Class: PathwaySearch

PathwaySearch

new PathwaySearch(baseURL, appID, appKey)

Parameters:
Name Type Description
baseURL string URL for the Open PHACTS API
appID string Application ID for the application being used. Created by https://dev.openphacts.org
appKey string Application Key for the application ID.
Author:
License:
Source:

Methods

byCompound(URI, organismopt, lensopt, pageopt, pageSizeopt, orderByopt, callback)

Get a list of pathways in which the given compound is active.
Parameters:
Name Type Attributes Default Description
URI string URI of the compound (e.g.: "http://purl.obolibrary.org/obo/CHEBI_57305")
organism string <optional>
Restricts to pathways in this organism, if given
lens string <optional>
The Lens name
page string <optional>
1 Which page of records to return.
pageSize string <optional>
10 How many records to return. Set to 'all' to return all records in a single page
orderBy string <optional>
Order the records by this field eg ?assay_type or DESC(?assay_type)
callback requestCallback Function that will be called with the result.
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byTarget(URI, organismopt, lensopt, pageopt, pageSizeopt, orderByopt, callback)

Get a list of pathways in which the given target is active.
Parameters:
Name Type Attributes Default Description
URI string URI of the target (e.g.: "http://identifiers.org/ncbigene/282478")
organism string <optional>
Restricts to pathways in this organism, if given
lens string <optional>
The Lens name
page string <optional>
1 Which page of records to return.
pageSize string <optional>
10 How many records to return. Set to 'all' to return all records in a single page
orderBy string <optional>
Order the records by this field eg ?assay_type or DESC(?assay_type)
callback requestCallback Function that will be called with the result.
Source:

countInteractionsByEntity(URI, organismopt, directionopt, interaction_typeopt, callback)

Give the count of interactions of the given entity (metabolite, gene, protein).
Parameters:
Name Type Attributes Description
URI string URI of the compound (e.g.: "http://purl.obolibrary.org/obo/CHEBI_57305")
organism string <optional>
Restricts to pathways in this organism, if given
direction string <optional>
Only interactions of this direction (values: "up", "down").
interaction_type string <optional>
Only interactions of this type (values: "directed" "undirected").
callback requestCallback Function that will be called with the result.
Source:

countPathways(organismopt, lensopt, callback)

Get a count of the pathways
Parameters:
Name Type Attributes Description
organism string <optional>
Restricts to pathways in this organism, if given
lens string <optional>
The Lens name
callback requestCallback Function that will be called with the result.
Source:

countPathwaysByCompound(URI, organismopt, lensopt, callback)

Get a count of the list of pathways in which the given compound is active.
Parameters:
Name Type Attributes Description
URI string URI of the compound (e.g.: "http://purl.obolibrary.org/obo/CHEBI_57305")
organism string <optional>
Restricts to pathways in this organism, if given
lens string <optional>
The Lens name
callback requestCallback Function that will be called with the result.
Source:

countPathwaysByTarget(URI, organismopt, lensopt, callback)

Get a count of the list of pathways in which the given target is active.
Parameters:
Name Type Attributes Description
URI string URI of the target (e.g.: "http://identifiers.org/ncbigene/282478")
organism string <optional>
Restricts to pathways in this organism, if given
lens string <optional>
The Lens name
callback requestCallback Function that will be called with the result.
Source:

getCompounds(URI, lensopt, callback)

Get a list of compounds that are part of the pathway specified
Parameters:
Name Type Attributes Description
URI string URI of the pathway (e.g.: "http://identifiers.org/wikipathways/WP1008")
lens string <optional>
The Lens name
callback requestCallback Function that will be called with the result.
Source:
Example
var searcher = new PathwaySearch("https://beta.openphacts.org/1.5", "appID", "appKey");
var callback=function(success, status, response){
   var compounds = searcher.parseGetCompoundsResponse(response);
};
searcher.getCompounds('http://identifiers.org/wikipathways/WP1008', null, callback);

getInteractions(URI, callback)

Give a list of interactions for the given pathway.
Parameters:
Name Type Description
URI string URI of the pathway (e.g.: "http://identifiers.org/wikipathways/WP1015")
callback requestCallback Function that will be called with the result.
Source:

getInteractionsByEntity(URI, organismopt, directionopt, interaction_typeopt, pageopt, pageSizeopt, orderByopt, callback)

Get a list of interactions of the given entity (metabolite, gene, protein).
Parameters:
Name Type Attributes Default Description
URI string URI of the compound (e.g.: "http://purl.obolibrary.org/obo/CHEBI_57305")
organism string <optional>
Restricts to pathways in this organism, if given
direction string <optional>
Only interactions of this direction (values: "up", "down").
interaction_type string <optional>
Only interactions of this type (values: "directed" "undirected").
page string <optional>
1 Which page of records to return.
pageSize string <optional>
10 How many records to return. Set to 'all' to return all records in a single page
orderBy string <optional>
Order the records by this field eg ?assay_type or DESC(?assay_type)
callback requestCallback Function that will be called with the result.
Source:

getTargets(URI, lensopt, callback)

Get a list of targets that are part of the pathway specified
Parameters:
Name Type Attributes Description
URI string URI of the pathway (e.g.: "http://identifiers.org/wikipathways/WP1008")
lens string <optional>
The Lens name
callback requestCallback Function that will be called with the result.
Source:
Example
var searcher = new PathwaySearch("https://beta.openphacts.org/2.1", "appID", "appKey");
var callback=function(success, status, response){
   var targets = searcher.parseGetTargetsResponse(response);
};
searcher.getTargets('http://identifiers.org/wikipathways/WP1008', null, callback);

list(organismopt, lensopt, pageopt, pageSizeopt, orderByopt, callback)

Get the pathways
Parameters:
Name Type Attributes Default Description
organism string <optional>
Restricts to pathways in this organism, if given
lens string <optional>
The Lens name
page string <optional>
1 Which page of records to return.
pageSize string <optional>
10 How many records to return. Set to 'all' to return all records in a single page
orderBy string <optional>
Order the records by this field eg ?assay_type or DESC(?assay_type)
callback requestCallback Function that will be called with the result.
Source:

organisms(lensopt, pageopt, pageSizeopt, orderByopt, callback)

Get the organisms
Parameters:
Name Type Attributes Default Description
lens string <optional>
The Lens name
page string <optional>
1 Which page of records to return.
pageSize string <optional>
10 How many records to return. Set to 'all' to return all records in a single page
orderBy string <optional>
Order the records by this field eg ?assay_type or DESC(?assay_type)
callback requestCallback Function that will be called with the result.
Source: