BioentityApi.md

BioentityApi

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

Method	HTTP request	Description
getAlleleObject	GET /bioentity/allele/{id}	TODO Returns allele object
getAnatomyGeneAssociations	GET /bioentity/anatomy/{id}/genes/	TODO Returns associations between anatomical entity and genes
getAnatomyObject	GET /bioentity/anatomy/{id}	TODO Returns anatomical entity
getAnatomyPhenotypeAssociations	GET /bioentity/anatomy/{id}/phenotypes/	TODO Returns associations between anatomical entity and phenotypes
getDiseaseAnatomyAssociations	GET /bioentity/disease/{id}/anatomy/	TODO Returns anatomical locations associated with a disease
getDiseaseFunctionAssociations	GET /bioentity/disease/{id}/function/	TODO Returns biological functions associated with a disease
getDiseaseGeneAssociations	GET /bioentity/disease/{id}/genes/	Returns genes associated with a disease
getDiseaseModelAssociations	GET /bioentity/disease/{id}/models/	Returns associations to models of the disease
getDiseaseModelTaxonAssociations	GET /bioentity/disease/{id}/models/{taxon}	Same as `/disease/<id>/models` but constrain models by taxon
getDiseaseObject	GET /bioentity/disease/{id}	TODO Returns disease object
getDiseasePhenotypeAssociations	GET /bioentity/disease/{id}/phenotypes/	Returns phenotypes associated with disease
getDiseaseSubstanceAssociations	GET /bioentity/disease/{id}/substance/	Returns substances associated with a disease
getDiseaseSubstanceAssociations_0	GET /bioentity/substance/{id}/treats/	Returns substances associated with a disease
getEnvironmentObject	GET /bioentity/environment/{id}	TODO Returns environment entity
getEnvironmentPhenotypeAssociations	GET /bioentity/environment/{id}/phenotypes/	TODO Returns list of associations
getGeneExpressionAssociations	GET /bioentity/gene/{id}/expressed/	TODO Returns expression events for a gene
getGeneFunctionAssociations	GET /bioentity/gene/{id}/function/	Returns function associations for a gene
getGeneHomologAssociations	GET /bioentity/gene/{id}/homologs/	Returns homologs for a gene
getGeneInteractions	GET /bioentity/gene/{id}/interactions/	Returns interactions for a gene
getGeneObject	GET /bioentity/gene/{id}	Returns gene object
getGenePhenotypeAssociations	GET /bioentity/gene/{id}/phenotypes/	Returns phenotypes associated with gene
getGenePublicationList	GET /bioentity/gene/{id}/pubs/	TODO Returns expression events for a gene
getGeneproductObject	GET /bioentity/geneproduct/{id}	TODO Returns gene product object
getGenericAssociations	GET /bioentity/{id}/associations/	Returns associations for an entity regardless of the type
getGenericObject	GET /bioentity/{id}	TODO Returns object of any type
getGenotypeDiseaseAssociations	GET /bioentity/genotype/{id}/diseases/	Returns diseases associated with a genotype
getGenotypeGeneAssociations	GET /bioentity/genotype/{id}/genes/	Returns genes associated with a genotype
getGenotypeGenotypeAssociations	GET /bioentity/genotype/{id}/genotypes/	Returns genotypes-genotype associations
getGenotypeObject	GET /bioentity/genotype/{id}	Returns genotype object
getGenotypePhenotypeAssociations	GET /bioentity/genotype/{id}/phenotypes/	Returns phenotypes associated with a genotype
getGotermGeneAssociations	GET /bioentity/goterm/{id}/genes/	TODO Returns associated phenotypes
getGotermObject	GET /bioentity/goterm/{id}	TODO Returns GO class object
getGotermPhenotypeAssociations	GET /bioentity/goterm/{id}/phenotype/	TODO Returns associated phenotypes
getLiteratureDiseaseAssociations	GET /bioentity/literature/{id}/diseases/	Returns associations between a lit entity and a disease
getLiteratureGeneAssociations	GET /bioentity/literature/{id}/genes/	Returns associations between a lit entity and a gene
getLiteratureGenotypeAssociations	GET /bioentity/literature/{id}/genotypes/	Returns associations between a lit entity and a genotype
getParentObject	GET /bioentity/individual/{id}	TODO Returns individual
getParentObject_0	GET /bioentity/investigation/{id}	TODO Returns investigation object
getPathwayGeneAssociations	GET /bioentity/pathway/{id}/genes/	TODO Returns list of genes associated with a pathway
getPathwayObject	GET /bioentity/pathway/{id}	TODO Returns pathway object
getPathwayParticipantAssociations	GET /bioentity/pathway/{id}/participants/	TODO Returns associations to participants (molecules, etc) for a pathway
getPhenotypeAnatomyAssociations	GET /bioentity/phenotype/{id}/anatomy/	Returns anatomical entities associated with a phenotype
getPhenotypeFunctionAssociations	GET /bioentity/phenotype/{id}/function/	TODO Returns biological functions associated with a Phenotype
getPhenotypeGeneAssociations	GET /bioentity/phenotype/{id}/gene/{taxid}/ids	Returns gene ids for all genes for a particular phenotype in a taxon
getPhenotypeGeneAssociations_0	GET /bioentity/phenotype/{id}/genes/	TODO Returns associated phenotypes
getPhenotypeObject	GET /bioentity/phenotype/{id}	TODO Returns phenotype class object
getPhenotypePhenotypeAssociations	GET /bioentity/phenotype/{id}/phenotype/	TODO Returns associated phenotypes
getPubObject	GET /bioentity/literature/{id}	TODO Returns publication object
getSequenceFeatureObject	GET /bioentity/sequence_feature/{id}	TODO Returns seqfeature
getSubstanceExposures	GET /bioentity/substance/{id}/exposures/	TODO Returns associations between a substance and related exposures
getSubstanceInteractions	GET /bioentity/substance/{id}/interactions/	TODO Returns associations between given drug and interactions
getSubstanceObject	GET /bioentity/substance/{id}	TODO Returns substance entity
getSubstanceParticipantInAssociations	GET /bioentity/substance/{id}/participant_in/	Returns associations between an activity and process and the specified substance
getSubstanceRelationships	GET /bioentity/substance/{id}/substances/	TODO Returns associations between a substance and other substances
getSubstanceRoleAssociations	GET /bioentity/substance/{id}/roles/	Returns associations between given drug and roles
getSubstanceTargetAssociations	GET /bioentity/substance/{id}/targets/	TODO Returns associations between given drug and targets
getVariantGeneAssociations	GET /bioentity/variant/{id}/genes/	Returns genes associated with a variant
getVariantGenotypeAssociations	GET /bioentity/variant/{id}/genotypes/	Returns genotypes associated with a variant
getVariantObject	GET /bioentity/variant/{id}	TODO Returns sequence variant entity
getVariantPhenotypeAssociations	GET /bioentity/variant/{id}/phenotypes/	Returns phenotypes associated with a variant

getAlleleObject

List<Allele> getAlleleObject(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

TODO Returns allele object

This is a composition of multiple smaller operations, including fetching allele metadata, plus allele associations TODO - should allele be subsumed into variant?

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | 
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<Allele> result = apiInstance.getAlleleObject(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getAlleleObject");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<Allele>

Authorization

No authorization required

HTTP request headers

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

getAnatomyGeneAssociations

List<Association> getAnatomyGeneAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

TODO Returns associations between anatomical entity and genes

Typically encompasses genes expressed in a particular location.

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | 
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<Association> result = apiInstance.getAnatomyGeneAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getAnatomyGeneAssociations");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<Association>

Authorization

No authorization required

HTTP request headers

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

getAnatomyObject

getAnatomyObject(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

TODO Returns anatomical entity

Anatomical entities span ranges from the subcellular (e.g. nucleus) through cells to tissues, organs and organ systems.

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | 
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    apiInstance.getAnatomyObject(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getAnatomyObject");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

null (empty response body)

Authorization

No authorization required

HTTP request headers

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

getAnatomyPhenotypeAssociations

List<Association> getAnatomyPhenotypeAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

TODO Returns associations between anatomical entity and phenotypes

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | 
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<Association> result = apiInstance.getAnatomyPhenotypeAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getAnatomyPhenotypeAssociations");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<Association>

Authorization

No authorization required

HTTP request headers

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

getDiseaseAnatomyAssociations

List<Association> getDiseaseAnatomyAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

TODO Returns anatomical locations associated with a disease

For example, neurodegeneratibe disease located in nervous system. For cancer, this may include both site of original and end location.

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | 
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<Association> result = apiInstance.getDiseaseAnatomyAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getDiseaseAnatomyAssociations");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<Association>

Authorization

No authorization required

HTTP request headers

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

getDiseaseFunctionAssociations

List<Association> getDiseaseFunctionAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

TODO Returns biological functions associated with a disease

This may come from a combination of asserted knowledge (e.g. Fanconi Anemia affects DNA repair) or from data-driven approach (cf Translator) Results are typically represented as GO classes

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | 
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<Association> result = apiInstance.getDiseaseFunctionAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getDiseaseFunctionAssociations");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<Association>

Authorization

No authorization required

HTTP request headers

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

getDiseaseGeneAssociations

List<AssociationResults> getDiseaseGeneAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

Returns genes associated with a disease

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<AssociationResults> result = apiInstance.getDiseaseGeneAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getDiseaseGeneAssociations");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String	CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<AssociationResults>

Authorization

No authorization required

HTTP request headers

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

getDiseaseModelAssociations

List<AssociationResults> getDiseaseModelAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

Returns associations to models of the disease

In the association object returned, the subject will be the disease, and the object will be the model. The model may be a gene or genetic element. If the query disease is a general class, the association subject may be to a specific disease. In some cases the association will be direct, for example if a paper asserts a genotype is a model of a disease. In other cases, the association will be indirect, for example, chaining over orthology. In these cases the chain will be reflected in the evidence graph * TODO: provide hook into owlsim for dynamic computation of models by similarity

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<AssociationResults> result = apiInstance.getDiseaseModelAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getDiseaseModelAssociations");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String	CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<AssociationResults>

Authorization

No authorization required

HTTP request headers

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

getDiseaseModelTaxonAssociations

List<AssociationResults> getDiseaseModelTaxonAssociations(taxon, id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

Same as `/disease/<id>/models` but constrain models by taxon

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String taxon = "taxon_example"; // String | CURIE of organism taxonomy class to constrain models, e.g NCBITaxon:6239 (C elegans).   Higher level taxa may be used
String id = "id_example"; // String | CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<AssociationResults> result = apiInstance.getDiseaseModelTaxonAssociations(taxon, id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getDiseaseModelTaxonAssociations");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
taxon	String	CURIE of organism taxonomy class to constrain models, e.g NCBITaxon:6239 (C elegans). Higher level taxa may be used
id	String	CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<AssociationResults>

Authorization

No authorization required

HTTP request headers

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

getDiseaseObject

getDiseaseObject(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

TODO Returns disease object

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | 
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    apiInstance.getDiseaseObject(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getDiseaseObject");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

null (empty response body)

Authorization

No authorization required

HTTP request headers

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

getDiseasePhenotypeAssociations

List<AssociationResults> getDiseasePhenotypeAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

Returns phenotypes associated with disease

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<AssociationResults> result = apiInstance.getDiseasePhenotypeAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getDiseasePhenotypeAssociations");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String	CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<AssociationResults>

Authorization

No authorization required

HTTP request headers

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

getDiseaseSubstanceAssociations

getDiseaseSubstanceAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

Returns substances associated with a disease

e.g. drugs or small molecules used to treat

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | CURIE identifier of disease, e.g. DOID:2841 (asthma). Equivalent IDs not yet supported
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    apiInstance.getDiseaseSubstanceAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getDiseaseSubstanceAssociations");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String	CURIE identifier of disease, e.g. DOID:2841 (asthma). Equivalent IDs not yet supported
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

null (empty response body)

Authorization

No authorization required

HTTP request headers

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

getDiseaseSubstanceAssociations_0

getDiseaseSubstanceAssociations_0(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

Returns substances associated with a disease

e.g. drugs or small molecules used to treat

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | 
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    apiInstance.getDiseaseSubstanceAssociations_0(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getDiseaseSubstanceAssociations_0");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

null (empty response body)

Authorization

No authorization required

HTTP request headers

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

getEnvironmentObject

getEnvironmentObject(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

TODO Returns environment entity

TODO consider renaming exposure

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | 
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    apiInstance.getEnvironmentObject(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getEnvironmentObject");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

null (empty response body)

Authorization

No authorization required

HTTP request headers

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

getEnvironmentPhenotypeAssociations

List<Association> getEnvironmentPhenotypeAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

TODO Returns list of associations

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | 
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<Association> result = apiInstance.getEnvironmentPhenotypeAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getEnvironmentPhenotypeAssociations");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<Association>

Authorization

No authorization required

HTTP request headers

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

getGeneExpressionAssociations

List<AssociationResults> getGeneExpressionAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

TODO Returns expression events for a gene

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | CURIE identifier of gene, e.g. NCBIGene:4750. Equivalent IDs can be used with same results
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<AssociationResults> result = apiInstance.getGeneExpressionAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getGeneExpressionAssociations");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String	CURIE identifier of gene, e.g. NCBIGene:4750. Equivalent IDs can be used with same results
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<AssociationResults>

Authorization

No authorization required

HTTP request headers

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

getGeneFunctionAssociations

List<AssociationResults> getGeneFunctionAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, type, homologTaxon, unselectEvidence, useCompactAssociations)

Returns function associations for a gene

Note: currently this is implemented as a query to the GO solr instance. A smaller set of identifiers may be supported: - ZFIN e.g. ZFIN:ZDB-GENE-050417-357 - MGI e.g. MGI:1342287 - Use UniProt for human (TODO: map this)

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | id, e.g. NCBIGene:3630. Equivalent IDs can be used with same results
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
String type = "type_example"; // String | P, O or LDO (paralog, ortholog or least-diverged).
String homologTaxon = "homologTaxon_example"; // String | Taxon CURIE of homolog, e.g. NCBITaxon:9606. Can be intermediate note, includes inferred by default
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<AssociationResults> result = apiInstance.getGeneFunctionAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, type, homologTaxon, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getGeneFunctionAssociations");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String	id, e.g. NCBIGene:3630. Equivalent IDs can be used with same results
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
type	String	P, O or LDO (paralog, ortholog or least-diverged).	[optional] [enum: P, O, LDO]
homologTaxon	String	Taxon CURIE of homolog, e.g. NCBITaxon:9606. Can be intermediate note, includes inferred by default	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<AssociationResults>

Authorization

No authorization required

HTTP request headers

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

getGeneHomologAssociations

List<AssociationResults> getGeneHomologAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, type, homologTaxon, unselectEvidence, useCompactAssociations)

Returns homologs for a gene

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | id, e.g. NCBIGene:3630. Equivalent IDs can be used with same results
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
String type = "type_example"; // String | P, O or LDO (paralog, ortholog or least-diverged).
String homologTaxon = "homologTaxon_example"; // String | Taxon CURIE of homolog, e.g. NCBITaxon:9606. Can be intermediate note, includes inferred by default
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<AssociationResults> result = apiInstance.getGeneHomologAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, type, homologTaxon, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getGeneHomologAssociations");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String	id, e.g. NCBIGene:3630. Equivalent IDs can be used with same results
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
type	String	P, O or LDO (paralog, ortholog or least-diverged).	[optional] [enum: P, O, LDO]
homologTaxon	String	Taxon CURIE of homolog, e.g. NCBITaxon:9606. Can be intermediate note, includes inferred by default	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<AssociationResults>

Authorization

No authorization required

HTTP request headers

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

getGeneInteractions

List<AssociationResults> getGeneInteractions(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

Returns interactions for a gene

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | id, e.g. NCBIGene:3630. Equivalent IDs can be used with same results
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<AssociationResults> result = apiInstance.getGeneInteractions(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getGeneInteractions");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String	id, e.g. NCBIGene:3630. Equivalent IDs can be used with same results
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<AssociationResults>

Authorization

No authorization required

HTTP request headers

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

getGeneObject

List<Gene> getGeneObject(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

Returns gene object

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | id, e.g. NCBIGene:84570
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<Gene> result = apiInstance.getGeneObject(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getGeneObject");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String	id, e.g. NCBIGene:84570
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<Gene>

Authorization

No authorization required

HTTP request headers

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

getGenePhenotypeAssociations

getGenePhenotypeAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

Returns phenotypes associated with gene

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | CURIE identifier of gene, e.g. NCBIGene:4750. Equivalent IDs can be used with same results
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    apiInstance.getGenePhenotypeAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getGenePhenotypeAssociations");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String	CURIE identifier of gene, e.g. NCBIGene:4750. Equivalent IDs can be used with same results
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

null (empty response body)

Authorization

No authorization required

HTTP request headers

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

getGenePublicationList

List<AssociationResults> getGenePublicationList(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

TODO Returns expression events for a gene

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | CURIE identifier of gene, e.g. NCBIGene:4750. Equivalent IDs can be used with same results
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<AssociationResults> result = apiInstance.getGenePublicationList(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getGenePublicationList");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String	CURIE identifier of gene, e.g. NCBIGene:4750. Equivalent IDs can be used with same results
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<AssociationResults>

Authorization

No authorization required

HTTP request headers

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

getGeneproductObject

getGeneproductObject(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

TODO Returns gene product object

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | 
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    apiInstance.getGeneproductObject(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getGeneproductObject");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

null (empty response body)

Authorization

No authorization required

HTTP request headers

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

getGenericAssociations

List<AssociationResults> getGenericAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

Returns associations for an entity regardless of the type

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | 
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<AssociationResults> result = apiInstance.getGenericAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getGenericAssociations");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<AssociationResults>

Authorization

No authorization required

HTTP request headers

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

getGenericObject

List<BioObject> getGenericObject(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

TODO Returns object of any type

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | id, e.g. NCBIGene:84570
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<BioObject> result = apiInstance.getGenericObject(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getGenericObject");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String	id, e.g. NCBIGene:84570
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<BioObject>

Authorization

No authorization required

HTTP request headers

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

getGenotypeDiseaseAssociations

List<AssociationResults> getGenotypeDiseaseAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

Returns diseases associated with a genotype

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-4286 (if non-human will return models)
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<AssociationResults> result = apiInstance.getGenotypeDiseaseAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getGenotypeDiseaseAssociations");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String	CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-4286 (if non-human will return models)
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<AssociationResults>

Authorization

No authorization required

HTTP request headers

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

getGenotypeGeneAssociations

List<AssociationResults> getGenotypeGeneAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

Returns genes associated with a genotype

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-6607
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<AssociationResults> result = apiInstance.getGenotypeGeneAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getGenotypeGeneAssociations");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String	CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-6607
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<AssociationResults>

Authorization

No authorization required

HTTP request headers

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

getGenotypeGenotypeAssociations

List<AssociationResults> getGenotypeGenotypeAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

Returns genotypes-genotype associations

Genotypes may be related to one another according to the GENO model

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-6607
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<AssociationResults> result = apiInstance.getGenotypeGenotypeAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getGenotypeGenotypeAssociations");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String	CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-6607
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<AssociationResults>

Authorization

No authorization required

HTTP request headers

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

getGenotypeObject

List<Genotype> getGenotypeObject(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

Returns genotype object

The genotype object will have the following association sets populated: * gene * phenotype * disease

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-6607
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<Genotype> result = apiInstance.getGenotypeObject(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getGenotypeObject");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String	CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-6607
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<Genotype>

Authorization

No authorization required

HTTP request headers

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

getGenotypePhenotypeAssociations

List<AssociationResults> getGenotypePhenotypeAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

Returns phenotypes associated with a genotype

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-4286
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<AssociationResults> result = apiInstance.getGenotypePhenotypeAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getGenotypePhenotypeAssociations");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String	CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-4286
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<AssociationResults>

Authorization

No authorization required

HTTP request headers

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

getGotermGeneAssociations

List<Association> getGotermGeneAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

TODO Returns associated phenotypes

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | 
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<Association> result = apiInstance.getGotermGeneAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getGotermGeneAssociations");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<Association>

Authorization

No authorization required

HTTP request headers

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

getGotermObject

getGotermObject(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

TODO Returns GO class object

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | GO class CURIE identifier, e.g GO:0016301 (kinase activity)
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    apiInstance.getGotermObject(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getGotermObject");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String	GO class CURIE identifier, e.g GO:0016301 (kinase activity)
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

null (empty response body)

Authorization

No authorization required

HTTP request headers

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

getGotermPhenotypeAssociations

List<Association> getGotermPhenotypeAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

TODO Returns associated phenotypes

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | 
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<Association> result = apiInstance.getGotermPhenotypeAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getGotermPhenotypeAssociations");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<Association>

Authorization

No authorization required

HTTP request headers

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

getLiteratureDiseaseAssociations

List<Association> getLiteratureDiseaseAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

Returns associations between a lit entity and a disease

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | 
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<Association> result = apiInstance.getLiteratureDiseaseAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getLiteratureDiseaseAssociations");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<Association>

Authorization

No authorization required

HTTP request headers

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

getLiteratureGeneAssociations

List<Association> getLiteratureGeneAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

Returns associations between a lit entity and a gene

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | 
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<Association> result = apiInstance.getLiteratureGeneAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getLiteratureGeneAssociations");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<Association>

Authorization

No authorization required

HTTP request headers

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

getLiteratureGenotypeAssociations

List<Association> getLiteratureGenotypeAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

Returns associations between a lit entity and a genotype

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | 
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<Association> result = apiInstance.getLiteratureGenotypeAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getLiteratureGenotypeAssociations");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<Association>

Authorization

No authorization required

HTTP request headers

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

getParentObject

getParentObject(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

TODO Returns individual

Individuals may typically encompass patients, but can be individuals of any species

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | 
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    apiInstance.getParentObject(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getParentObject");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

null (empty response body)

Authorization

No authorization required

HTTP request headers

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

getParentObject_0

getParentObject_0(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

TODO Returns investigation object

Investigations encompass clinical trials, molecular biology experiments or any kind of study

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | 
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    apiInstance.getParentObject_0(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getParentObject_0");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

null (empty response body)

Authorization

No authorization required

HTTP request headers

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

getPathwayGeneAssociations

List<Association> getPathwayGeneAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

TODO Returns list of genes associated with a pathway

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | 
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<Association> result = apiInstance.getPathwayGeneAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getPathwayGeneAssociations");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<Association>

Authorization

No authorization required

HTTP request headers

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

getPathwayObject

getPathwayObject(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

TODO Returns pathway object

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | CURIE any pathway element. May be a GO ID or a pathway database ID
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    apiInstance.getPathwayObject(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getPathwayObject");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String	CURIE any pathway element. May be a GO ID or a pathway database ID
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

null (empty response body)

Authorization

No authorization required

HTTP request headers

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

getPathwayParticipantAssociations

List<Association> getPathwayParticipantAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

TODO Returns associations to participants (molecules, etc) for a pathway

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | 
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<Association> result = apiInstance.getPathwayParticipantAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getPathwayParticipantAssociations");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<Association>

Authorization

No authorization required

HTTP request headers

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

getPhenotypeAnatomyAssociations

List<NamedObject> getPhenotypeAnatomyAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

Returns anatomical entities associated with a phenotype

Example IDs: * ZP:0004204 * MP:0008521 abnormal Bowman membrane For example, abnormal limb development will map to limb

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | 
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<NamedObject> result = apiInstance.getPhenotypeAnatomyAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getPhenotypeAnatomyAssociations");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<NamedObject>

Authorization

No authorization required

HTTP request headers

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

getPhenotypeFunctionAssociations

List<Association> getPhenotypeFunctionAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

TODO Returns biological functions associated with a Phenotype

This may come from a combination of asserted knowledge (e.g. abnormal levels of metabolite to corresponding GO activity) or from data-driven approach (cf Translator) Results are typically represented as GO classes

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | 
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<Association> result = apiInstance.getPhenotypeFunctionAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getPhenotypeFunctionAssociations");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<Association>

Authorization

No authorization required

HTTP request headers

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

getPhenotypeGeneAssociations

getPhenotypeGeneAssociations(taxid, id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

Returns gene ids for all genes for a particular phenotype in a taxon

For example, + NCBITaxon:10090 (mouse)

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String taxid = "taxid_example"; // String | Species or high level taxon grouping, e.g  NCBITaxon:10090 (Mus musculus)
String id = "id_example"; // String | Pheno class CURIE identifier, e.g  MP:0001569 (abnormal circulating bilirubin level)
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    apiInstance.getPhenotypeGeneAssociations(taxid, id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getPhenotypeGeneAssociations");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
taxid	String	Species or high level taxon grouping, e.g NCBITaxon:10090 (Mus musculus)
id	String	Pheno class CURIE identifier, e.g MP:0001569 (abnormal circulating bilirubin level)
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

null (empty response body)

Authorization

No authorization required

HTTP request headers

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

getPhenotypeGeneAssociations_0

List<Association> getPhenotypeGeneAssociations_0(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

TODO Returns associated phenotypes

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | 
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<Association> result = apiInstance.getPhenotypeGeneAssociations_0(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getPhenotypeGeneAssociations_0");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<Association>

Authorization

No authorization required

HTTP request headers

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

getPhenotypeObject

getPhenotypeObject(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

TODO Returns phenotype class object

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | 
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    apiInstance.getPhenotypeObject(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getPhenotypeObject");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

null (empty response body)

Authorization

No authorization required

HTTP request headers

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

getPhenotypePhenotypeAssociations

List<Association> getPhenotypePhenotypeAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

TODO Returns associated phenotypes

Includes phenologs, as well as equivalent phenotypes in other species

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | 
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<Association> result = apiInstance.getPhenotypePhenotypeAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getPhenotypePhenotypeAssociations");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<Association>

Authorization

No authorization required

HTTP request headers

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

getPubObject

getPubObject(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

TODO Returns publication object

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | 
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    apiInstance.getPubObject(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getPubObject");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

null (empty response body)

Authorization

No authorization required

HTTP request headers

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

getSequenceFeatureObject

getSequenceFeatureObject(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

TODO Returns seqfeature

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | 
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    apiInstance.getSequenceFeatureObject(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getSequenceFeatureObject");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

null (empty response body)

Authorization

No authorization required

HTTP request headers

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

getSubstanceExposures

List<Association> getSubstanceExposures(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

TODO Returns associations between a substance and related exposures

E.g. between pesticide and occupational exposure class

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | 
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<Association> result = apiInstance.getSubstanceExposures(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getSubstanceExposures");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<Association>

Authorization

No authorization required

HTTP request headers

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

getSubstanceInteractions

List<Association> getSubstanceInteractions(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

TODO Returns associations between given drug and interactions

Interactions can encompass drugs or environments

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | 
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<Association> result = apiInstance.getSubstanceInteractions(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getSubstanceInteractions");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<Association>

Authorization

No authorization required

HTTP request headers

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

getSubstanceObject

List<Substance> getSubstanceObject(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

TODO Returns substance entity

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | 
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<Substance> result = apiInstance.getSubstanceObject(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getSubstanceObject");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<Substance>

Authorization

No authorization required

HTTP request headers

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

getSubstanceParticipantInAssociations

List<Association> getSubstanceParticipantInAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

Returns associations between an activity and process and the specified substance

Examples relationships: * substance is a metabolite of a process * substance is synthesized by a process * substance is modified by an activity * substance elicits a response program/pathway * substance is transported by activity or pathway For example, CHEBI:40036 (amitrole)

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | 
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<Association> result = apiInstance.getSubstanceParticipantInAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getSubstanceParticipantInAssociations");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<Association>

Authorization

No authorization required

HTTP request headers

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

getSubstanceRelationships

List<Association> getSubstanceRelationships(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

TODO Returns associations between a substance and other substances

E.g. metabolite-of, tautomer-of, parent-of, ...

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | 
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<Association> result = apiInstance.getSubstanceRelationships(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getSubstanceRelationships");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<Association>

Authorization

No authorization required

HTTP request headers

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

getSubstanceRoleAssociations

List<Association> getSubstanceRoleAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

Returns associations between given drug and roles

Roles may be human-oriented (e.g. pesticide) or molecular (e.g. enzyme inhibitor)

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | 
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<Association> result = apiInstance.getSubstanceRoleAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getSubstanceRoleAssociations");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<Association>

Authorization

No authorization required

HTTP request headers

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

getSubstanceTargetAssociations

List<Association> getSubstanceTargetAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

TODO Returns associations between given drug and targets

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | 
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<Association> result = apiInstance.getSubstanceTargetAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getSubstanceTargetAssociations");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<Association>

Authorization

No authorization required

HTTP request headers

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

getVariantGeneAssociations

List<AssociationResults> getVariantGeneAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

Returns genes associated with a variant

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<AssociationResults> result = apiInstance.getVariantGeneAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getVariantGeneAssociations");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String	CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<AssociationResults>

Authorization

No authorization required

HTTP request headers

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

getVariantGenotypeAssociations

List<AssociationResults> getVariantGenotypeAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

Returns genotypes associated with a variant

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<AssociationResults> result = apiInstance.getVariantGenotypeAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getVariantGenotypeAssociations");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String	CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<AssociationResults>

Authorization

No authorization required

HTTP request headers

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

getVariantObject

getVariantObject(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

TODO Returns sequence variant entity

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    apiInstance.getVariantObject(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getVariantObject");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String	CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

null (empty response body)

Authorization

No authorization required

HTTP request headers

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

getVariantPhenotypeAssociations

List<AssociationResults> getVariantPhenotypeAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations)

Returns phenotypes associated with a variant

Example

// Import classes:
//import io.swagger.client.ApiException;
//import io.swagger.client.api.BioentityApi;


BioentityApi apiInstance = new BioentityApi();
String id = "id_example"; // String | CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783
Boolean fetchObjects = true; // Boolean | If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
Integer rows = 20; // Integer | number of rows
Boolean excludeAutomaticAssertions = true; // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
Boolean unselectEvidence = true; // Boolean | If set, excludes evidence objects in response
Boolean useCompactAssociations = true; // Boolean | If true, returns results in compact associations format
try {
    List<AssociationResults> result = apiInstance.getVariantPhenotypeAssociations(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling BioentityApi#getVariantPhenotypeAssociations");
    e.printStackTrace();
}

Parameters

Name	Type	Description	Notes
id	String	CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783
fetchObjects	Boolean	If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload	[optional] [default to true]
rows	Integer	number of rows	[optional] [default to 20]
excludeAutomaticAssertions	Boolean	If set, excludes associations that involve IEAs (ECO:0000501)	[optional]
unselectEvidence	Boolean	If set, excludes evidence objects in response	[optional]
useCompactAssociations	Boolean	If true, returns results in compact associations format	[optional]

Return type

List<AssociationResults>

Authorization

No authorization required

HTTP request headers

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