"type":"string"}}],"responses":{"200":{"description":"everything ok"}},"tags":["Organism list","All functions"]}},"/listPathways":{"get":{"description":"listPathways","parameters":[{"description":"The organism to filter by (optional)","in":"query","name":"organism","required":false,"schema":{"type":"string"}},{"in":"query","name":"format","required":false,"schema":{"default":"xml","enum":["json","xml","html","dump","jpg","pdf"],"type":"string"}}],"responses":{"200":{"description":"everything ok"}},"tags":["Pathway list","All functions"]}},"/login":{"get":{"description":"loginStart a logged in session, using an existing WikiPathways account. This function will return an authentication code that can be used to excecute methods that need authentication (e.g. updatePathway).","parameters":[{"description":"The usernameset_include_path(get_include_path().PATH_SEPARATOR.realpath('../includes').PATH_SEPARATOR.realpath('../').PATH_SEPARATOR);","in":"query","name":"name","required":true,"schema":{"type":"string"}},{"description":"The password","in":"query","name":"pass","required":true,"schema":{"type":"string"}},{"in":"query","name":"format","required":false,"schema":{"default":"xml","enum":["json","xml","html","dump","jpg","pdf"],"type":"string"}}],"responses":{"200":{"description":"everything ok"}},"tags":["User management","All functions"]}},"/removeCurationTag":{"get":{"description":"removeCurationTagRemove a curation tag from a pathway.","parameters":[{"description":"The pathway identifier","in":"query","name":"pwId","required":true,"schema":{"type":"string"}},{"description":"The name of the tag to apply","in":"query","name":"tagName","required":true,"schema":{"type":"string"}},{"description":"The authentication data","in":"query","name":"auth","required":true,"schema":{"type":"string"}},{"description":"The user name","in":"query","name":"username","required":true,"schema":{"type":"string"}},{"in":"query","name":"format","required":false,"schema":{"default":"xml","enum":["json","xml","html","dump","jpg","pdf"],"type":"string"}}],"responses":{"200":{"description":"everything ok"}},"tags":["All functions","Search"]}},"/removeOntologyTag":{"get":{"description":"removeOntologyTag","parameters":[{"description":"The pathway identifier","in":"query","name":"pwId","required":true,"schema":{"type":"string"}},{"description":"The ontology term identifier in the ontology","in":"query","name":"termId","required":true,"schema":{"type":"string"}},{"description":"The authentication key","in":"query","name":"auth","required":true,"schema":{"type":"string"}},{"description":"The username","in":"query","name":"user","required":true,"schema":{"type":"string"}},{"in":"query","name":"format","required":false,"schema":{"default":"xml","enum":["json","xml","html","dump","jpg","pdf"],"type":"string"}}],"responses":{"200":{"description":"everything ok"}},"tags":["Write (create/update/delete)","Ontology tags","All functions"]}},"/saveCurationTag":{"get":{"description":"saveCurationTag","parameters":[{"description":"The pathway identifier","in":"query","name":"pwId","required":true,"schema":{"type":"string"}},{"description":"The name of the tag to apply","in":"query","name":"tagName","required":true,"schema":{"type":"string"}},{"description":"string","in":"query","name":"text","required":true,"schema":{"type":"string"}},{"description":"The revision this tag applies to","in":"query","name":"revision","required":true,"schema":{"type":"integer"}},{"description":"The authentication key","in":"query","name":"auth","required":true,"schema":{"type":"string"}},{"description":"The user name","in":"query","name":"username","required":true,"schema":{"type":"string"}},{"in":"query","name":"format","required":false,"schema":{"default":"xml","enum":["json","xml","html","dump","jpg","pdf"],"type":"string"}}],"responses":{"200":{"description":"everything ok"}},"tags":["All functions","Write (create/update/delete)","Curation tags"]}},"/saveOntologyTag":{"get":{"description":"saveOntologyTag","parameters":[{"description":"The pathway identifier","in":"query","name":"pwId","required":true,"schema":{"type":"string"}},{"description":"The ontology term to apply","in":"query","name":"term","required":true,"schema":{"type":"string"}},{"description":"The identifier of the term in the ontology","in":"query","name":"termId","required":true,"schema":{"type":"string"}},{"description":"The authentication key","in":"query","name":"auth","required":true,"schema":{"type":"string"}},{"description":"The username","in":"query","name":"user","required":true,"schema":{"type":"string"}},{"in":"query","name":"format","required":false,"schema":{"default":"xml","enum":["json","xml","html","dump","jpg","pdf"],"type":"string"}}],"responses":{"200":{"description":"everything ok"}},"tags":["Write (create/update/delete)","Ontology tags","All functions"]}},"/updatePathway":{"get":{"description":"updatePathwayUpdate a pathway on the wiki with the given GPML code.<br>Note: To create/modify pathways via the web service, you need to have an account with web service write permissions. Please contact us to request write access for the web service.","parameters":[{"description":"The pathway identifier","in":"query","name":"pwId","required":true,"schema":{"type":"string"}},{"description":"A description of the modifications","in":"query","name":"description","required":true,"schema":{"type":"string"}},{"description":"The updated GPML code","in":"query","name":"gpml","required":true,"schema":{"type":"string"}},{"description":"The revision the GPML code is based on","in":"query","name":"revision","required":true,"schema":{"type":"integer"}},{"description":"The authentication key","in":"query","name":"auth","required":true,"schema":{"type":"string"}},{"description":"The username","in":"query","name":"username","required":true,"schema":{"type":"string"}},{"in":"query","name":"format","required":false,"schema":{"default":"xml","enum":["json","xml","html","dump","jpg","pdf"],"type":"string"}}],"responses":{"200":{"description":"everything ok"}},"tags":["Write (create/update/delete)","All functions"]}}}}