Class: CompoundSearch

CompoundSearch

new CompoundSearch(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

compoundClassifications(URI, tree, callback)

The classes the given compound URI has been classified with eg ChEBI
Parameters:
Name Type Description
URI string The URI for the compound of interest
tree string Restrict results by hierarchy eg chebi
callback requestCallback Function that will be called with the result
Source:

compoundClassMembers(URI, pageopt, pageSizeopt, orderByopt, lensopt, callback)

Fetch compounds for the class represented by the URI provided.
Parameters:
Name Type Attributes Default Description
URI string The URI for the compound class of interest
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)
lens string <optional>
Which chemistry lens to apply to the records
callback requestCallback Function that will be called with the result
Source:
Example
var searcher = new CompoundSearch("https://beta.openphacts.org/2.1", "appID", "appKey");
var callback=function(success, status, response){
    var classMembersResult == searcher.parseCompoundClassMembersResponse(response);
};
searcher.compoundClassMembers('http://purl.obolibrary.org/obo/CHEBI_24431', 1, 20, null, null, callback);

compoundClassMembersCount(URI, lensopt, callback)

Count the number of compounds classified with the class represented by the URI provided.
Parameters:
Name Type Attributes Description
URI string The URI for the class of interest.
lens string <optional>
An optional lens to apply to the result.
callback requestCallback Function that will be called with the result.
Source:
Example
var searcher = new CompoundSearch("https://beta.openphacts.org/2.1", "appID", "appKey");
var callback=function(success, status, response){
   var result = searcher.parseCompoundClassMembersCountResponse(response);
};
searcher.compoundClassMembersCount('http://purl.obolibrary.org/obo/CHEBI_24431', null, callback);

compoundPharmacology(URI, assayOrganismopt, targetOrganismopt, activityTypeopt, activityValueopt, minActivityValueopt, minExActivityValueopt, maxActivityValueopt, maxExActivityValueopt, activityUnitopt, activityRelationopt, pChemblopt, minpChemblopt, minExpChemblopt, maxpChemblopt, maxExpChemblopt, targetTypeopt, pageopt, pageSizeopt, orderByopt, lensopt, callback)

Fetch pharmacology records for the compound represented by the URI provided.
Parameters:
Name Type Attributes Default Description
URI string The URI for the compound of interest
assayOrganism string <optional>
Filter by assay organism eg Homo Sapiens
targetOrganism string <optional>
Filter by target organism eg Rattus Norvegicus
activityType string <optional>
Filter by activity type eg IC50
activityValue string <optional>
Return pharmacology records with activity values equal to this number
minActivityValue string <optional>
Return pharmacology records with activity values greater than or equal to this number
minExActivityValue string <optional>
Return pharmacology records with activity values greater than this number
maxActivityValue string <optional>
Return pharmacology records with activity values less than or equal to this number
maxExActivityValue string <optional>
Return pharmacology records with activity values less than this number
activityUnit string <optional>
Return pharmacology records which have this activity unit eg nanomolar
activityRelation string <optional>
Return pharmacology records which have this activity relation eg =
pChembl string <optional>
Return pharmacology records with pChembl equal to this number
minpChembl string <optional>
Return pharmacology records with pChembl values greater than or equal to this number
minExpChembl string <optional>
Return pharmacology records with pChembl values greater than this number
maxpChembl string <optional>
Return pharmacology records with pChembl values less than or equal to this number
maxExpChembl string <optional>
Return pharmacology records with pChembl values less than this number
targetType string <optional>
Filter by one of the available target types. e.g. single_protein
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)
lens string <optional>
Which chemistry lens to apply to the records
callback requestCallback Function that will be called with the result
Source:
Example
var searcher = new CompoundSearch("https://beta.openphacts.org/2.1", "appID", "appKey");
var callback=function(success, status, response){
    var pharmacologyResult == searcher.parseCompoundPharmacologyResponse(response);
};
searcher.compoundPharmacology('http://www.conceptwiki.org/concept/38932552-111f-4a4e-a46a-4ed1d7bdf9d5', null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, 1, 20, null, null, callback);

compoundPharmacologyCount(URI, assayOrganismopt, targetOrganismopt, activityTypeopt, activityValueopt, minActivityValueopt, minExActivityValueopt, maxActivityValueopt, maxExActivityValueopt, activityUnitopt, activityRelationopt, pChemblopt, minpChemblopt, minExpChemblopt, maxpChemblopt, maxExpChemblopt, targetTypeopt, lensopt, callback)

Fetch a count of the pharmacology records belonging to the compound represented by the URI provided.
Parameters:
Name Type Attributes Description
URI string The URI for the compound of interest
assayOrganism string <optional>
Filter by assay organism eg Homo Sapiens
targetOrganism string <optional>
Filter by target organism eg Rattus Norvegicus
activityType string <optional>
Filter by activity type eg IC50
activityValue string <optional>
Return pharmacology records with activity values equal to this number
minActivityValue string <optional>
Return pharmacology records with activity values greater than or equal to this number
minExActivityValue string <optional>
Return pharmacology records with activity values greater than this number
maxActivityValue string <optional>
Return pharmacology records with activity values less than or equal to this number
maxExActivityValue string <optional>
Return pharmacology records with activity values less than this number
activityUnit string <optional>
Return pharmacology records which have this activity unit eg nanomolar
activityRelation string <optional>
Return pharmacology records which have this activity relation eg =
pChembl string <optional>
Return pharmacology records with pChembl equal to this number
minpChembl string <optional>
Return pharmacology records with pChembl values greater than or equal to this number
minExpChembl string <optional>
Return pharmacology records with pChembl values greater than this number
maxpChembl string <optional>
Return pharmacology records with pChembl values less than or equal to this number
maxExpChembl string <optional>
Return pharmacology records with pChembl values less than this number
targetType string <optional>
Filter by one of the available target types. e.g. single_protein
lens string <optional>
Which chemistry lens to apply to the records
callback requestCallback Function that will be called with the result
Source:
Example
var searcher = new CompoundSearch("https://beta.openphacts.org/2.1", "appID", "appKey");
var callback=function(success, status, response){
    var pharmacologyResult == searcher.parseCompoundPharmacologyCountResponse(response);
};
searcher.compoundPharmacologyCount('http://www.conceptwiki.org/concept/38932552-111f-4a4e-a46a-4ed1d7bdf9d5', null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, callback);

fetchCompound(URI, lensopt, callback)

Fetch the compound represented by the URI provided.
Parameters:
Name Type Attributes Description
URI string The URI for the compound of interest.
lens string <optional>
An optional lens to apply to the result.
callback requestCallback Function that will be called with the result.
Source:
Example
var searcher = new CompoundSearch("https://beta.openphacts.org/2.1", "appID", "appKey");
var callback=function(success, status, response){
   var compoundResult = searcher.parseCompoundResponse(response);
};
searcher.fetchCompound('http://www.conceptwiki.org/concept/38932552-111f-4a4e-a46a-4ed1d7bdf9d5', null, callback);

fetchCompoundBatch(URIList, lensopt, callback)

Fetch the compounds matching the list of URIs provided.
Parameters:
Name Type Attributes Description
URIList Array An array of URIs for the compounds of interest.
lens string <optional>
An optional lens to apply to the result.
callback requestCallback Function that will be called with the result.
Source:
Example
var searcher = new CompoundSearch("https://beta.openphacts.org/2.1", "appID", "appKey");
var callback=function(success, status, response){
   var compoundResults = searcher.parseCompoundBatchResponse(response);
};
searcher.fetchCompoundBatch(['http://www.conceptwiki.org/concept/38932552-111f-4a4e-a46a-4ed1d7bdf9d5', 'http://www.conceptwiki.org/concept/dd758846-1dac-4f0d-a329-06af9a7fa413'], null, callback);

parseCompoundBatchResponse(response) → {FetchCompoundBatchResponse}

Parse the results from CompoundSearch#fetchCompoundBatch
Parameters:
Name Type Description
response Object the JSON response from CompoundSearch#fetchCompoundBatch
Source:
Returns:
Containing the flattened response
Type
FetchCompoundBatchResponse

parseCompoundClassMembersCountResponse(response) → {Number}

Parameters:
Name Type Description
response Object the JSON response from CompoundSearch#compoundClassMembersCount
Source:
Returns:
Count of the number of compounds classified for a particular class
Type
Number

parseCompoundClassMembersResponse(response) → {Number}

Parse the results from CompoundSearch#compoundClassMembers
Parameters:
Name Type Description
response Object the JSON response from CompoundSearch#compoundClassMembers
Source:
Returns:
Compounds classified for a particular class
Type
Number

parseCompoundLensResponse(response) → {FetchCompoundLensResponse}

Parse the results from CompoundSearch#fetchCompound which have a lens applied
Parameters:
Name Type Description
response Object the JSON response from CompoundSearch#fetchCompound
Source:
Returns:
Containing the flattened response
Type
FetchCompoundLensResponse

parseCompoundPharmacologyCountResponse(response) → {Number}

Parameters:
Name Type Description
response Object the JSON response from CompoundSearch#compoundPharmacologyCount
Source:
Returns:
Count of the number of pharmacology entries for the compound
Type
Number

parseCompoundPharmacologyResponse(response) → {FetchCompoundPharmacologyResponse}

Parse the results from CompoundSearch#fetchCompoundPharmacology
Parameters:
Name Type Description
response Object the JSON response from CompoundSearch#fetchCompoundPharmacology
Source:
Returns:
Containing the flattened response
Type
FetchCompoundPharmacologyResponse

parseCompoundResponse(response) → {FetchCompoundResponse}

Parse the results from CompoundSearch#fetchCompound
Parameters:
Name Type Description
response Object the JSON response from CompoundSearch#fetchCompound
Source:
Returns:
Containing the flattened response
Type
FetchCompoundResponse