README.md

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

For Node.js

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

• BioLinkApi.APageOfResults
• BioLinkApi.AbstractPropertyValue
• BioLinkApi.Allele
• BioLinkApi.AnnotationExtension
• BioLinkApi.Association
• BioLinkApi.AssociationPropertyValue
• BioLinkApi.AssociationResults
• BioLinkApi.BioObject
• BioLinkApi.Chromosome
• BioLinkApi.CompactAssociationSet
• BioLinkApi.Edge
• BioLinkApi.Exon
• BioLinkApi.Gene
• BioLinkApi.Genotype
• BioLinkApi.Graph
• BioLinkApi.NamedObject
• BioLinkApi.Node
• BioLinkApi.PageOfVariantSets
• BioLinkApi.Publication
• BioLinkApi.Relation
• BioLinkApi.SearchResult
• BioLinkApi.Seq
• BioLinkApi.SequenceFeature
• BioLinkApi.SequenceLocation
• BioLinkApi.SequencePosition
• BioLinkApi.Substance
• BioLinkApi.SummaryPropertyValue
• BioLinkApi.Taxon
• BioLinkApi.Transcript
• BioLinkApi.VariantSet

Documentation for Authorization

All endpoints do not require authorization.