Help:WikiPathways Webservice/API
From WikiPathways
Functions
listOrganisms
Get a list of all available organisms.
listPathways
Get a list of all available pathways.
Arguments:
-
string
organism- Only return pathways for this organism (optional).
getPathway
Download the pathway from WikiPathways.
Arguments:
-
string
pwId- The pathway identifier.
-
integer
revision- The revision number of the pathway (use '0' for most recent version).
getPathwayInfo
Get some general info about the pathway, such as the name, species, without downloading the GPML.
Arguments:
-
string
pwId- The pathway identifier.
getPathwayHistory
Get the revision history of a pathway.
Arguments:
-
string
pwId- The pathway identifier.
-
string
timestamp- Limit the results by date, only history items after the given timestamp will be included.
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:
-
string
timestamp- Only get changes from after this time. Timestamp format: yyyymmddMMHHSS.
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:
-
string
name- The username of the WikiPathways account.
-
string
pass- The password of the WikiPathways account.
getPathwayAs
Download a pathway in the specified file format.
Arguments:
-
string
fileType- Download a pathway in the specified file format.
- gpml
- png
- svg
- txt
- pwf
See the download page for an explanation of these file formats.
-
string
pwId- The pathway identifier.
-
integer
revision- The revision number of the pathway (use '0' for most recent version).
updatePathway
Update 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.
Arguments:
-
string
pwId- The pathway identifier.
-
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.
createPathway
Create 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.
Arguments:
-
string
gpml- The GPML code.
-
object WSAuth
auth- The authentication info.
findPathwaysByText
Find pathways using a textual search on the description and text labels of the pathway objects. The query syntax offers several options:
- Combine terms with AND and OR. Combining terms with a space is equal to using OR ('p53 OR apoptosis' gives the same result as 'p53 apoptosis').
- Group terms with parentheses, e.g. '(apoptosis OR mapk) AND p53'
- You can use wildcards * and ?. * searches for one or more characters, ? searchers for only one character.
- Use quotes to escape special characters. E.g. '"apoptosis*"' will include the * in the search and not use it as wildcard.
Arguments:
-
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).
findPathwaysByXref
Find pathways by searching on the external references of DataNodes (gene/protein/metabolite identifiers).
Arguments:
-
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.
findInteractions
Find interactions defined in WikiPathways pathways.
Arguments:
-
string
query- The name of an entity to find interactions for (e.g. 'P53')
saveCurationTag
Apply a curation tag to a pahtway. This operation will overwrite any existing tag with the same name.
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.
Arguments:
-
string
pwId- The pathway identifier.
-
string
tagName- The name of the tag to apply.
-
string
tagText- The tag text (optional).
-
integer
revision- The revision this tag applies to.
-
object WSAuth
auth- The authentication info.
removeCurationTag
Remove a curation tag from a pathway.
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.
Arguments:
-
string
pwId- The pathway identifier.
-
string
tagName- The name of the tag to remove.
-
object WSAuth
auth- The authentication info.
getCurationTags
Get all curation tags for the given pathway.
Arguments:
-
string
pwId- The pathway identifier.
getCurationTagsByName
Get 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.
Arguments:
-
string
tagName- The tag name (see Special:SpecialCurationTags for an overview of available tag names).
getColoredPathway
Get a colored image version of the pathway.
Arguments:
-
string
pwId- The pathway identifier.
-
integer
revision- The revision number of the pathway (use '0' for most recent version).
-
array of string
graphId- An array with graphIds of the objects to color.
-
array of string
color- An array with colors of the objects (should be the same length as graphId).
Colors should be encoded as a hexadecimal number, e.g. FF0000 for red).
-
string
fileType- The image type (One of 'svg', 'pdf' or 'png').
getXrefList
Get a list of external references on the pathway (gene, protein or metabolite ids), translated to the given database system.
Arguments:
-
string
pwId- The pathway identifier.
-
string
code- The code of the system to translate to (e.g. 'S' for UniProt).
findPathwaysByLiterature
Find pathways by their literature references.
Arguments:
-
string
query- The query, can be a pubmed id, author name or title keyword.
Objects
This section explains the different object classes defined in the WSDL.
WSPathwayInfo
Container for pathway metadata, such as name, organism and url.
Fields:
-
string
id- The pathway identifier
-
string
name- The name of the pathway
-
string
species- The species (organism) of the pathway
-
string
revision- The revision number of the pathway
-
string
url- The url to the pathway
WSPathway
Extends WSPathwayInfo.
Container for pathway metadata and content. This object inherits all fields from WSPathwayInfo and has one additional field:
Fields:
-
string
gpml- The content of the pathway (as GPML).
WSPathwayHistory
Extends WSPathwayInfo.
Container for pathway revision history. This object inherits all fields from WSPathwayInfo and has one additional field:
Fields:
-
array of WSHistoryRow
history- The revision history of the pathway.
WSHistoryRow
Info about a single revision of a pathway.
Fields:
-
string
revision- The revision number of this revision
-
string
comment- The edit description
-
string
user- The username of the user that edited this revision
-
string
timestamp- The timestamp of this revision
WSAuth
Container for authentication data for a logged in WikiPathways session.
Fields:
-
string
user- The username of a WikiPathways account
-
string
key- The authentication key of the session (can be obtained by calling the login function).
WSSearchResult
Container for a single search result.
Fields:
-
double
score- The score of the search result
-
string
id- The pathway identifier
-
string
name- The name of the pathway
-
string
species- The species (organism) of the pathway
-
string
revision- The revision number of the pathway
-
string
url- The url to the pathway
-
array of WSIndexField
fields- An array of index fields that were returned with the search. The included fields vary among different search functions. For example, it includes an array of hashes of arrays to represent interactions involving grouped objects.
WSIndexField
Container for a single index field.
Fields:
-
string
name- The name of the index field.
-
array of string
values- An array with the value(s) of the field.
WSCurationTag
Container for a single index field.
Fields:
-
string
name- The internal tag name.
-
string
displayName- The display name of the tag.
-
object WSPathwayInfo
pathway- The pathway this tag applies to.
-
string
revision- The revision this tag applies to. '0' is used for tags that apply to all revisions.
-
string
text- The tag text.
-
long
timeModified- The timestamp of the last modified date.
-
string
userModified- The username of the user that last modified the tag.