BioLinkApi.AssociationApi

All URIs are relative to https://localhost/api

Method	HTTP request	Description
getAssociationObject	GET /association/{id}	Returns the association with a given identifier
getAssociationSearch	GET /association/find/	Returns list of matching associations
getAssociationSearch_0	GET /association/find/{subject_category}/	Returns list of matching associations
getAssociationSearch_1	GET /association/find/{subject_category}/{object_category}/	Returns list of matching associations
getAssociationsFrom	GET /association/between/{subject}/{object}	Returns associations connecting two entities
getAssociationsFrom_0	GET /association/from/{subject}	Returns list of matching associations
getAssociationsTo	GET /association/to/{object}	Returns list of matching associations

getAssociationObject

[Association] getAssociationObject(id, opts)

Returns the association with a given identifier

An association connects, at a minimum, two things, designated subject and object, via some relationship. Associations also include evidence, provenance etc.

Example

var BioLinkApi = require('bio_link_api');

var apiInstance = new BioLinkApi.AssociationApi();

var id = "id_example"; // String | 

var opts = { 
  'evidence': "evidence_example", // String | Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default)                     or a specific publication or other supporting ibject, e.g. ZFIN:ZDB-PUB-060503-2.                     
  'mapIdentifiers': "mapIdentifiers_example", // String | Prefix to map all IDs to. E.g. NCBIGene
  '_object': "_object_example", // String | OBJECT id, e.g. HP:0011927. Includes inferred by default
  'graphize': true, // Boolean | If set, includes graph object in response
  'subjectTaxon': "subjectTaxon_example", // String | SUBJECT TAXON id, e.g. NCBITaxon:9606. Includes inferred by default
  'page': 1, // Integer | Page number
  'subject': "subject_example", // String | SUBJECT id, e.g. NCBIGene:84570, ZFIN:ZDB-GENE-050417-357. Includes inferred by default
  'flExcludesEvidence': true, // Boolean | If set, excludes evidence objects in response
  'rows': 10 // Integer | number of rows
};

var callback = function(error, data, response) {
  if (error) {
    console.error(error);
  } else {
    console.log('API called successfully. Returned data: ' + data);
  }
};
apiInstance.getAssociationObject(id, opts, callback);

Parameters

Name	Type	Description	Notes
id	String
evidence	String	Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting ibject, e.g. ZFIN:ZDB-PUB-060503-2.	[optional]
mapIdentifiers	String	Prefix to map all IDs to. E.g. NCBIGene	[optional]
_object	String	OBJECT id, e.g. HP:0011927. Includes inferred by default	[optional]
graphize	Boolean	If set, includes graph object in response	[optional]
subjectTaxon	String	SUBJECT TAXON id, e.g. NCBITaxon:9606. Includes inferred by default	[optional]
page	Integer	Page number	[optional] [default to 1]
subject	String	SUBJECT id, e.g. NCBIGene:84570, ZFIN:ZDB-GENE-050417-357. Includes inferred by default	[optional]
flExcludesEvidence	Boolean	If set, excludes evidence objects in response	[optional]
rows	Integer	number of rows	[optional] [default to 10]

Return type

[Association]

Authorization

No authorization required

HTTP request headers

Content-Type: application/json
Accept: application/json

getAssociationSearch

[AssociationResults] getAssociationSearch(opts)

Returns list of matching associations

Example

var BioLinkApi = require('bio_link_api');

var apiInstance = new BioLinkApi.AssociationApi();

var opts = { 
  'evidence': "evidence_example", // String | Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default)                     or a specific publication or other supporting ibject, e.g. ZFIN:ZDB-PUB-060503-2.                     
  'mapIdentifiers': "mapIdentifiers_example", // String | Prefix to map all IDs to. E.g. NCBIGene
  '_object': "_object_example", // String | OBJECT id, e.g. HP:0011927. Includes inferred by default
  'graphize': true, // Boolean | If set, includes graph object in response
  'subjectTaxon': "subjectTaxon_example", // String | SUBJECT TAXON id, e.g. NCBITaxon:9606. Includes inferred by default
  'page': 1, // Integer | Page number
  'subject': "subject_example", // String | SUBJECT id, e.g. NCBIGene:84570, ZFIN:ZDB-GENE-050417-357. Includes inferred by default
  'flExcludesEvidence': true, // Boolean | If set, excludes evidence objects in response
  'rows': 10 // Integer | number of rows
};

var callback = function(error, data, response) {
  if (error) {
    console.error(error);
  } else {
    console.log('API called successfully. Returned data: ' + data);
  }
};
apiInstance.getAssociationSearch(opts, callback);

Parameters

Name	Type	Description	Notes
evidence	String	Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting ibject, e.g. ZFIN:ZDB-PUB-060503-2.	[optional]
mapIdentifiers	String	Prefix to map all IDs to. E.g. NCBIGene	[optional]
_object	String	OBJECT id, e.g. HP:0011927. Includes inferred by default	[optional]
graphize	Boolean	If set, includes graph object in response	[optional]
subjectTaxon	String	SUBJECT TAXON id, e.g. NCBITaxon:9606. Includes inferred by default	[optional]
page	Integer	Page number	[optional] [default to 1]
subject	String	SUBJECT id, e.g. NCBIGene:84570, ZFIN:ZDB-GENE-050417-357. Includes inferred by default	[optional]
flExcludesEvidence	Boolean	If set, excludes evidence objects in response	[optional]
rows	Integer	number of rows	[optional] [default to 10]

Return type

[AssociationResults]

Authorization

No authorization required

HTTP request headers

Content-Type: application/json
Accept: application/json

getAssociationSearch_0

[AssociationResults] getAssociationSearch_0(objectCategory, subjectCategory, opts)

Returns list of matching associations

Example

var BioLinkApi = require('bio_link_api');

var apiInstance = new BioLinkApi.AssociationApi();

var objectCategory = "objectCategory_example"; // String | CATEGORY of entity at link OBJECT (target), e.g. phenotype, disease

var subjectCategory = "subjectCategory_example"; // String | CATEGORY of entity at link SUBJECT (source), e.g. gene, disease, genotype

var opts = { 
  'evidence': "evidence_example", // String | Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default)                     or a specific publication or other supporting ibject, e.g. ZFIN:ZDB-PUB-060503-2.                     
  'mapIdentifiers': "mapIdentifiers_example", // String | Prefix to map all IDs to. E.g. NCBIGene
  '_object': "_object_example", // String | OBJECT id, e.g. HP:0011927. Includes inferred by default
  'graphize': true, // Boolean | If set, includes graph object in response
  'subjectTaxon': "subjectTaxon_example", // String | SUBJECT TAXON id, e.g. NCBITaxon:9606. Includes inferred by default
  'page': 1, // Integer | Page number
  'subject': "subject_example", // String | SUBJECT id, e.g. NCBIGene:84570, ZFIN:ZDB-GENE-050417-357. Includes inferred by default
  'flExcludesEvidence': true, // Boolean | If set, excludes evidence objects in response
  'rows': 10 // Integer | number of rows
};

var callback = function(error, data, response) {
  if (error) {
    console.error(error);
  } else {
    console.log('API called successfully. Returned data: ' + data);
  }
};
apiInstance.getAssociationSearch_0(objectCategory, subjectCategory, opts, callback);

Parameters

Name	Type	Description	Notes
objectCategory	String	CATEGORY of entity at link OBJECT (target), e.g. phenotype, disease
subjectCategory	String	CATEGORY of entity at link SUBJECT (source), e.g. gene, disease, genotype
evidence	String	Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting ibject, e.g. ZFIN:ZDB-PUB-060503-2.	[optional]
mapIdentifiers	String	Prefix to map all IDs to. E.g. NCBIGene	[optional]
_object	String	OBJECT id, e.g. HP:0011927. Includes inferred by default	[optional]
graphize	Boolean	If set, includes graph object in response	[optional]
subjectTaxon	String	SUBJECT TAXON id, e.g. NCBITaxon:9606. Includes inferred by default	[optional]
page	Integer	Page number	[optional] [default to 1]
subject	String	SUBJECT id, e.g. NCBIGene:84570, ZFIN:ZDB-GENE-050417-357. Includes inferred by default	[optional]
flExcludesEvidence	Boolean	If set, excludes evidence objects in response	[optional]
rows	Integer	number of rows	[optional] [default to 10]

Return type

[AssociationResults]

Authorization

No authorization required

HTTP request headers

Content-Type: application/json
Accept: application/json

getAssociationSearch_1

[AssociationResults] getAssociationSearch_1(objectCategory, subjectCategory, opts)

Returns list of matching associations

Example

var BioLinkApi = require('bio_link_api');

var apiInstance = new BioLinkApi.AssociationApi();

var objectCategory = "objectCategory_example"; // String | CATEGORY of entity at link OBJECT (target), e.g. phenotype, disease

var subjectCategory = "subjectCategory_example"; // String | CATEGORY of entity at link SUBJECT (source), e.g. gene, disease, genotype

var opts = { 
  'evidence': "evidence_example", // String | Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default)                     or a specific publication or other supporting ibject, e.g. ZFIN:ZDB-PUB-060503-2.                     
  'mapIdentifiers': "mapIdentifiers_example", // String | Prefix to map all IDs to. E.g. NCBIGene
  '_object': "_object_example", // String | OBJECT id, e.g. HP:0011927. Includes inferred by default
  'graphize': true, // Boolean | If set, includes graph object in response
  'subjectTaxon': "subjectTaxon_example", // String | SUBJECT TAXON id, e.g. NCBITaxon:9606. Includes inferred by default
  'page': 1, // Integer | Page number
  'subject': "subject_example", // String | SUBJECT id, e.g. NCBIGene:84570, ZFIN:ZDB-GENE-050417-357. Includes inferred by default
  'flExcludesEvidence': true, // Boolean | If set, excludes evidence objects in response
  'rows': 10 // Integer | number of rows
};

var callback = function(error, data, response) {
  if (error) {
    console.error(error);
  } else {
    console.log('API called successfully. Returned data: ' + data);
  }
};
apiInstance.getAssociationSearch_1(objectCategory, subjectCategory, opts, callback);

Parameters

Name	Type	Description	Notes
objectCategory	String	CATEGORY of entity at link OBJECT (target), e.g. phenotype, disease
subjectCategory	String	CATEGORY of entity at link SUBJECT (source), e.g. gene, disease, genotype
evidence	String	Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting ibject, e.g. ZFIN:ZDB-PUB-060503-2.	[optional]
mapIdentifiers	String	Prefix to map all IDs to. E.g. NCBIGene	[optional]
_object	String	OBJECT id, e.g. HP:0011927. Includes inferred by default	[optional]
graphize	Boolean	If set, includes graph object in response	[optional]
subjectTaxon	String	SUBJECT TAXON id, e.g. NCBITaxon:9606. Includes inferred by default	[optional]
page	Integer	Page number	[optional] [default to 1]
subject	String	SUBJECT id, e.g. NCBIGene:84570, ZFIN:ZDB-GENE-050417-357. Includes inferred by default	[optional]
flExcludesEvidence	Boolean	If set, excludes evidence objects in response	[optional]
rows	Integer	number of rows	[optional] [default to 10]

Return type

[AssociationResults]

Authorization

No authorization required

HTTP request headers

Content-Type: application/json
Accept: application/json

getAssociationsFrom

[AssociationResults] getAssociationsFrom(subject, _object, opts)

Returns associations connecting two entities

Given two entities (e.g. a particular gene and a particular disease), if these two entities are connected (directly or indirectly), then return the association objects describing the connection.

Example

var BioLinkApi = require('bio_link_api');

var apiInstance = new BioLinkApi.AssociationApi();

var subject = "subject_example"; // String | E.g. e.g. MGI:1342287

var _object = "_object_example"; // String | E.g. e.g. MP:0013765, can also be a biological entity such as a gene

var opts = { 
  'objectCategory': "objectCategory_example", // String | e.g. disease, phenotype, gene
  'evidence': "evidence_example", // String | Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default)                     or a specific publication or other supporting ibject, e.g. ZFIN:ZDB-PUB-060503-2.                     
  'mapIdentifiers': "mapIdentifiers_example", // String | Prefix to map all IDs to. E.g. NCBIGene
  'page': 1, // Integer | Page number
  'graphize': true, // Boolean | If set, includes graph object in response
  'subjectTaxon': "subjectTaxon_example", // String | SUBJECT TAXON id, e.g. NCBITaxon:9606. Includes inferred by default
  'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
  'subjectCategory': "subjectCategory_example", // String | e.g. gene, genotype, disease
  'rows': 10, // Integer | number of rows
  'flExcludesEvidence': true // Boolean | If set, excludes evidence objects in response
};

var callback = function(error, data, response) {
  if (error) {
    console.error(error);
  } else {
    console.log('API called successfully. Returned data: ' + data);
  }
};
apiInstance.getAssociationsFrom(subject, _object, opts, callback);

Parameters

Name	Type	Description	Notes
subject	String	E.g. e.g. MGI:1342287
_object	String	E.g. e.g. MP:0013765, can also be a biological entity such as a gene
objectCategory	String	e.g. disease, phenotype, gene	[optional]
evidence	String	Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting ibject, e.g. ZFIN:ZDB-PUB-060503-2.	[optional]
mapIdentifiers	String	Prefix to map all IDs to. E.g. NCBIGene	[optional]
page	Integer	Page number	[optional] [default to 1]
graphize	Boolean	If set, includes graph object in response	[optional]
subjectTaxon	String	SUBJECT TAXON id, e.g. NCBITaxon:9606. Includes inferred by default	[optional]
slim	[String]	Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]
subjectCategory	String	e.g. gene, genotype, disease	[optional]
rows	Integer	number of rows	[optional] [default to 10]
flExcludesEvidence	Boolean	If set, excludes evidence objects in response	[optional]

Return type

[AssociationResults]

Authorization

No authorization required

HTTP request headers

Content-Type: application/json
Accept: application/json

getAssociationsFrom_0

[AssociationResults] getAssociationsFrom_0(subject, opts)

Returns list of matching associations

Example

var BioLinkApi = require('bio_link_api');

var apiInstance = new BioLinkApi.AssociationApi();

var subject = "subject_example"; // String | E.g. e.g. NCBIGene:84570

var opts = { 
  'objectCategory': "objectCategory_example", // String | e.g. disease, phenotype, gene
  'evidence': "evidence_example", // String | Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default)                     or a specific publication or other supporting ibject, e.g. ZFIN:ZDB-PUB-060503-2.                     
  'mapIdentifiers': "mapIdentifiers_example", // String | Prefix to map all IDs to. E.g. NCBIGene
  'page': 1, // Integer | Page number
  'graphize': true, // Boolean | If set, includes graph object in response
  'subjectTaxon': "subjectTaxon_example", // String | SUBJECT TAXON id, e.g. NCBITaxon:9606. Includes inferred by default
  'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
  'subjectCategory': "subjectCategory_example", // String | e.g. gene, genotype, disease
  'rows': 10, // Integer | number of rows
  'flExcludesEvidence': true // Boolean | If set, excludes evidence objects in response
};

var callback = function(error, data, response) {
  if (error) {
    console.error(error);
  } else {
    console.log('API called successfully. Returned data: ' + data);
  }
};
apiInstance.getAssociationsFrom_0(subject, opts, callback);

Parameters

Name	Type	Description	Notes
subject	String	E.g. e.g. NCBIGene:84570
objectCategory	String	e.g. disease, phenotype, gene	[optional]
evidence	String	Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting ibject, e.g. ZFIN:ZDB-PUB-060503-2.	[optional]
mapIdentifiers	String	Prefix to map all IDs to. E.g. NCBIGene	[optional]
page	Integer	Page number	[optional] [default to 1]
graphize	Boolean	If set, includes graph object in response	[optional]
subjectTaxon	String	SUBJECT TAXON id, e.g. NCBITaxon:9606. Includes inferred by default	[optional]
slim	[String]	Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]
subjectCategory	String	e.g. gene, genotype, disease	[optional]
rows	Integer	number of rows	[optional] [default to 10]
flExcludesEvidence	Boolean	If set, excludes evidence objects in response	[optional]

Return type

[AssociationResults]

Authorization

No authorization required

HTTP request headers

Content-Type: application/json
Accept: application/json

getAssociationsTo

[AssociationResults] getAssociationsTo(_object, opts)

Returns list of matching associations

Example

var BioLinkApi = require('bio_link_api');

var apiInstance = new BioLinkApi.AssociationApi();

var _object = "_object_example"; // String | E.g. e.g. MP:0013765, can also be a biological entity such as a gene

var opts = { 
  'objectCategory': "objectCategory_example", // String | e.g. disease, phenotype, gene
  'evidence': "evidence_example", // String | Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default)                     or a specific publication or other supporting ibject, e.g. ZFIN:ZDB-PUB-060503-2.                     
  'mapIdentifiers': "mapIdentifiers_example", // String | Prefix to map all IDs to. E.g. NCBIGene
  'page': 1, // Integer | Page number
  'graphize': true, // Boolean | If set, includes graph object in response
  'subjectTaxon': "subjectTaxon_example", // String | SUBJECT TAXON id, e.g. NCBITaxon:9606. Includes inferred by default
  'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
  'subjectCategory': "subjectCategory_example", // String | e.g. gene, genotype, disease
  'rows': 10, // Integer | number of rows
  'flExcludesEvidence': true // Boolean | If set, excludes evidence objects in response
};

var callback = function(error, data, response) {
  if (error) {
    console.error(error);
  } else {
    console.log('API called successfully. Returned data: ' + data);
  }
};
apiInstance.getAssociationsTo(_object, opts, callback);

Parameters

Name	Type	Description	Notes
_object	String	E.g. e.g. MP:0013765, can also be a biological entity such as a gene
objectCategory	String	e.g. disease, phenotype, gene	[optional]
evidence	String	Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting ibject, e.g. ZFIN:ZDB-PUB-060503-2.	[optional]
mapIdentifiers	String	Prefix to map all IDs to. E.g. NCBIGene	[optional]
page	Integer	Page number	[optional] [default to 1]
graphize	Boolean	If set, includes graph object in response	[optional]
subjectTaxon	String	SUBJECT TAXON id, e.g. NCBITaxon:9606. Includes inferred by default	[optional]
slim	[String]	Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]
subjectCategory	String	e.g. gene, genotype, disease	[optional]
rows	Integer	number of rows	[optional] [default to 10]
flExcludesEvidence	Boolean	If set, excludes evidence objects in response	[optional]

Return type

[AssociationResults]

Authorization

No authorization required

HTTP request headers

Content-Type: application/json
Accept: application/json

Files

AssociationApi.md

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AssociationApi.md

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BioLinkApi.AssociationApi

getAssociationObject

Example

Parameters

Return type

Authorization

HTTP request headers

getAssociationSearch

Example

Parameters

Return type

Authorization

HTTP request headers

getAssociationSearch_0

Example

Parameters

Return type

Authorization

HTTP request headers

getAssociationSearch_1

Example

Parameters

Return type

Authorization

HTTP request headers

getAssociationsFrom

Example

Parameters

Return type

Authorization

HTTP request headers

getAssociationsFrom_0

Example

Parameters

Return type

Authorization

HTTP request headers

getAssociationsTo

Example

Parameters

Return type

Authorization

HTTP request headers