--- 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 ## CLI ```bash # Update this spec to the latest version npx @lap-platform/lapsh get wikipathways-webservices -o references/api-spec.lap # Search for related APIs npx @lap-platform/lapsh search wikipathways-webservices ``` ## 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](https://lap.sh)