{"swagger":"2.0","info":{"title":"WikiPathways Webservices","version":"1.0"},"host":"webservice.wikipathways.org","schemes":["https"],"basePath":"\/","paths":{"\/listOrganisms":{"get":{"description":"listOrganisms","produces":["application\/json","application\/xml","text\/html","text\/xml"],"parameters":[{"name":"format","required":false,"in":"query","type":"string","default":"xml","enum":["json","xml","html","dump","jpg","pdf"]}],"responses":{"200":{"description":"everything ok"}},"tags":["Organism list","All functions"]}},"\/listPathways":{"get":{"description":"listPathways","produces":["application\/json","application\/xml","text\/html","text\/xml"],"parameters":[{"name":"organism","required":false,"in":"query","type":"string","description":"The organism to filter by (optional)"},{"name":"format","required":false,"in":"query","type":"string","default":"xml","enum":["json","xml","html","dump","jpg","pdf"]}],"responses":{"200":{"description":"everything ok"}},"tags":["Pathway list","All functions"]}},"\/getPathway":{"get":{"description":"getPathway","produces":["application\/json","application\/xml","text\/html","text\/xml"],"parameters":[{"name":"pwId","required":true,"in":"query","type":"string","description":"The pathway identifier"},{"name":"revision","required":false,"in":"query","type":"integer","description":"The revision number of the pathway (use 0 for most recent)"},{"name":"format","required":false,"in":"query","type":"string","default":"xml","enum":["json","xml","html","dump","jpg","pdf"]}],"responses":{"200":{"description":"everything ok"}},"tags":["Pathway information","All functions"]}},"\/getPathwayInfo":{"get":{"description":"getPathwayInfoGet some general info about the pathway, such as the name, species, without downloading the GPML.","produces":["application\/json","application\/xml","text\/html","text\/xml"],"parameters":[{"name":"pwId","required":true,"in":"query","type":"string","description":"The pathway identifier"},{"name":"format","required":false,"in":"query","type":"string","default":"xml","enum":["json","xml","html","dump","jpg","pdf"]}],"responses":{"200":{"description":"everything ok"}},"tags":["Pathway information","All functions"]}},"\/getPathwayHistory":{"get":{"description":"getPathwayHistoryGet the revision history of a pathway.","produces":["application\/json","application\/xml","text\/html","text\/xml"],"parameters":[{"name":"pwId","required":true,"in":"query","type":"string","description":"The pathway identifier"},{"name":"timestamp","required":true,"in":"query","type":"string","description":"Limit by time, only history items after the given"},{"name":"format","required":false,"in":"query","type":"string","default":"xml","enum":["json","xml","html","dump","jpg","pdf"]}],"responses":{"200":{"description":"everything ok"}},"tags":["History","All functions"]}},"\/getRecentChanges":{"get":{"description":"getRecentChangesGet the recently changed pathways.
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.","produces":["application\/json","application\/xml","text\/html","text\/xml"],"parameters":[{"name":"timestamp","required":true,"in":"query","type":"string","description":"Get the changes after this time"},{"name":"format","required":false,"in":"query","type":"string","default":"xml","enum":["json","xml","html","dump","jpg","pdf"]}],"responses":{"200":{"description":"everything ok"}},"tags":["History","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).","produces":["application\/json","application\/xml","text\/html","text\/xml"],"parameters":[{"name":"name","required":true,"in":"query","type":"string","description":"The usernameset_include_path(get_include_path().PATH_SEPARATOR.realpath('..\/includes').PATH_SEPARATOR.realpath('..\/').PATH_SEPARATOR);"},{"name":"pass","required":true,"in":"query","type":"string","description":"The password"},{"name":"format","required":false,"in":"query","type":"string","default":"xml","enum":["json","xml","html","dump","jpg","pdf"]}],"responses":{"200":{"description":"everything ok"}},"tags":["User management","All functions"]}},"\/getPathwayAs":{"get":{"description":"getPathwayAsDownload a pathway in the specified file format.","produces":["application\/json","application\/xml","text\/html","text\/xml"],"parameters":[{"name":"fileType","required":true,"in":"query","type":"string","description":"The file type to convert to, e.g."},{"name":"pwId","required":true,"in":"query","type":"string","description":"The pathway identifier"},{"name":"revision","required":false,"in":"query","type":"integer","description":"The revision number of the pathway (use 0 for most recent)"},{"name":"format","required":false,"in":"query","type":"string","default":"xml","enum":["json","xml","html","dump","jpg","pdf"]}],"responses":{"200":{"description":"everything ok"}},"tags":["Download","All functions"]}},"\/updatePathway":{"get":{"description":"updatePathwayUpdate a pathway on the wiki with the given GPML code.
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.","produces":["application\/json","application\/xml","text\/html","text\/xml"],"parameters":[{"name":"pwId","required":true,"in":"query","type":"string","description":"The pathway identifier"},{"name":"description","required":true,"in":"query","type":"string","description":"A description of the modifications"},{"name":"gpml","required":true,"in":"query","type":"string","description":"The updated GPML code"},{"name":"revision","required":true,"in":"query","type":"integer","description":"The revision the GPML code is based on"},{"name":"auth","required":true,"in":"query","type":"string","description":"The authentication key"},{"name":"username","required":true,"in":"query","type":"string","description":"The username"},{"name":"format","required":false,"in":"query","type":"string","default":"xml","enum":["json","xml","html","dump","jpg","pdf"]}],"responses":{"200":{"description":"everything ok"}},"tags":["Write (create\/update\/delete)","All functions"]}},"\/createPathway":{"post":{"description":"createPathwayCreate a new pathway on the wiki with the given GPML code.
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.","produces":["application\/json","application\/xml","text\/html","text\/xml"],"parameters":[{"name":"gpml","required":true,"in":"query","type":"string","description":"The GPML code for the new pathway"},{"name":"auth","required":true,"in":"query","type":"string","description":"The authentication info"},{"name":"username","required":true,"in":"query","type":"string","description":"The user name"},{"name":"format","required":false,"in":"query","type":"string","default":"xml","enum":["json","xml","html","dump","jpg","pdf"]}],"responses":{"200":{"description":"everything ok"}},"tags":["All functions","Write (create\/update\/delete)"]}},"\/findPathwaysByText":{"get":{"description":"findPathwaysByText","produces":["application\/json","application\/xml","text\/html","text\/xml"],"parameters":[{"name":"query","required":true,"in":"query","type":"string","description":"The query, e.g. 'apoptosis'"},{"name":"species","required":false,"in":"query","type":"string","description":"Optional, limit the query by species. Leave"},{"name":"format","required":false,"in":"query","type":"string","default":"xml","enum":["json","xml","html","dump","jpg","pdf"]}],"responses":{"200":{"description":"everything ok"}},"tags":["All functions","Search"]}},"\/findPathwaysByXref":{"get":{"description":"findPathwaysByXref","produces":["application\/json","application\/xml","text\/html","text\/xml"],"parameters":[{"name":"ids","required":true,"in":"query","type":"array","description":"string"},{"name":"codes","required":false,"in":"query","type":"array","description":"string"},{"name":"format","required":false,"in":"query","type":"string","default":"xml","enum":["json","xml","html","dump","jpg","pdf"]}],"responses":{"200":{"description":"everything ok"}},"tags":["All functions","Search"]}},"\/removeCurationTag":{"get":{"description":"removeCurationTagRemove a curation tag from a pathway.","produces":["application\/json","application\/xml","text\/html","text\/xml"],"parameters":[{"name":"pwId","required":true,"in":"query","type":"string","description":"The pathway identifier"},{"name":"tagName","required":true,"in":"query","type":"string","description":"The name of the tag to apply"},{"name":"auth","required":true,"in":"query","type":"string","description":"The authentication data"},{"name":"username","required":true,"in":"query","type":"string","description":"The user name"},{"name":"format","required":false,"in":"query","type":"string","default":"xml","enum":["json","xml","html","dump","jpg","pdf"]}],"responses":{"200":{"description":"everything ok"}},"tags":["All functions","Search"]}},"\/saveCurationTag":{"get":{"description":"saveCurationTag","produces":["application\/json","application\/xml","text\/html","text\/xml"],"parameters":[{"name":"pwId","required":true,"in":"query","type":"string","description":"The pathway identifier"},{"name":"tagName","required":true,"in":"query","type":"string","description":"The name of the tag to apply"},{"name":"text","required":true,"in":"query","type":"string","description":"string"},{"name":"revision","required":true,"in":"query","type":"integer","description":"The revision this tag applies to"},{"name":"auth","required":true,"in":"query","type":"string","description":"The authentication key"},{"name":"username","required":true,"in":"query","type":"string","description":"The user name"},{"name":"format","required":false,"in":"query","type":"string","default":"xml","enum":["json","xml","html","dump","jpg","pdf"]}],"responses":{"200":{"description":"everything ok"}},"tags":["All functions","Write (create\/update\/delete)","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.","produces":["application\/json","application\/xml","text\/html","text\/xml"],"parameters":[{"name":"pwId","required":true,"in":"query","type":"string","description":"The pathway identifier"},{"name":"format","required":false,"in":"query","type":"string","default":"xml","enum":["json","xml","html","dump","jpg","pdf"]}],"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.","produces":["application\/json","application\/xml","text\/html","text\/xml"],"parameters":[{"name":"tagName","required":true,"in":"query","type":"string","description":"The tag name"},{"name":"format","required":false,"in":"query","type":"string","default":"xml","enum":["json","xml","html","dump","jpg","pdf"]}],"responses":{"200":{"description":"everything ok"}},"tags":["All functions","Pathway list","Curation tags"]}},"\/getCurationTagHistory":{"get":{"description":"getCurationTagHistory","produces":["application\/json","application\/xml","text\/html","text\/xml"],"parameters":[{"name":"pwId","required":true,"in":"query","type":"string","description":"The pathway identifier"},{"name":"timestamp","required":false,"in":"query","type":"string","description":"Only include history from after the given date"},{"name":"format","required":false,"in":"query","type":"string","default":"xml","enum":["json","xml","html","dump","jpg","pdf"]}],"responses":{"200":{"description":"everything ok"}},"tags":["All functions","History","Curation tags"]}},"\/getColoredPathway":{"get":{"description":"getColoredPathwayGet a colored image version of the pathway.","produces":["application\/json","application\/xml","text\/html","text\/xml"],"parameters":[{"name":"pwId","required":true,"in":"query","type":"string","description":"The pathway identifier"},{"name":"revision","required":true,"in":"query","type":"string","description":"The revision of the pathway (use '0' for most recent)"},{"name":"graphId","required":true,"in":"query","type":"array","description":"string"},{"name":"color","required":true,"in":"query","type":"array","description":"string"},{"name":"fileType","required":true,"in":"query","type":"string","description":"The image type (One of 'svg', 'pdf' or 'png')."},{"name":"format","required":false,"in":"query","type":"string","default":"xml","enum":["json","xml","html","dump","jpg","pdf"]}],"responses":{"200":{"description":"everything ok"}},"tags":["All functions","Download"]}},"\/findInteractions":{"get":{"description":"findInteractionsFind interactions defined in WikiPathways pathways.","produces":["application\/json","application\/xml","text\/html","text\/xml"],"parameters":[{"name":"query","required":true,"in":"query","type":"string","description":"The name of an entity to find interactions for (e.g. 'P53')"},{"name":"format","required":false,"in":"query","type":"string","default":"xml","enum":["json","xml","html","dump","jpg","pdf"]}],"responses":{"200":{"description":"everything ok"}},"tags":["Search","All functions"]}},"\/getXrefList":{"get":{"description":"getXrefList","produces":["application\/json","application\/xml","text\/html","text\/xml"],"parameters":[{"name":"pwId","required":true,"in":"query","type":"string","description":"The pathway identifier."},{"name":"code","required":true,"in":"query","type":"string","description":"The database code to translate to (e.g. 'S' for UniProt)."},{"name":"format","required":false,"in":"query","type":"string","default":"xml","enum":["json","xml","html","dump","jpg","pdf"]}],"responses":{"200":{"description":"everything ok"}},"tags":["Download","All functions"]}},"\/findPathwaysByLiterature":{"get":{"description":"findPathwaysByLiterature","produces":["application\/json","application\/xml","text\/html","text\/xml"],"parameters":[{"name":"query","required":true,"in":"query","type":"string","description":"The query, can be a pubmed id, author name or title keyword."},{"name":"format","required":false,"in":"query","type":"string","default":"xml","enum":["json","xml","html","dump","jpg","pdf"]}],"responses":{"200":{"description":"everything ok"}},"tags":["Search","All functions"]}},"\/saveOntologyTag":{"get":{"description":"saveOntologyTag","produces":["application\/json","application\/xml","text\/html","text\/xml"],"parameters":[{"name":"pwId","required":true,"in":"query","type":"string","description":"The pathway identifier"},{"name":"term","required":true,"in":"query","type":"string","description":"The ontology term to apply"},{"name":"termId","required":true,"in":"query","type":"string","description":"The identifier of the term in the ontology"},{"name":"auth","required":true,"in":"query","type":"string","description":"The authentication key"},{"name":"user","required":true,"in":"query","type":"string","description":"The username"},{"name":"format","required":false,"in":"query","type":"string","default":"xml","enum":["json","xml","html","dump","jpg","pdf"]}],"responses":{"200":{"description":"everything ok"}},"tags":["Write (create\/update\/delete)","Ontology tags","All functions"]}},"\/removeOntologyTag":{"get":{"description":"removeOntologyTag","produces":["application\/json","application\/xml","text\/html","text\/xml"],"parameters":[{"name":"pwId","required":true,"in":"query","type":"string","description":"The pathway identifier"},{"name":"termId","required":true,"in":"query","type":"string","description":"The ontology term identifier in the ontology"},{"name":"auth","required":true,"in":"query","type":"string","description":"The authentication key"},{"name":"user","required":true,"in":"query","type":"string","description":"The username"},{"name":"format","required":false,"in":"query","type":"string","default":"xml","enum":["json","xml","html","dump","jpg","pdf"]}],"responses":{"200":{"description":"everything ok"}},"tags":["Write (create\/update\/delete)","Ontology tags","All functions"]}},"\/getOntologyTermsByPathway":{"get":{"description":"getOntologyTermsByPathway","produces":["application\/json","application\/xml","text\/html","text\/xml"],"parameters":[{"name":"pwId","required":true,"in":"query","type":"string","description":"The pathway identifier"},{"name":"format","required":false,"in":"query","type":"string","default":"xml","enum":["json","xml","html","dump","jpg","pdf"]}],"responses":{"200":{"description":"everything ok"}},"tags":["Pathway information","Curation tags","All functions"]}},"\/getPathwaysByOntologyTerm":{"get":{"description":"getPathwaysByOntologyTerm","produces":["application\/json","application\/xml","text\/html","text\/xml"],"parameters":[{"name":"term","required":true,"in":"query","type":"string","description":"The Ontology term"},{"name":"format","required":false,"in":"query","type":"string","default":"xml","enum":["json","xml","html","dump","jpg","pdf"]}],"responses":{"200":{"description":"everything ok"}},"tags":["Pathway list","Ontology tags","All functions"]}},"\/getPathwaysByParentOntologyTerm":{"get":{"description":"getPathwaysByParentOntologyTerm","produces":["application\/json","application\/xml","text\/html","text\/xml"],"parameters":[{"name":"term","required":true,"in":"query","type":"string","description":"The Ontology term"},{"name":"format","required":false,"in":"query","type":"string","default":"xml","enum":["json","xml","html","dump","jpg","pdf"]}],"responses":{"200":{"description":"everything ok"}},"tags":["Pathway list","Ontology tags","All functions"]}},"\/getUserByOrcid":{"get":{"description":"getUserByOrcid","produces":["application\/json","application\/xml","text\/html","text\/xml"],"parameters":[{"name":"orcid","required":true,"in":"query","type":"string","description":"string"},{"name":"format","required":false,"in":"query","type":"string","default":"xml","enum":["json","xml","html","dump","jpg","pdf"]}],"responses":{"200":{"description":"everything ok"}},"tags":["User management","All functions"]}}}}