Ubergraph Adapter
About
Ubergraph is a SPARQL endpoint serving multiple OBO ontologies, pre-processed with
relation-graph
information content scores
biolink categories
This implementation is a specialization of the sparql interface, tuned for Ubergraph
Note
This is a remote endpoint implementation - as such, throttling is implemented to limit overuse
Interfaces Implemented
This implements most interfaces. It also attempts to implement each in the most performant way, avoiding iterative queries, attempting instead to batch queries into larger SPARQL query
Connecting
Use ubergraph: as a selector.
To restrict queries to a particular ontology, use the ontology ID as a suffix, e.g. ubergraph:uberon
Search
runoak -i ubergraph: search hippocampus
Code
- class oaklib.implementations.ubergraph.ubergraph_implementation.UbergraphImplementation(resource: ~oaklib.resource.OntologyResource = None, strict: bool = False, _multilingual: bool = None, autosave: bool = <factory>, exclude_owl_top_and_bottom: bool = <factory>, ontology_metamodel_mapper: ~oaklib.mappers.ontology_metadata_mapper.OntologyMetadataMapper | None = None, _converter: ~curies.api.Converter | None = None, auto_relax_axioms: bool = None, cache_lookups: bool = False, property_cache: ~oaklib.utilities.keyval_cache.KeyValCache = <factory>, _edge_index: ~oaklib.indexes.edge_index.EdgeIndex | None = None, _entailed_edge_index: ~oaklib.indexes.edge_index.EdgeIndex | None = None, _prefix_map: ~typing.Mapping[str, str] | None = None, sparql_wrapper: <module 'SPARQLWrapper' from '/home/runner/.cache/pypoetry/virtualenvs/oaklib-5bvmowLS-py3.9/lib/python3.9/site-packages/SPARQLWrapper/__init__.py'> = None, graph: ~rdflib.graph.Graph = None, _list_of_named_graphs: ~typing.List[str] = None, **_kwargs)[source]
Wraps the Ubergraph sparql endpoint
See: https://github.com/INCATools/ubergraph
This is a specialization of the more generic
SparqlImplementation, which has knowledge of some of the specialized patterns found in UbergraphAn UbergraphImplementation can be initialed by:
>>> from oaklib.implementations.ubergraph.ubergraph_implementation import UbergraphImplementation >>> adapter = UbergraphImplementation()
or
>>> from oaklib import get_adapter >>> adapter = get_adapter("ubergraph:")
to use a specific ontology or named graph within ubergraph:
>>> adapter = get_adapter("ubergraph:cl")