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 |
[Allele] getAlleleObject(id, opts)
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?
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String |
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getAlleleObject(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | ||
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
[Association] getAnatomyGeneAssociations(id, opts)
TODO Returns associations between anatomical entity and genes
Typically encompasses genes expressed in a particular location.
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String |
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getAnatomyGeneAssociations(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | ||
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
getAnatomyObject(id, opts)
TODO Returns anatomical entity
Anatomical entities span ranges from the subcellular (e.g. nucleus) through cells to tissues, organs and organ systems.
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String |
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully.');
}
};
apiInstance.getAnatomyObject(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | ||
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
null (empty response body)
No authorization required
- Content-Type: application/json
- Accept: application/json
[Association] getAnatomyPhenotypeAssociations(id, opts)
TODO Returns associations between anatomical entity and phenotypes
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String |
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getAnatomyPhenotypeAssociations(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | ||
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
[Association] getDiseaseAnatomyAssociations(id, opts)
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.
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String |
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getDiseaseAnatomyAssociations(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | ||
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
[Association] getDiseaseFunctionAssociations(id, opts)
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
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String |
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getDiseaseFunctionAssociations(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | ||
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
[AssociationResults] getDiseaseGeneAssociations(id, opts)
Returns genes associated with a disease
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String | CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getDiseaseGeneAssociations(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results | |
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
[AssociationResults] getDiseaseModelAssociations(id, opts)
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
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String | CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getDiseaseModelAssociations(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results | |
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
[AssociationResults] getDiseaseModelTaxonAssociations(taxon, id, opts)
Same as `/disease/<id>/models` but constrain models by taxon
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var taxon = "taxon_example"; // String | CURIE of organism taxonomy class to constrain models, e.g NCBITaxon:6239 (C elegans). Higher level taxa may be used
var id = "id_example"; // String | CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getDiseaseModelTaxonAssociations(taxon, id, opts, callback);| 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 | |
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
getDiseaseObject(id, opts)
TODO Returns disease object
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String |
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully.');
}
};
apiInstance.getDiseaseObject(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | ||
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
null (empty response body)
No authorization required
- Content-Type: application/json
- Accept: application/json
[AssociationResults] getDiseasePhenotypeAssociations(id, opts)
Returns phenotypes associated with disease
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String | CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getDiseasePhenotypeAssociations(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results | |
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
getDiseaseSubstanceAssociations(id, opts)
Returns substances associated with a disease
e.g. drugs or small molecules used to treat
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String | CURIE identifier of disease, e.g. DOID:2841 (asthma). Equivalent IDs not yet supported
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully.');
}
};
apiInstance.getDiseaseSubstanceAssociations(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | CURIE identifier of disease, e.g. DOID:2841 (asthma). Equivalent IDs not yet supported | |
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
null (empty response body)
No authorization required
- Content-Type: application/json
- Accept: application/json
getDiseaseSubstanceAssociations_0(id, opts)
Returns substances associated with a disease
e.g. drugs or small molecules used to treat
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String |
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully.');
}
};
apiInstance.getDiseaseSubstanceAssociations_0(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | ||
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
null (empty response body)
No authorization required
- Content-Type: application/json
- Accept: application/json
getEnvironmentObject(id, opts)
TODO Returns environment entity
TODO consider renaming exposure
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String |
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully.');
}
};
apiInstance.getEnvironmentObject(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | ||
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
null (empty response body)
No authorization required
- Content-Type: application/json
- Accept: application/json
[Association] getEnvironmentPhenotypeAssociations(id, opts)
TODO Returns list of associations
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String |
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getEnvironmentPhenotypeAssociations(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | ||
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
[AssociationResults] getGeneExpressionAssociations(id, opts)
TODO Returns expression events for a gene
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String | CURIE identifier of gene, e.g. NCBIGene:4750. Equivalent IDs can be used with same results
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getGeneExpressionAssociations(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | CURIE identifier of gene, e.g. NCBIGene:4750. Equivalent IDs can be used with same results | |
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
[AssociationResults] getGeneFunctionAssociations(id, opts)
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)
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String | id, e.g. NCBIGene:3630. Equivalent IDs can be used with same results
var opts = {
'type': "type_example", // String | P, O or LDO (paralog, ortholog or least-diverged).
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'homologTaxon': "homologTaxon_example", // String | Taxon CURIE of homolog, e.g. NCBITaxon:9606. Can be intermediate note, includes inferred by default
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'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
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getGeneFunctionAssociations(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | id, e.g. NCBIGene:3630. Equivalent IDs can be used with same results | |
| type | String | P, O or LDO (paralog, ortholog or least-diverged). | [optional] |
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| homologTaxon | String | Taxon CURIE of homolog, e.g. NCBITaxon:9606. Can be intermediate note, includes inferred by default | [optional] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| 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] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
[AssociationResults] getGeneHomologAssociations(id, opts)
Returns homologs for a gene
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String | id, e.g. NCBIGene:3630. Equivalent IDs can be used with same results
var opts = {
'type': "type_example", // String | P, O or LDO (paralog, ortholog or least-diverged).
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'homologTaxon': "homologTaxon_example", // String | Taxon CURIE of homolog, e.g. NCBITaxon:9606. Can be intermediate note, includes inferred by default
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20, // Integer | number of rows
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getGeneHomologAssociations(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | id, e.g. NCBIGene:3630. Equivalent IDs can be used with same results | |
| type | String | P, O or LDO (paralog, ortholog or least-diverged). | [optional] |
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| homologTaxon | String | Taxon CURIE of homolog, e.g. NCBITaxon:9606. Can be intermediate note, includes inferred by default | [optional] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
No authorization required
- Content-Type: application/json
- Accept: application/json
[AssociationResults] getGeneInteractions(id, opts)
Returns interactions for a gene
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String | id, e.g. NCBIGene:3630. Equivalent IDs can be used with same results
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getGeneInteractions(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | id, e.g. NCBIGene:3630. Equivalent IDs can be used with same results | |
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
[Gene] getGeneObject(id, opts)
Returns gene object
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String | id, e.g. NCBIGene:84570
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getGeneObject(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | id, e.g. NCBIGene:84570 | |
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
getGenePhenotypeAssociations(id, opts)
Returns phenotypes associated with gene
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String | CURIE identifier of gene, e.g. NCBIGene:4750. Equivalent IDs can be used with same results
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully.');
}
};
apiInstance.getGenePhenotypeAssociations(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | CURIE identifier of gene, e.g. NCBIGene:4750. Equivalent IDs can be used with same results | |
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
null (empty response body)
No authorization required
- Content-Type: application/json
- Accept: application/json
[AssociationResults] getGenePublicationList(id, opts)
TODO Returns expression events for a gene
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String | CURIE identifier of gene, e.g. NCBIGene:4750. Equivalent IDs can be used with same results
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getGenePublicationList(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | CURIE identifier of gene, e.g. NCBIGene:4750. Equivalent IDs can be used with same results | |
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
getGeneproductObject(id, opts)
TODO Returns gene product object
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String |
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully.');
}
};
apiInstance.getGeneproductObject(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | ||
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
null (empty response body)
No authorization required
- Content-Type: application/json
- Accept: application/json
[AssociationResults] getGenericAssociations(id, opts)
Returns associations for an entity regardless of the type
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String |
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getGenericAssociations(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | ||
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
[BioObject] getGenericObject(id, opts)
TODO Returns object of any type
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String | id, e.g. NCBIGene:84570
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getGenericObject(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | id, e.g. NCBIGene:84570 | |
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
[AssociationResults] getGenotypeDiseaseAssociations(id, opts)
Returns diseases associated with a genotype
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String | CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-4286 (if non-human will return models)
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getGenotypeDiseaseAssociations(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-4286 (if non-human will return models) | |
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
[AssociationResults] getGenotypeGeneAssociations(id, opts)
Returns genes associated with a genotype
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String | CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-6607
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getGenotypeGeneAssociations(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-6607 | |
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
[AssociationResults] getGenotypeGenotypeAssociations(id, opts)
Returns genotypes-genotype associations
Genotypes may be related to one another according to the GENO model
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String | CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-6607
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getGenotypeGenotypeAssociations(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-6607 | |
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
[Genotype] getGenotypeObject(id, opts)
Returns genotype object
The genotype object will have the following association sets populated: * gene * phenotype * disease
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String | CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-6607
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getGenotypeObject(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-6607 | |
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
[AssociationResults] getGenotypePhenotypeAssociations(id, opts)
Returns phenotypes associated with a genotype
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String | CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-4286
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getGenotypePhenotypeAssociations(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-4286 | |
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
[Association] getGotermGeneAssociations(id, opts)
TODO Returns associated phenotypes
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String |
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getGotermGeneAssociations(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | ||
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
getGotermObject(id, opts)
TODO Returns GO class object
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String | GO class CURIE identifier, e.g GO:0016301 (kinase activity)
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully.');
}
};
apiInstance.getGotermObject(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | GO class CURIE identifier, e.g GO:0016301 (kinase activity) | |
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
null (empty response body)
No authorization required
- Content-Type: application/json
- Accept: application/json
[Association] getGotermPhenotypeAssociations(id, opts)
TODO Returns associated phenotypes
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String |
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getGotermPhenotypeAssociations(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | ||
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
[Association] getLiteratureDiseaseAssociations(id, opts)
Returns associations between a lit entity and a disease
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String |
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getLiteratureDiseaseAssociations(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | ||
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
[Association] getLiteratureGeneAssociations(id, opts)
Returns associations between a lit entity and a gene
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String |
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getLiteratureGeneAssociations(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | ||
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
[Association] getLiteratureGenotypeAssociations(id, opts)
Returns associations between a lit entity and a genotype
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String |
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getLiteratureGenotypeAssociations(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | ||
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
getParentObject(id, opts)
TODO Returns individual
Individuals may typically encompass patients, but can be individuals of any species
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String |
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully.');
}
};
apiInstance.getParentObject(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | ||
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
null (empty response body)
No authorization required
- Content-Type: application/json
- Accept: application/json
getParentObject_0(id, opts)
TODO Returns investigation object
Investigations encompass clinical trials, molecular biology experiments or any kind of study
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String |
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully.');
}
};
apiInstance.getParentObject_0(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | ||
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
null (empty response body)
No authorization required
- Content-Type: application/json
- Accept: application/json
[Association] getPathwayGeneAssociations(id, opts)
TODO Returns list of genes associated with a pathway
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String |
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getPathwayGeneAssociations(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | ||
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
getPathwayObject(id, opts)
TODO Returns pathway object
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String | CURIE any pathway element. May be a GO ID or a pathway database ID
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully.');
}
};
apiInstance.getPathwayObject(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | CURIE any pathway element. May be a GO ID or a pathway database ID | |
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
null (empty response body)
No authorization required
- Content-Type: application/json
- Accept: application/json
[Association] getPathwayParticipantAssociations(id, opts)
TODO Returns associations to participants (molecules, etc) for a pathway
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String |
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getPathwayParticipantAssociations(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | ||
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
[NamedObject] getPhenotypeAnatomyAssociations(id, opts)
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
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String |
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getPhenotypeAnatomyAssociations(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | ||
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
[Association] getPhenotypeFunctionAssociations(id, opts)
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
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String |
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getPhenotypeFunctionAssociations(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | ||
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
getPhenotypeGeneAssociations(id, taxid, opts)
Returns gene ids for all genes for a particular phenotype in a taxon
For example, + NCBITaxon:10090 (mouse)
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String | Pheno class CURIE identifier, e.g MP:0001569 (abnormal circulating bilirubin level)
var taxid = "taxid_example"; // String | Species or high level taxon grouping, e.g NCBITaxon:10090 (Mus musculus)
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully.');
}
};
apiInstance.getPhenotypeGeneAssociations(id, taxid, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | Pheno class CURIE identifier, e.g MP:0001569 (abnormal circulating bilirubin level) | |
| taxid | String | Species or high level taxon grouping, e.g NCBITaxon:10090 (Mus musculus) | |
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
null (empty response body)
No authorization required
- Content-Type: application/json
- Accept: application/json
[Association] getPhenotypeGeneAssociations_0(id, opts)
TODO Returns associated phenotypes
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String |
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getPhenotypeGeneAssociations_0(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | ||
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
getPhenotypeObject(id, opts)
TODO Returns phenotype class object
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String |
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully.');
}
};
apiInstance.getPhenotypeObject(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | ||
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
null (empty response body)
No authorization required
- Content-Type: application/json
- Accept: application/json
[Association] getPhenotypePhenotypeAssociations(id, opts)
TODO Returns associated phenotypes
Includes phenologs, as well as equivalent phenotypes in other species
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String |
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getPhenotypePhenotypeAssociations(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | ||
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
getPubObject(id, opts)
TODO Returns publication object
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String |
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully.');
}
};
apiInstance.getPubObject(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | ||
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
null (empty response body)
No authorization required
- Content-Type: application/json
- Accept: application/json
getSequenceFeatureObject(id, opts)
TODO Returns seqfeature
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String |
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully.');
}
};
apiInstance.getSequenceFeatureObject(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | ||
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
null (empty response body)
No authorization required
- Content-Type: application/json
- Accept: application/json
[Association] getSubstanceExposures(id, opts)
TODO Returns associations between a substance and related exposures
E.g. between pesticide and occupational exposure class
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String |
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getSubstanceExposures(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | ||
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
[Association] getSubstanceInteractions(id, opts)
TODO Returns associations between given drug and interactions
Interactions can encompass drugs or environments
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String |
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getSubstanceInteractions(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | ||
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
[Substance] getSubstanceObject(id, opts)
TODO Returns substance entity
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String |
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getSubstanceObject(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | ||
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
[Association] getSubstanceParticipantInAssociations(id, opts)
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)
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String |
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getSubstanceParticipantInAssociations(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | ||
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
[Association] getSubstanceRelationships(id, opts)
TODO Returns associations between a substance and other substances
E.g. metabolite-of, tautomer-of, parent-of, ...
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String |
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getSubstanceRelationships(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | ||
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
[Association] getSubstanceRoleAssociations(id, opts)
Returns associations between given drug and roles
Roles may be human-oriented (e.g. pesticide) or molecular (e.g. enzyme inhibitor)
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String |
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getSubstanceRoleAssociations(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | ||
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
[Association] getSubstanceTargetAssociations(id, opts)
TODO Returns associations between given drug and targets
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String |
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getSubstanceTargetAssociations(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | ||
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
[AssociationResults] getVariantGeneAssociations(id, opts)
Returns genes associated with a variant
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String | CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getVariantGeneAssociations(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783 | |
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
[AssociationResults] getVariantGenotypeAssociations(id, opts)
Returns genotypes associated with a variant
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String | CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getVariantGenotypeAssociations(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783 | |
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json
getVariantObject(id, opts)
TODO Returns sequence variant entity
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String | CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully.');
}
};
apiInstance.getVariantObject(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783 | |
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
null (empty response body)
No authorization required
- Content-Type: application/json
- Accept: application/json
[AssociationResults] getVariantPhenotypeAssociations(id, opts)
Returns phenotypes associated with a variant
var BioLinkApi = require('bio_link_api');
var apiInstance = new BioLinkApi.BioentityApi();
var id = "id_example"; // String | CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783
var opts = {
'excludeAutomaticAssertions': true, // Boolean | If set, excludes associations that involve IEAs (ECO:0000501)
'unselectEvidence': true, // Boolean | If set, excludes evidence objects in response
'slim': ["slim_example"], // [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
'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
'useCompactAssociations': true, // Boolean | If true, returns results in compact associations format
'rows': 20 // Integer | number of rows
};
var callback = function(error, data, response) {
if (error) {
console.error(error);
} else {
console.log('API called successfully. Returned data: ' + data);
}
};
apiInstance.getVariantPhenotypeAssociations(id, opts, callback);| Name | Type | Description | Notes |
|---|---|---|---|
| id | String | CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783 | |
| excludeAutomaticAssertions | Boolean | If set, excludes associations that involve IEAs (ECO:0000501) | [optional] |
| unselectEvidence | Boolean | If set, excludes evidence objects in response | [optional] |
| slim | [String] | Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID | [optional] |
| 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] |
| useCompactAssociations | Boolean | If true, returns results in compact associations format | [optional] |
| rows | Integer | number of rows | [optional] [default to 20] |
No authorization required
- Content-Type: application/json
- Accept: application/json