ENDPOINTS

Endpoint: ubergraph

ubergraph is a merged set of mutually referential OBO ontologies, pre-reasoned, and implementing relation-graph triples

  • URL: https://stars-app.renci.org/ubergraph/sparql
  • Implements Profiles:
    • relation_graph: Implementing endpoints must have reflexive inferred triples asserted with named graph indicating method as per balhoff/relation-graph
    • taxon: Implementing endpoints must have NCBITaxon, or a relevant subset of NCBITaxon loaded
    • owl_as_rdf: Implementing endpoints must OWL axioms loaded as per the OWL2 mapping to RDF specification
    • omo: Implementing endpoints must use OBO ontology-metadata (OMO) compliant annotations on terms
    • biolink_categories: Implementing endpoints must tag elements to biolink categories using biolink:category
    • biolink_ontology: Implementing endpoints must have the biolink OWL ontology loaded

EXAMPLES

PairwiseCommonSubClassAncestor

Finds common ancestors between pyridine biosynthetic process and spermidine biosynthetic process

sparqlfun query -e ubergraph -T PairwiseCommonSubClassAncestor node1=GO:0046220 node2=GO:0008295

PairwiseMostRecentCommonSubClassAncestor

Finds most recent common ancestors between pyridine biosynthetic process and spermidine biosynthetic process

sparqlfun query -e ubergraph -T PairwiseMostRecentCommonSubClassAncestor node1=GO:0046220 node2=GO:0008295

Endpoint: dbpedia

a project aiming to extract structured content from the information created in the Wikipedia project, implementing the dbpedia ontology

  • URL: http://dbpedia.org/sparql
  • Implements Profiles:

Endpoint: go

public endpoint for GO-CAMs

  • URL: http://rdf.geneontology.org/sparql
  • Implements Profiles:
    • taxon: Implementing endpoints must have NCBITaxon, or a relevant subset of NCBITaxon loaded
    • owl_as_rdf: Implementing endpoints must OWL axioms loaded as per the OWL2 mapping to RDF specification
    • omo: Implementing endpoints must use OBO ontology-metadata (OMO) compliant annotations on terms

Endpoint: uniprot

Contains all UniProt data.

  • URL: https://sparql.uniprot.org/sparql
  • Implements Profiles:
    • ontobee: Implementing endpoints must use ontobee patterns for indicating source of ontology as Named Graph
    • taxon: Implementing endpoints must have NCBITaxon, or a relevant subset of NCBITaxon loaded
    • owl_as_rdf: Implementing endpoints must OWL axioms loaded as per the OWL2 mapping to RDF specification
    • omo: Implementing endpoints must use OBO ontology-metadata (OMO) compliant annotations on terms

Endpoint: nextprot

endpoint for nextprot database of human proteins

  • URL: https://api.nextprot.org/sparql
  • Implements Profiles:

Endpoint: kghub

endpoint for the KG-Hub project, which amalgamates multiple Knowledge Graphs following the Biolink Model

  • URL: http://kg-hub-rdf.berkeleybop.io/sparql
  • Implements Profiles:
    • biolink_categories: Implementing endpoints must tag elements to biolink categories using biolink:category
    • ontologies_as_kgx: Implementing endpoints must use kgx/rdf reification patterns for ontology edges

Endpoint: ontobee

Endpoint for OBO ontologies, provided by the He Group

  • URL: http://sparql.hegroup.org/sparql
  • Implements Profiles:
    • ontobee: Implementing endpoints must use ontobee patterns for indicating source of ontology as Named Graph
    • taxon: Implementing endpoints must have NCBITaxon, or a relevant subset of NCBITaxon loaded
    • owl_as_rdf: Implementing endpoints must OWL axioms loaded as per the OWL2 mapping to RDF specification
    • omo: Implementing endpoints must use OBO ontology-metadata (OMO) compliant annotations on terms

Endpoint: rhea

Endpoint for the Rhea database of enzymatic reactions

  • URL: https://sparql.rhea-db.org/sparql
  • Implements Profiles:

Endpoint: wikidata

Wikidata triple store

  • URL: http://query.wikidata.org/sparql
  • Implements Profiles:
    • wikidata: Implementing endpoints must use Wikidata properties and Wikidata-style reification