BioLink API

Tools (170)

Extracted live via the executor SDK.

• association.getAssociationBySubjectAndAssocType

  Returns list of matching associations of a given type

• association.getAssociationBySubjectAndObjectCategorySearch

  Returns list of matching associations between a given subject and object category

• association.getAssociationBySubjectCategorySearch

  Returns list of matching associations for a given subject category

• association.getAssociationObject

  An association connects, at a minimum, two things, designated subject and object, via some relationship. Associations also include evidence, provenance etc.

• association.getAssociationsBetween

  Given two entities (e.g. a particular gene and a particular disease), if these two entities are connected (directly or indirectly), then return the association objects describing the connection.

• association.getAssociationsFrom

  Returns list of matching associations starting from a given subject (source)

• association.getAssociationsTo

  Returns list of matching associations pointing to a given object (target)

• bioentity.getAnatomyGeneAssociations

  Returns genes associated with a given anatomy

• bioentity.getAnatomyGeneByTaxonAssociations

  For example, + NCBITaxon:10090 (mouse)

• bioentity.getCaseDiseaseAssociations

  Returns diseases associated with a case

• bioentity.getCaseGenotypeAssociations

  Returns genotypes associated with a case

• bioentity.getCaseModelAssociations

  Returns models associated with a case

• bioentity.getCasePhenotypeAssociations

  Returns phenotypes associated with a case

• bioentity.getCaseVariantAssociations

  Returns variants associated with a case

• bioentity.getDiseaseCaseAssociations

  Returns cases associated with a disease

• bioentity.getDiseaseGeneAssociations

  Returns genes associated with a disease

• bioentity.getDiseaseGenotypeAssociations

  Returns genotypes associated with a disease

• bioentity.getDiseaseModelAssociations

  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
• bioentity.getDiseaseModelTaxonAssociations

  See /disease//models route for full details

• bioentity.getDiseasePathwayAssociations

  Returns pathways associated with a disease

• bioentity.getDiseasePhenotypeAssociations

  Returns phenotypes associated with disease

• bioentity.getDiseasePublicationAssociations

  Returns publications associated with a disease

• bioentity.getDiseaseSubstanceAssociations

  e.g. drugs or small molecules used to treat

• bioentity.getDiseaseVariantAssociations

  Returns variants associated with a disease

• bioentity.getFunctionAssociations

  Returns annotations associated to a function term

• bioentity.getFunctionGeneAssociations

  Returns genes associated to a GO term

• bioentity.getFunctionPublicationAssociations

  Returns publications associated to a GO term

• bioentity.getFunctionTaxonAssociations

  Returns taxons associated to a GO term

• bioentity.getGeneAnatomyAssociations

  Returns anatomical entities associated with a gene

• bioentity.getGeneCaseAssociations

  Returns cases associated with a gene

• bioentity.getGeneDiseaseAssociations

  Returns diseases associated with gene

• bioentity.getGeneExpressionAssociations

  Returns expression events for a gene

• bioentity.getGeneFunctionAssociations

  IMPLEMENTATION DETAILS

  Note: currently this is implemented as a query to the GO/AmiGO solr instance. This directly supports IDs such as:

  • ZFIN e.g. ZFIN:ZDB-GENE-050417-357

  Note that the AmiGO GOlr natively stores MGI annotations to MGI:MGI:nn. However, the standard for biolink is MGI:nnnn, so you should use this (will be transparently mapped to legacy ID)

  Additionally, for some species such as Human, GO has the annotation attached to the UniProt ID. Again, this should be transparently handled; e.g. you can use NCBIGene:6469, and this will be mapped behind the scenes for querying.

• bioentity.getGeneGenotypeAssociations

  Returns genotypes associated with a gene

• bioentity.getGeneHomologAssociations

  Returns homologs for a gene

• bioentity.getGeneInteractions

  Returns interactions for a gene

• bioentity.getGeneModelAssociations

  Returns models associated with a gene

• bioentity.getGeneOrthologDiseaseAssociations

  Return diseases associated with orthologs of a gene

• bioentity.getGeneOrthologPhenotypeAssociations

  Return phenotypes associated with orthologs for a gene

• bioentity.getGenePathwayAssociations

  Returns pathways associated with gene

• bioentity.getGenePhenotypeAssociations

  Returns phenotypes associated with gene

• bioentity.getGenePublicationAssociations

  Returns publications associated with a gene

• bioentity.getGenericAssociations

  Returns associations for an entity regardless of the type

• bioentity.getGenericObject

  Returns basic info on object of any type

• bioentity.getGenericObjectByType

  Return basic info on an object for a given type

• bioentity.getGeneVariantAssociations

  Returns variants associated with a gene

• bioentity.getGenotypeCaseAssociations

  Returns cases associated with a genotype

• bioentity.getGenotypeDiseaseAssociations

  Returns diseases associated with a genotype

• bioentity.getGenotypeGeneAssociations

  Returns genes associated with a genotype

• bioentity.getGenotypeGenotypeAssociations

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

• bioentity.getGenotypeModelAssociations

  Returns models associated with a genotype

• bioentity.getGenotypePhenotypeAssociations

  Returns phenotypes associated with a genotype

• bioentity.getGenotypePublicationAssociations

  Returns publications associated with a genotype

• bioentity.getGenotypeVariantAssociations

  Returns genotypes-variant associations

• bioentity.getGotermGeneAssociations

  Returns associations to GO terms for a gene

• bioentity.getModelCaseAssociations

  Returns cases associated with a model

• bioentity.getModelDiseaseAssociations

  Returns diseases associated with a model

• bioentity.getModelGeneAssociations

  Returns genes associated with a model

• bioentity.getModelGenotypeAssociations

  Returns genotypes associated with a model

• bioentity.getModelPhenotypeAssociations

  Returns phenotypes associated with a model

• bioentity.getModelPublicationAssociations

  Returns publications associated with a model

• bioentity.getModelVariantAssociations

  Returns variants associated with a model

• bioentity.getPathwayDiseaseAssociations

  Returns diseases associated with a pathway

• bioentity.getPathwayGeneAssociations

  Returns genes associated with a pathway

• bioentity.getPathwayPhenotypeAssociations

  Returns phenotypes associated with a pathway

• bioentity.getPhenotypeAnatomyAssociations

  Example IDs:

  • MP:0008521 abnormal Bowman membrane
• bioentity.getPhenotypeCaseAssociations

  Returns cases associated with a phenotype

• bioentity.getPhenotypeDiseaseAssociations

  Returns diseases associated with a phenotype

• bioentity.getPhenotypeGeneAssociations

  Returns genes associated with a phenotype

• bioentity.getPhenotypeGeneByTaxonAssociations

  For example, MP:0001569 + NCBITaxon:10090 (mouse)

• bioentity.getPhenotypeGenotypeAssociations

  Returns genotypes associated with a phenotype

• bioentity.getPhenotypePathwayAssociations

  Returns pathways associated with a phenotype

• bioentity.getPhenotypePublicationAssociations

  Returns publications associated with a phenotype

• bioentity.getPhenotypeVariantAssociations

  Returns variants associated with a phenotype

• bioentity.getPublicationDiseaseAssociations

  Returns diseases associated with a publication

• bioentity.getPublicationGeneAssociations

  Returns genes associated with a publication

• bioentity.getPublicationGenotypeAssociations

  Returns genotypes associated with a publication

• bioentity.getPublicationModelAssociations

  Returns models associated with a publication

• bioentity.getPublicationPhenotypeAssociations

  Returns phenotypes associated with a publication

• bioentity.getPublicationVariantAssociations

  Returns variants associated with a publication

• bioentity.getSubstanceParticipantInAssociations

  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)

• bioentity.getSubstanceRoleAssociations

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

• bioentity.getSubstanceTreatsAssociations

  e.g. drugs or small molecules used to treat

• bioentity.getVariantCaseAssociations

  Returns cases associated with a variant

• bioentity.getVariantDiseaseAssociations

  Returns diseases associated with a variant

• bioentity.getVariantGeneAssociations

  Returns genes associated with a variant

• bioentity.getVariantGenotypeAssociations

  Returns genotypes associated with a variant

• bioentity.getVariantModelAssociations

  Returns models associated with a variant

• bioentity.getVariantPhenotypeAssociations

  Returns phenotypes associated with a variant

• bioentity.getVariantPublicationAssociations

  Returns publications associated with a variant

• bioentityset.getEntitySetAssociations

  Returns compact associations for a given input set

• bioentityset.getEntitySetGraphResource

  TODO Graph object spanning all entities

• bioentityset.getEntitySetSummary

  Summary statistics for objects associated

• bioentityset.getOverRepresentation

  Summary statistics for objects associated

• bioentitysetHomologs.getEntitySetHomologs

  Returns homology associations for a given input set of genes

• bioentitysetSlimmer.getEntitySetAnatomySlimmer

  For a given gene(s), summarize its annotations over a defined set of slim

• bioentitysetSlimmer.getEntitySetFunctionSlimmer

  For a given gene(s), summarize its annotations over a defined set of slim

• bioentitysetSlimmer.getEntitySetPhenotypeSlimmer

  For a given gene(s), summarize its annotations over a defined set of slim

• cam.getActivityCollection

  Returns list of models

• cam.getInstanceObject

  Returns list of matches

• cam.getModelCollection

  Returns list of ALL models

• cam.getModelContributors

  Returns list of all contributors across all models

• cam.getModelInstances

  Returns list of all instances

• cam.getModelObject

  Returns a complete model

• cam.getModelProperties

  Returns list of all properties used across all models

• cam.getModelPropertyValues

  Returns list property-values for all models

• cam.getModelQuery

  Returns list of models matching query

• cam.getPhysicalInteraction

  Returns list of models

• evidenceGraph.getEvidenceGraphObject

  Note that every association is assumed to have a unique ID

• evidenceGraph.getEvidenceGraphTable

  Note that every association is assumed to have a unique ID

• genomeFeatures.getFeaturesWithinResource

  Returns list of matches

• graph.getEdgeResource

  Returns edges emanating from a given node

• graph.getNodeResource

  A node is an abstract representation of some kind of entity. The entity may be a physical thing such as a patient, a molecular entity such as a gene or protein, or a conceptual entity such as a class from an ontology.

• identifierMapper.getIdentifierMapper

  TODO maps a list of identifiers from a source to a target

• identifierPrefixes.getPrefixCollection

  Returns list of prefixes

• identifierPrefixes.getPrefixContract

  Returns contracted URI

• identifierPrefixes.getPrefixExpand

  Returns expanded URI

• individual.getIndividual

  Returns list of matches

• individual.getPedigree

  Returns list of matches

• mart.getMartCaseAssociationsResource

  NOTE: this route has a limiter on it, you may be restricted in the number of downloads per hour. Use carefully.

• mart.getMartDiseaseAssociationsResource

  NOTE: this route has a limiter on it, you may be restricted in the number of downloads per hour. Use carefully.

• mart.getMartGeneAssociationsResource

  NOTE: this route has a limiter on it, you may be restricted in the number of downloads per hour. Use carefully.

• mart.getMartOrthologAssociationsResource

  Bulk download of orthologs

• mart.getMartParalogAssociationsResource

  Bulk download of paralogs

• metadata.getMetadataForDatasets

  Get metadata for all datasets from SciGraph

• mme.postDiseaseMme

  Match a patient to diseases based on their phenotypes

• mme.postFlyMme

  Match a patient to fruit fly genes based on similar phenotypes

• mme.postMouseMme

  Match a patient to mouse genes based on similar phenotypes

• mme.postNematodeMme

  Match a patient to nematode genes based on similar phenotypes

• mme.postZebrafishMme

  Match a patient to zebrafish genes based on similar phenotypes

• nlpAnnotate.getAnnotate

  Annotate a given text using SciGraph annotator

• nlpAnnotate.getAnnotateEntities

  Annotate a given content using SciGraph annotator and get all entities from content

• nlpAnnotate.postAnnotate

  Annotate a given text using SciGraph annotator

• nlpAnnotate.postAnnotateEntities

  Annotate a given content using SciGraph annotator and get all entities from content

• ontol.getExtractOntologySubgraphResource

  Extract a subgraph from an ontology

• ontol.getInformationContentResource
  IC = -log2( freq(t) / popSize )

  Here the frequency and population is calculated for a particular dataset: e.g. all human disease-phenotype associations

• ontol.postExtractOntologySubgraphResource

  Extract a subgraph from an ontology

• ontolIdentifier.getOntolIdentifierResource

  Fetches a map from CURIEs/IDs to labels

• ontolIdentifier.postOntolIdentifierResource

  Takes 'label' list argument either as a querystring argument or as a key in the POST body when content-type is application/json.

• ontolLabeler.getOntolLabelerResource

  Fetches a map from CURIEs/IDs to labels

• ontology.getOntologySubset

  Returns meta data of an ontology subset (slim)

• ontology.getOntologyTerm

  Returns meta data of an ontology term

• ontology.getOntologyTermGraph

  Returns graph of an ontology term

• ontology.getOntologyTermsSharedAncestor

  Returns the ancestor ontology terms shared by two ontology terms

• ontology.getOntologyTermSubgraph

  Extract a subgraph from an ontology term

• ontology.getOntologyTermSubsets

  Returns subsets (slims) associated to an ontology term

• owlOntology.getDlQuery

  Placeholder - use OWLery for now

• owlOntology.getSparqlQuery

  Placeholder - use direct SPARQL endpoint for now

• pairSim.getPairSimJaccardResource

  Get pairwise similarity

• relationUsage.getRelationUsageBetweenResource

  All relations used plus count of associations

• relationUsage.getRelationUsagePivotLabelResource

  Relation usage count for all subj x obj category combinations, showing label

• relationUsage.getRelationUsagePivotResource

  Relation usage count for all subj x obj category combinations

• relationUsage.getRelationUsageResource

  All relations used plus count of associations

• search.getAutocomplete

  Returns list of matching concepts or entities using lexical search

• search.getSearchEntities

  Returns list of matching concepts or entities using lexical search

• search.getSearchHpoEntities

  Returns list of matching concepts or entities using lexical search

• sim.getAnnotationScore

  Get annotation score

• sim.getSimCompare

  Compare a reference profile vs one profiles

• sim.getSimSearch

  Search for phenotypically similar diseases or model genes

• sim.postAnnotationScore

  Get annotation score

• sim.postSimCompare

  Compare a reference profile vs one or more profiles

• variationSet.deleteVariantSetItem

  Deletes variant set

• variationSet.getVariantAnalyze

  Returns list of matches

• variationSet.getVariantSetItem

  Returns a variant set

• variationSet.getVariantSetsArchiveCollection

  Returns list of variant sets from a specified time period

• variationSet.getVariantSetsCollection

  Returns list of variant sets

• variationSet.postVariantSetsCollection

  Creates a new variant set

• variationSet.putVariantSetItem

  Updates a variant set

• openapi.previewSpec

  Preview an OpenAPI document before adding it as a source

• openapi.addSource

  Add an OpenAPI source and register its operations as tools