biolinkapi

BioLinkApi - JavaScript client for biolinkapi 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:

shell npm install bio_link_api --save

git

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

shell 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):

shell 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:

```javascript var BioLinkApi = require('biolinkapi');

var api = new BioLinkApi.AssociationApi()

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

var opts = { 'evidence': "evidenceexample", // {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': "mapIdentifiersexample", // {String} Prefix to map all IDs to. E.g. NCBIGene 'object': "objectexample", // {String} OBJECT id, e.g. HP:0011927. Includes inferred by default 'graphize': true, // {Boolean} If set, includes graph object in response 'subjectTaxon': "subjectTaxonexample", // {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/{subjectcategory}/ | Returns list of matching associations BioLinkApi.AssociationApi | getAssociationSearch_1 | GET /association/find/{subjectcategory}/{objectcategory}/ | 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/sequencefeature/{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}/participantin/ | 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/{objectcategory}/ | 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/propertyvalues/ | 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/physicalinteraction/ | 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/informationcontent/{subjectcategory}/{objectcategory}/{subjecttaxon} | 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/{subjectcategory}/{objectcategory} | 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.