WikiPathways Webservices
Connect to WikiPathways Webservices with 1 MCP tools for AI-powered API automation.
COMMUNITYNO AUTH0 INSTALLS
OpenAPI Specificationv3.0
{
"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",
"x-logo": {
"url": "https://api.apis.guru/v2/cache/logo/https_apis.guru_assets_images_no-logo.svg"
}
},
"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"
]
}
}
}
}