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bio_link_api

BioLinkApi - JavaScript client for bio_link_api API integration layer for linked biological objects. Source: https://github.com/monarch-initiative/biolink-api/ This SDK is automatically generated by the Swagger Codegen project:

  • API version: 0.1
  • Package version: 0.1
  • Build date: 2017-02-07T16:19:27.567-08:00
  • Build package: class io.swagger.codegen.languages.JavascriptClientCodegen

Installation

npm

To publish the library as a npm, please follow the procedure in "Publishing npm packages".

Then install it via:

npm install bio_link_api --save

git

If the library is hosted at a git repository, e.g. https://github.com/GIT_USER_ID/GIT_REPO_ID then install it via:

    npm install GIT_USER_ID/GIT_REPO_ID --save

For browser

The library also works in the browser environment via npm and browserify. After following the above steps with Node.js and installing browserify with npm install -g browserify, perform the following (assuming main.js is your entry file):

browserify main.js > bundle.js

Then include bundle.js in the HTML pages.

Getting Started

Please follow the installation instruction and execute the following JS code:

var BioLinkApi = require('bio_link_api');

var api = new BioLinkApi.AssociationApi()

var id = "id_example"; // {String} 

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

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

Documentation for API Endpoints

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

Class Method HTTP request Description
BioLinkApi.AssociationApi getAssociationObject GET /association/{id} Returns the association with a given identifier
BioLinkApi.AssociationApi getAssociationSearch GET /association/find/ Returns list of matching associations
BioLinkApi.AssociationApi getAssociationSearch_0 GET /association/find/{subject_category}/ Returns list of matching associations
BioLinkApi.AssociationApi getAssociationSearch_1 GET /association/find/{subject_category}/{object_category}/ Returns list of matching associations
BioLinkApi.AssociationApi getAssociationsFrom GET /association/between/{subject}/{object} Returns associations connecting two entities
BioLinkApi.AssociationApi getAssociationsFrom_0 GET /association/from/{subject} Returns list of matching associations
BioLinkApi.AssociationApi getAssociationsTo GET /association/to/{object} Returns list of matching associations
BioLinkApi.BioentityApi getAlleleObject GET /bioentity/allele/{id} TODO Returns allele object
BioLinkApi.BioentityApi getAnatomyGeneAssociations GET /bioentity/anatomy/{id}/genes/ TODO Returns associations between anatomical entity and genes
BioLinkApi.BioentityApi getAnatomyObject GET /bioentity/anatomy/{id} TODO Returns anatomical entity
BioLinkApi.BioentityApi getAnatomyPhenotypeAssociations GET /bioentity/anatomy/{id}/phenotypes/ TODO Returns associations between anatomical entity and phenotypes
BioLinkApi.BioentityApi getDiseaseAnatomyAssociations GET /bioentity/disease/{id}/anatomy/ TODO Returns anatomical locations associated with a disease
BioLinkApi.BioentityApi getDiseaseFunctionAssociations GET /bioentity/disease/{id}/function/ TODO Returns biological functions associated with a disease
BioLinkApi.BioentityApi getDiseaseGeneAssociations GET /bioentity/disease/{id}/genes/ Returns genes associated with a disease
BioLinkApi.BioentityApi getDiseaseModelAssociations GET /bioentity/disease/{id}/models/ Returns associations to models of the disease
BioLinkApi.BioentityApi getDiseaseModelTaxonAssociations GET /bioentity/disease/{id}/models/{taxon} Same as `/disease/<id>/models` but constrain models by taxon
BioLinkApi.BioentityApi getDiseaseObject GET /bioentity/disease/{id} TODO Returns disease object
BioLinkApi.BioentityApi getDiseasePhenotypeAssociations GET /bioentity/disease/{id}/phenotypes/ Returns phenotypes associated with disease
BioLinkApi.BioentityApi getDiseaseSubstanceAssociations GET /bioentity/disease/{id}/substance/ Returns substances associated with a disease
BioLinkApi.BioentityApi getDiseaseSubstanceAssociations_0 GET /bioentity/substance/{id}/treats/ Returns substances associated with a disease
BioLinkApi.BioentityApi getEnvironmentObject GET /bioentity/environment/{id} TODO Returns environment entity
BioLinkApi.BioentityApi getEnvironmentPhenotypeAssociations GET /bioentity/environment/{id}/phenotypes/ TODO Returns list of associations
BioLinkApi.BioentityApi getGeneExpressionAssociations GET /bioentity/gene/{id}/expressed/ TODO Returns expression events for a gene
BioLinkApi.BioentityApi getGeneFunctionAssociations GET /bioentity/gene/{id}/function/ Returns function associations for a gene
BioLinkApi.BioentityApi getGeneHomologAssociations GET /bioentity/gene/{id}/homologs/ Returns homologs for a gene
BioLinkApi.BioentityApi getGeneInteractions GET /bioentity/gene/{id}/interactions/ Returns interactions for a gene
BioLinkApi.BioentityApi getGeneObject GET /bioentity/gene/{id} Returns gene object
BioLinkApi.BioentityApi getGenePhenotypeAssociations GET /bioentity/gene/{id}/phenotypes/ Returns phenotypes associated with gene
BioLinkApi.BioentityApi getGenePublicationList GET /bioentity/gene/{id}/pubs/ TODO Returns expression events for a gene
BioLinkApi.BioentityApi getGeneproductObject GET /bioentity/geneproduct/{id} TODO Returns gene product object
BioLinkApi.BioentityApi getGenericAssociations GET /bioentity/{id}/associations/ Returns associations for an entity regardless of the type
BioLinkApi.BioentityApi getGenericObject GET /bioentity/{id} TODO Returns object of any type
BioLinkApi.BioentityApi getGenotypeDiseaseAssociations GET /bioentity/genotype/{id}/diseases/ Returns diseases associated with a genotype
BioLinkApi.BioentityApi getGenotypeGeneAssociations GET /bioentity/genotype/{id}/genes/ Returns genes associated with a genotype
BioLinkApi.BioentityApi getGenotypeGenotypeAssociations GET /bioentity/genotype/{id}/genotypes/ Returns genotypes-genotype associations
BioLinkApi.BioentityApi getGenotypeObject GET /bioentity/genotype/{id} Returns genotype object
BioLinkApi.BioentityApi getGenotypePhenotypeAssociations GET /bioentity/genotype/{id}/phenotypes/ Returns phenotypes associated with a genotype
BioLinkApi.BioentityApi getGotermGeneAssociations GET /bioentity/goterm/{id}/genes/ TODO Returns associated phenotypes
BioLinkApi.BioentityApi getGotermObject GET /bioentity/goterm/{id} TODO Returns GO class object
BioLinkApi.BioentityApi getGotermPhenotypeAssociations GET /bioentity/goterm/{id}/phenotype/ TODO Returns associated phenotypes
BioLinkApi.BioentityApi getLiteratureDiseaseAssociations GET /bioentity/literature/{id}/diseases/ Returns associations between a lit entity and a disease
BioLinkApi.BioentityApi getLiteratureGeneAssociations GET /bioentity/literature/{id}/genes/ Returns associations between a lit entity and a gene
BioLinkApi.BioentityApi getLiteratureGenotypeAssociations GET /bioentity/literature/{id}/genotypes/ Returns associations between a lit entity and a genotype
BioLinkApi.BioentityApi getParentObject GET /bioentity/individual/{id} TODO Returns individual
BioLinkApi.BioentityApi getParentObject_0 GET /bioentity/investigation/{id} TODO Returns investigation object
BioLinkApi.BioentityApi getPathwayGeneAssociations GET /bioentity/pathway/{id}/genes/ TODO Returns list of genes associated with a pathway
BioLinkApi.BioentityApi getPathwayObject GET /bioentity/pathway/{id} TODO Returns pathway object
BioLinkApi.BioentityApi getPathwayParticipantAssociations GET /bioentity/pathway/{id}/participants/ TODO Returns associations to participants (molecules, etc) for a pathway
BioLinkApi.BioentityApi getPhenotypeAnatomyAssociations GET /bioentity/phenotype/{id}/anatomy/ Returns anatomical entities associated with a phenotype
BioLinkApi.BioentityApi getPhenotypeFunctionAssociations GET /bioentity/phenotype/{id}/function/ TODO Returns biological functions associated with a Phenotype
BioLinkApi.BioentityApi getPhenotypeGeneAssociations GET /bioentity/phenotype/{id}/gene/{taxid}/ids Returns gene ids for all genes for a particular phenotype in a taxon
BioLinkApi.BioentityApi getPhenotypeGeneAssociations_0 GET /bioentity/phenotype/{id}/genes/ TODO Returns associated phenotypes
BioLinkApi.BioentityApi getPhenotypeObject GET /bioentity/phenotype/{id} TODO Returns phenotype class object
BioLinkApi.BioentityApi getPhenotypePhenotypeAssociations GET /bioentity/phenotype/{id}/phenotype/ TODO Returns associated phenotypes
BioLinkApi.BioentityApi getPubObject GET /bioentity/literature/{id} TODO Returns publication object
BioLinkApi.BioentityApi getSequenceFeatureObject GET /bioentity/sequence_feature/{id} TODO Returns seqfeature
BioLinkApi.BioentityApi getSubstanceExposures GET /bioentity/substance/{id}/exposures/ TODO Returns associations between a substance and related exposures
BioLinkApi.BioentityApi getSubstanceInteractions GET /bioentity/substance/{id}/interactions/ TODO Returns associations between given drug and interactions
BioLinkApi.BioentityApi getSubstanceObject GET /bioentity/substance/{id} TODO Returns substance entity
BioLinkApi.BioentityApi getSubstanceParticipantInAssociations GET /bioentity/substance/{id}/participant_in/ Returns associations between an activity and process and the specified substance
BioLinkApi.BioentityApi getSubstanceRelationships GET /bioentity/substance/{id}/substances/ TODO Returns associations between a substance and other substances
BioLinkApi.BioentityApi getSubstanceRoleAssociations GET /bioentity/substance/{id}/roles/ Returns associations between given drug and roles
BioLinkApi.BioentityApi getSubstanceTargetAssociations GET /bioentity/substance/{id}/targets/ TODO Returns associations between given drug and targets
BioLinkApi.BioentityApi getVariantGeneAssociations GET /bioentity/variant/{id}/genes/ Returns genes associated with a variant
BioLinkApi.BioentityApi getVariantGenotypeAssociations GET /bioentity/variant/{id}/genotypes/ Returns genotypes associated with a variant
BioLinkApi.BioentityApi getVariantObject GET /bioentity/variant/{id} TODO Returns sequence variant entity
BioLinkApi.BioentityApi getVariantPhenotypeAssociations GET /bioentity/variant/{id}/phenotypes/ Returns phenotypes associated with a variant
BioLinkApi.BioentitysetApi getEntitySetAssociations GET /bioentityset/associations/ Returns compact associations for a given input set
BioLinkApi.BioentitysetApi getEntitySetGraphResource GET /bioentityset/graph/ TODO Graph object spanning all entities
BioLinkApi.BioentitysetApi getEntitySetHomologsDeprecated GET /bioentityset/DEPRECATEDhomologs/ Returns homology associations for a given input set of genes
BioLinkApi.BioentitysetApi getEntitySetOverRepresentationAnalysis GET /bioentityset/ora/ TODO Over-representation analysis
BioLinkApi.BioentitysetApi getEntitySetOverRepresentationAnalysis_0 GET /bioentityset/ora/{object_category}/ TODO Over-representation analysis
BioLinkApi.BioentitysetApi getEntitySetSummary GET /bioentityset/descriptor/counts/ Summary statistics for objects associated
BioLinkApi.BioentitysethomologsApi getEntitySetHomologs GET /bioentityset/homologs/homologs/ Returns homology associations for a given input set of genes
BioLinkApi.CamApi getActivityCollection GET /cam/activity/ Returns list of models
BioLinkApi.CamApi getInstance GET /cam/instance/{id} Returns list of matches
BioLinkApi.CamApi getModel GET /cam/model/{id} Returns a complete model
BioLinkApi.CamApi getModelCollection GET /cam/model/ Returns list of ALL models
BioLinkApi.CamApi getModelCollection_0 GET /cam/model/properties/ Returns list of all properties used across all models
BioLinkApi.CamApi getModelCollection_1 GET /cam/model/property_values/ Returns list property-values for all models
BioLinkApi.CamApi getModelCollection_2 GET /cam/model/query/ Returns list of models matching query
BioLinkApi.CamApi getModelContibutors GET /cam/instances/ Returns list of all instances
BioLinkApi.CamApi getModelContibutors_0 GET /cam/model/contributors/ Returns list of all contributors across all models
BioLinkApi.CamApi getPhysicalInteraction GET /cam/physical_interaction/ Returns list of models
BioLinkApi.EvidencegraphApi getAssociationObject GET /evidence/graph/{id} Returns evidence graph object for a given association
BioLinkApi.EvidencegraphApi getAssociationObject_0 GET /evidence/graph/{id}/image Returns evidence graph as a png
BioLinkApi.GenomefeaturesApi getFeaturesWithinResource GET /genome/features/within/{build}/{reference}/{begin}/{end} Returns list of matches
BioLinkApi.GraphApi getEdgeResource GET /graph/edges/from/{id} Returns edges emanating from a node
BioLinkApi.GraphApi getNodeResource GET /graph/node/{id} Returns a graph node
BioLinkApi.IdentifiermapperApi getPrefixCollection GET /identifier/mapper/{source}/{target}/ TODO maps a list of identifiers from a source to a target
BioLinkApi.IdentifierprefixesApi getPrefixCollection GET /identifier/prefixes/ Returns list of prefixes
BioLinkApi.IdentifierprefixesApi getPrefixCollection_0 GET /identifier/prefixes/contract/{uri} Returns contracted URI
BioLinkApi.IdentifierprefixesApi getPrefixCollection_1 GET /identifier/prefixes/expand/{id} Returns expanded URI
BioLinkApi.IndividualApi getIndividual GET /individual/{id} Returns list of matches
BioLinkApi.IndividualApi getPedigree GET /individual/pedigree/{id} Returns list of matches
BioLinkApi.NlpannotateApi getAnnotate GET /nlp/annotate/{text} Returns list of matches
BioLinkApi.OntolApi getInformationContentResource GET /ontol/information_content/{subject_category}/{object_category}/{subject_taxon} Calculates information content
BioLinkApi.OntolslimmerApi getFoo GET /ontol/slimmer/{subset} Maps to slim
BioLinkApi.OwlontologyApi getDlQuery GET /owl/ontology/dlquery/{query} Returns list of matches
BioLinkApi.OwlontologyApi getDlQuery_0 GET /owl/ontology/sparql/{query} Returns list of matches
BioLinkApi.PairsimApi getPairSimJaccardResource GET /pair/sim/jaccard/{id1}/{id2}/ Get pairwise similarity
BioLinkApi.PubpubsApi getFoo GET /pub/pubs/{term} Returns list of matches
BioLinkApi.RelationusageApi getRelationUsageBetweenResource GET /relation/usage/between/{subject_category}/{object_category} All relations used plus count of associations
BioLinkApi.RelationusageApi getRelationUsagePivotLabelResource GET /relation/usage/pivot/label Relation usage count for all subj x obj category combinations, showing label
BioLinkApi.RelationusageApi getRelationUsagePivotResource GET /relation/usage/pivot/ Relation usage count for all subj x obj category combinations
BioLinkApi.RelationusageApi getRelationUsageResource GET /relation/usage/ All relations used plus count of associations
BioLinkApi.SearchentityApi getAuthocomplete GET /search/entity/autocomplete/{term} Returns list of matches
BioLinkApi.SearchentityApi getAuthocomplete_0 GET /search/entity/query/ Returns list of matches
BioLinkApi.SearchentityApi getSearchEntities GET /search/entity/{term} Returns list of matches
BioLinkApi.VariationsetApi deleteVariantSetItem DELETE /variation/set/{id} Deletes variant set
BioLinkApi.VariationsetApi getAnalyze GET /variation/set/analyze/{id} Returns list of matches
BioLinkApi.VariationsetApi getVariantSetItem GET /variation/set/{id} Returns a variant set
BioLinkApi.VariationsetApi getVariantSetsArchiveCollection GET /variation/set/archive/{year}/{month}/{day}/ Returns list of variant sets from a specified time period
BioLinkApi.VariationsetApi getVariantSetsCollection GET /variation/set/ Returns list of variant sets
BioLinkApi.VariationsetApi postVariantSetsCollection POST /variation/set/ Creates a new variant set
BioLinkApi.VariationsetApi putVariantSetItem PUT /variation/set/{id} Updates a variant set

Documentation for Models

Documentation for Authorization

All endpoints do not require authorization.