Help:WikiPathways Webservice/API
From WikiPathways
Contents |
Functions
listOrganisms
Get a list of all available organisms.
| returns | ||
| array of string | The names of the supported organisms | |
listPathways
Get a list of all available pathways.
| returns | ||
| array of object WSPathwayInfo | The available pathways. | |
getPathway
Download the pathway from WikiPathways.
| Arguments | ||
| Type | Name | Description |
| string | pwName | The pathway name |
| string | pwSpecies | The pathway species |
| integer | revision | The revision number of the pathway (use '0' for most recent version) |
| Returns | ||
| array of object WSPathwayInfo | The available pathways. | |
getRecentChanges
Get 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.
| Arguments | ||
| Type | Name | Description |
| string | timestamp | Only get changes from after this time. Timestamp format: yyyymmddMMHHSS. |
| Returns | ||
| array of object WSPathwayInfo | The changed pathways. | |
login
Start 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).
| Arguments | ||
| Type | Name | Description |
| string | name | The username of the WikiPathways account |
| string | pass | The password of the WikiPathways account |
| Returns | ||
| string | The authentication code for this session | |
getPathwayAs
Download a pathway in the specified file format.
| Arguments | ||
| Type | Name | Description |
| string | fileType | The file format. This can be one of:
See the download page for an explanation of these file formats. |
| string | pwName | The pathway name |
| string | pwSpecies | The pathway species |
| integer | revision | The revision number of the pathway (use '0' for most recent version) |
| Returns | ||
| base64Binary | The file contents (base64 encoded) | |
updatePathway
Update a pathway on the wiki with the given GPML code.
| Arguments | ||
| Type | Name | Description |
| string | pwName | The pathway name |
| string | pwSpecies | The pathway species |
| string | description | A description of the modifications |
| string | gpml | The updated GPML code |
| integer | revision | The revision number of the version this GPML code was based on. This is used to prevent edit conflicts in case another client edited the pathway after this client downloaded it. |
| object WSAuth | auth | The authentication info. |
| Returns | ||
| boolean | True if the pathway was updated sucessfully. | |
findPathwaysByText
Find pathways using a textual search on the description and text labels of the pathway objects.
| Arguments | ||
| Type | Name | Description |
| string | query | The search query (e.g. 'apoptosis' or 'p53'). |
| string | species | The species to limit the search to (leave blank to search on all species). |
| Returns | ||
| array of object WSSearchResult | An array of search results. | |
findPathwaysByXref
Find pathways by searching on the external references of DataNodes (gene/protein/metabolite identifiers).
| Arguments | ||
| Type | Name | Description |
| string | id | The DataNode identifier (e.g. 'P45985'). |
| string | code | The code of the database system to limit the search to. Leave blank to search on all database systems. See this page for an overview of available system codes. |
| Returns | ||
| array of object WSSearchResult | An array of search results. | |
Objects
This section explains the different object classes defined in the WSDL.
WSPathwayInfo
Container for pathway metadata, such as name, organism and url.
| fields | ||
| name | string | The name of the pathway |
| species | string | The species (organism) of the pathway |
| url | string | The url to the pathway |
| revision | string | The revision number of the pathway ('0' can be used for the most recent revision) |
WSPathway
Extends WSPathwayInfo.
Container for pathway metadata and content. This object inherits all fields from WSPathwayInfo and has one additional field:
| fields | ||
| gpml | string | The content of the pathway (as GPML). |
WSAuth
Container for authentication data for a logged in WikiPathways session.
| fields | ||
| user | string | The username of a WikiPathways account |
| key | string | The authentication key of the session (can be obtained by calling the login function). |
WSSearchResult
Container for a single search result.
| fields | ||
| score | double | The score of the search result |
| fields | array of object WSIndexField | An array of index fields that were returned with the search. The included fields may vary among different search functions. |
WSIndexField
Container for a single index field.
| fields | ||
| name | string | The name of the index field. |
| fields | array of string | An array with the value(s) of the field. |
