@datafire/wikipathways

Client library for WikiPathways Webservices

Installation and Usage

npm install --save @datafire/wikipathways

let wikipathways = require('@datafire/wikipathways').create();

.then(data => {
  console.log(data);
});

Description

Actions

createPathway.post

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.

wikipathways.createPathway.post({
  "gpml": "",
  "auth": "",
  "username": ""
}, context)

Input

• input object
  • gpml required string: The GPML code for the new pathway
  • auth required string: The authentication info
  • username required string: The user name
  • format string (values: json, xml, html, dump, jpg, pdf)

Output

Output schema unknown

findInteractions.get

findInteractionsFind interactions defined in WikiPathways pathways.

wikipathways.findInteractions.get({
  "query": ""
}, context)

Input

• input object
  • query required string: The name of an entity to find interactions for (e.g. 'P53')
  • format string (values: json, xml, html, dump, jpg, pdf)

Output

Output schema unknown

findPathwaysByLiterature.get

findPathwaysByLiterature

wikipathways.findPathwaysByLiterature.get({
  "query": ""
}, context)

Input

• input object
  • query required string: The query, can be a pubmed id, author name or title keyword.
  • format string (values: json, xml, html, dump, jpg, pdf)

Output

Output schema unknown

findPathwaysByText.get

findPathwaysByText

wikipathways.findPathwaysByText.get({
  "query": ""
}, context)

Input

• input object
  • query required string: The query, e.g. 'apoptosis'
  • species string: Optional, limit the query by species. Leave
  • format string (values: json, xml, html, dump, jpg, pdf)

Output

Output schema unknown

findPathwaysByXref.get

findPathwaysByXref

wikipathways.findPathwaysByXref.get({
  "ids": []
}, context)

Input

• input object
  • ids required array: string
  • codes array: string
  • format string (values: json, xml, html, dump, jpg, pdf)

Output

Output schema unknown

getColoredPathway.get

getColoredPathwayGet a colored image version of the pathway.

wikipathways.getColoredPathway.get({
  "pwId": "",
  "revision": "",
  "graphId": [],
  "color": [],
  "fileType": ""
}, context)

Input

• input object
  • pwId required string: The pathway identifier
  • revision required string: The revision of the pathway (use '0' for most recent)
  • graphId required array: string
  • color required array: string
  • fileType required string: The image type (One of 'svg', 'pdf' or 'png').
  • format string (values: json, xml, html, dump, jpg, pdf)

Output

Output schema unknown

getCurationTagHistory.get

getCurationTagHistory

wikipathways.getCurationTagHistory.get({
  "pwId": ""
}, context)

Input

• input object
  • pwId required string: The pathway identifier
  • timestamp string: Only include history from after the given date
  • format string (values: json, xml, html, dump, jpg, pdf)

Output

Output schema unknown

getCurationTags.get

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.

wikipathways.getCurationTags.get({
  "pwId": ""
}, context)

Input

• input object
  • pwId required string: The pathway identifier
  • format string (values: json, xml, html, dump, jpg, pdf)

Output

Output schema unknown

getCurationTagsByName.get

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.

wikipathways.getCurationTagsByName.get({
  "tagName": ""
}, context)

Input

• input object
  • tagName required string: The tag name
  • format string (values: json, xml, html, dump, jpg, pdf)

Output

Output schema unknown

getOntologyTermsByPathway.get

getOntologyTermsByPathway

wikipathways.getOntologyTermsByPathway.get({
  "pwId": ""
}, context)

Input

• input object
  • pwId required string: The pathway identifier
  • format string (values: json, xml, html, dump, jpg, pdf)

Output

Output schema unknown

getPathway.get

getPathway

wikipathways.getPathway.get({
  "pwId": ""
}, context)

Input

• input object
  • pwId required string: The pathway identifier
  • revision integer: The revision number of the pathway (use 0 for most recent)
  • format string (values: json, xml, html, dump, jpg, pdf)

Output

Output schema unknown

getPathwayAs.get

getPathwayAsDownload a pathway in the specified file format.

wikipathways.getPathwayAs.get({
  "fileType": "",
  "pwId": ""
}, context)

Input

• input object
  • fileType required string: The file type to convert to, e.g.
  • pwId required string: The pathway identifier
  • revision integer: The revision number of the pathway (use 0 for most recent)
  • format string (values: json, xml, html, dump, jpg, pdf)

Output

Output schema unknown

getPathwayHistory.get

getPathwayHistoryGet the revision history of a pathway.

wikipathways.getPathwayHistory.get({
  "pwId": "",
  "timestamp": ""
}, context)

Input

• input object
  • pwId required string: The pathway identifier
  • timestamp required string: Limit by time, only history items after the given
  • format string (values: json, xml, html, dump, jpg, pdf)

Output

Output schema unknown

getPathwayInfo.get

getPathwayInfoGet some general info about the pathway, such as the name, species, without downloading the GPML.

wikipathways.getPathwayInfo.get({
  "pwId": ""
}, context)

Input

• input object
  • pwId required string: The pathway identifier
  • format string (values: json, xml, html, dump, jpg, pdf)

Output

Output schema unknown

getPathwaysByOntologyTerm.get

getPathwaysByOntologyTerm

wikipathways.getPathwaysByOntologyTerm.get({
  "term": ""
}, context)

Input

• input object
  • term required string: The Ontology term
  • format string (values: json, xml, html, dump, jpg, pdf)

Output

Output schema unknown

getPathwaysByParentOntologyTerm.get

getPathwaysByParentOntologyTerm

wikipathways.getPathwaysByParentOntologyTerm.get({
  "term": ""
}, context)

Input

• input object
  • term required string: The Ontology term
  • format string (values: json, xml, html, dump, jpg, pdf)

Output

Output schema unknown

getRecentChanges.get

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.

wikipathways.getRecentChanges.get({
  "timestamp": ""
}, context)

Input

• input object
  • timestamp required string: Get the changes after this time
  • format string (values: json, xml, html, dump, jpg, pdf)

Output

Output schema unknown

getUserByOrcid.get

getUserByOrcid

wikipathways.getUserByOrcid.get({
  "orcid": ""
}, context)

Input

• input object
  • orcid required string: string
  • format string (values: json, xml, html, dump, jpg, pdf)

Output

Output schema unknown

getXrefList.get

getXrefList

wikipathways.getXrefList.get({
  "pwId": "",
  "code": ""
}, context)

Input

• input object
  • pwId required string: The pathway identifier.
  • code required string: The database code to translate to (e.g. 'S' for UniProt).
  • format string (values: json, xml, html, dump, jpg, pdf)

Output

Output schema unknown

listOrganisms.get

listOrganisms

wikipathways.listOrganisms.get({}, context)

Input

• input object
  • format string (values: json, xml, html, dump, jpg, pdf)

Output

Output schema unknown

listPathways.get

listPathways

wikipathways.listPathways.get({}, context)

Input

• input object
  • organism string: The organism to filter by (optional)
  • format string (values: json, xml, html, dump, jpg, pdf)

Output

Output schema unknown

login.get

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).

wikipathways.login.get({
  "name": "",
  "pass": ""
}, context)

Input

• input object
  • name required string: The usernameset_include_path(get_include_path().PATH_SEPARATOR.realpath('../includes').PATH_SEPARATOR.realpath('../').PATH_SEPARATOR);
  • pass required string: The password
  • format string (values: json, xml, html, dump, jpg, pdf)

Output

Output schema unknown

removeCurationTag.get

removeCurationTagRemove a curation tag from a pathway.

wikipathways.removeCurationTag.get({
  "pwId": "",
  "tagName": "",
  "auth": "",
  "username": ""
}, context)

Input

• input object
  • pwId required string: The pathway identifier
  • tagName required string: The name of the tag to apply
  • auth required string: The authentication data
  • username required string: The user name
  • format string (values: json, xml, html, dump, jpg, pdf)

Output

Output schema unknown

removeOntologyTag.get

removeOntologyTag

wikipathways.removeOntologyTag.get({
  "pwId": "",
  "termId": "",
  "auth": "",
  "user": ""
}, context)

Input

• input object
  • pwId required string: The pathway identifier
  • termId required string: The ontology term identifier in the ontology
  • auth required string: The authentication key
  • user required string: The username
  • format string (values: json, xml, html, dump, jpg, pdf)

Output

Output schema unknown

saveCurationTag.get

saveCurationTag

wikipathways.saveCurationTag.get({
  "pwId": "",
  "tagName": "",
  "text": "",
  "revision": 0,
  "auth": "",
  "username": ""
}, context)

Input

• input object
  • pwId required string: The pathway identifier
  • tagName required string: The name of the tag to apply
  • text required string: string
  • revision required integer: The revision this tag applies to
  • auth required string: The authentication key
  • username required string: The user name
  • format string (values: json, xml, html, dump, jpg, pdf)

Output

Output schema unknown

saveOntologyTag.get

saveOntologyTag

wikipathways.saveOntologyTag.get({
  "pwId": "",
  "term": "",
  "termId": "",
  "auth": "",
  "user": ""
}, context)

Input

• input object
  • pwId required string: The pathway identifier
  • term required string: The ontology term to apply
  • termId required string: The identifier of the term in the ontology
  • auth required string: The authentication key
  • user required string: The username
  • format string (values: json, xml, html, dump, jpg, pdf)

Output

Output schema unknown

updatePathway.get

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.

wikipathways.updatePathway.get({
  "pwId": "",
  "description": "",
  "gpml": "",
  "revision": 0,
  "auth": "",
  "username": ""
}, context)

Input

• input object
  • pwId required string: The pathway identifier
  • description required string: A description of the modifications
  • gpml required string: The updated GPML code
  • revision required integer: The revision the GPML code is based on
  • auth required string: The authentication key
  • username required string: The username
  • format string (values: json, xml, html, dump, jpg, pdf)

Output

Output schema unknown

Definitions

This integration has no definitions