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