BioLink

All relations used plus count of associations

All relations used plus count of associations

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

Annotate a given text using SciGraph annotator

Compare a reference profile vs one or more profiles

Compare a reference profile vs one profiles

Creates a new variant set

Deletes variant set

Extract a subgraph from an ontology

Extract a subgraph from an ontology

Extract a subgraph from an ontology term

Fetches a map from CURIEs/IDs to labels

Fetches a map from CURIEs/IDs to labels

Fetches a map from CURIEs/IDs to labels

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

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

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

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

Get annotation score

Get annotation score

Get metadata for all datasets from SciGraph

Get pairwise similarity

Match a patient to diseases based on their phenotypes

Match a patient to fruit fly genes based on similar phenotypes

Match a patient to mouse genes based on similar phenotypes

Match a patient to nematode genes based on similar phenotypes

Match a patient to zebrafish genes based on similar phenotypes

Placeholder - use direct SPARQL endpoint for now

Placeholder - use OWLery for now

Relation usage count for all subj x obj category combinations

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

Returns a complete model

Returns a graph node

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.

Returns a variant set

Returns anatomical entities associated with a gene

Returns annotations associated to a function term

Returns associations connecting two entities

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.

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

Returns associations to models of the disease constrained by taxon

See /disease/<id>/models route for full details

Returns cases associated with a disease

Returns cases associated with a gene

Returns compact associations for a given input set

Returns contracted URI

Returns diseases associated with a case

Returns diseases associated with gene

Returns edges emanating from a given node

Returns evidence as a association_results object given an association

Note that every association is assumed to have a unique ID

Returns evidence graph object for a given association

Note that every association is assumed to have a unique ID

Returns expanded URI

Returns expression events for a gene

Returns function associations for a gene

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.

Returns gene IDs for all genes associated with a given anatomy, filtered by taxon

For example, + NCBITaxon:10090 (mouse)

Returns genes associated to a GO term

Returns genes associated with a disease

Returns genes associated with a given anatomy

Returns genotypes associated with a case

Returns genotypes associated with a disease

Returns graph of an ontology term

Returns homology associations for a given input set of genes

Returns information content (IC) for a set of relevant ontology classes

``` IC = -log2( freq(t) / popSize ) ``` Here the frequency and population is calculated for a particular dataset: e.g. all human disease-phenotype associations

Returns list of all contributors across all models

Returns list of all instances

Returns list of ALL models

Returns list of all properties used across all models

Returns list of matches

Returns list of matches

Returns list of matches

Returns list of matches

Returns list of matches

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

Returns list of matching associations for a given subject category

Returns list of matching associations of a given type

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

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

Returns list of matching concepts or entities using lexical search

Returns list of models

Returns list of models

Returns list of models matching query

Returns list of prefixes

Returns list of variant sets

Returns list of variant sets from a specified time period

Returns list property-values for all models

Returns meta data of an ontology subset (slim)

Returns meta data of an ontology term

Returns models associated with a case

Returns pathways associated with a disease

Returns phenotypes associated with a case

Returns phenotypes associated with disease

Returns publications associated to a GO term

Returns publications associated with a disease

Returns subsets (slims) associated to an ontology term

Returns substances associated with a disease

e.g. drugs or small molecules used to treat

Returns taxons associated to a GO term

Returns the ancestor ontology terms shared by two ontology terms

Returns the association with a given identifier

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

Returns variants associated with a case

Returns variants associated with a disease

Search for phenotypically similar diseases or model genes

Summary statistics for objects associated

TODO Graph object spanning all entities

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