wikipathways-webservices

name	wikipathways-webservices
description	WikiPathways Webservices API skill. Use when working with WikiPathways Webservices for listOrganisms, listPathways, getPathway. Covers 26 endpoints.
version	1.0.0
generator	lapsh

WikiPathways Webservices

API version: 1.0

Auth

ApiKey auth in query

Base URL

https://webservice.wikipathways.org/

Setup

1. Set your API key in the appropriate header
2. GET /listOrganisms -- verify access
3. POST /createPathway -- create first createPathway

Endpoints

26 endpoints across 26 groups. See references/api-spec.lap for full details.

listOrganisms

Method	Path	Description
GET	/listOrganisms	listOrganisms

listPathways

Method	Path	Description
GET	/listPathways	listPathways

getPathway

Method	Path	Description
GET	/getPathway	getPathway

getPathwayInfo

Method	Path	Description
GET	/getPathwayInfo	getPathwayInfoGet some general info about the pathway, such as the name, species, without downloading the GPML.

getPathwayHistory

Method	Path	Description
GET	/getPathwayHistory	getPathwayHistoryGet the revision history of a pathway.

getRecentChanges

Method	Path	Description
GET	/getRecentChanges	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.

login

Method	Path	Description
GET	/login	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).

updatePathway

Method	Path	Description
GET	/updatePathway	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.

createPathway

Method	Path	Description
POST	/createPathway	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.

findPathwaysByText

Method	Path	Description
GET	/findPathwaysByText	findPathwaysByText

findPathwaysByXref

Method	Path	Description
GET	/findPathwaysByXref	findPathwaysByXref

removeCurationTag

Method	Path	Description
GET	/removeCurationTag	removeCurationTagRemove a curation tag from a pathway.

saveCurationTag

Method	Path	Description
GET	/saveCurationTag	saveCurationTag

getCurationTags

Method	Path	Description
GET	/getCurationTags	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.

getCurationTagsByName

Method	Path	Description
GET	/getCurationTagsByName	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.

getCurationTagHistory

Method	Path	Description
GET	/getCurationTagHistory	getCurationTagHistory

getColoredPathway

Method	Path	Description
GET	/getColoredPathway	getColoredPathwayGet a colored image version of the pathway.

findInteractions

Method	Path	Description
GET	/findInteractions	findInteractionsFind interactions defined in WikiPathways pathways.

getXrefList

Method	Path	Description
GET	/getXrefList	getXrefList

findPathwaysByLiterature

Method	Path	Description
GET	/findPathwaysByLiterature	findPathwaysByLiterature

saveOntologyTag

Method	Path	Description
GET	/saveOntologyTag	saveOntologyTag

removeOntologyTag

Method	Path	Description
GET	/removeOntologyTag	removeOntologyTag

getOntologyTermsByPathway

Method	Path	Description
GET	/getOntologyTermsByPathway	getOntologyTermsByPathway

getPathwaysByOntologyTerm

Method	Path	Description
GET	/getPathwaysByOntologyTerm	getPathwaysByOntologyTerm

getPathwaysByParentOntologyTerm

Method	Path	Description
GET	/getPathwaysByParentOntologyTerm	getPathwaysByParentOntologyTerm

getUserByOrcid

Method	Path	Description
GET	/getUserByOrcid	getUserByOrcid

Common Questions

Match user requests to endpoints in references/api-spec.lap. Key patterns:

• "List all listOrganisms?" -> GET /listOrganisms
• "List all listPathways?" -> GET /listPathways
• "List all getPathway?" -> GET /getPathway
• "List all getPathwayInfo?" -> GET /getPathwayInfo
• "List all getPathwayHistory?" -> GET /getPathwayHistory
• "List all getRecentChanges?" -> GET /getRecentChanges
• "List all login?" -> GET /login
• "List all updatePathway?" -> GET /updatePathway
• "Create a createPathway?" -> POST /createPathway
• "Search findPathwaysByText?" -> GET /findPathwaysByText
• "List all findPathwaysByXref?" -> GET /findPathwaysByXref
• "List all removeCurationTag?" -> GET /removeCurationTag
• "List all saveCurationTag?" -> GET /saveCurationTag
• "List all getCurationTags?" -> GET /getCurationTags
• "List all getCurationTagsByName?" -> GET /getCurationTagsByName
• "List all getCurationTagHistory?" -> GET /getCurationTagHistory
• "List all getColoredPathway?" -> GET /getColoredPathway
• "Search findInteractions?" -> GET /findInteractions
• "List all getXrefList?" -> GET /getXrefList
• "Search findPathwaysByLiterature?" -> GET /findPathwaysByLiterature
• "List all saveOntologyTag?" -> GET /saveOntologyTag
• "List all removeOntologyTag?" -> GET /removeOntologyTag
• "List all getOntologyTermsByPathway?" -> GET /getOntologyTermsByPathway
• "List all getPathwaysByOntologyTerm?" -> GET /getPathwaysByOntologyTerm
• "List all getPathwaysByParentOntologyTerm?" -> GET /getPathwaysByParentOntologyTerm
• "List all getUserByOrcid?" -> GET /getUserByOrcid
• "How to authenticate?" -> See Auth section

Response Tips

• Check response schemas in references/api-spec.lap for field details
• Create/update endpoints typically return the created/updated object

References

• Full spec: See references/api-spec.lap for complete endpoint details, parameter tables, and response schemas

Generated from the official API spec by LAP