sparqlfun schema

SPARQL Templates

Classes

• Binding
• ResultSet
  • DescribeEquivalentExpression
  • OboClassQuery
• Charge
• DeprecatedOboClassQuery
• Node - The basic unit of representation in an RDF or OWL graph
  • BasicClass
  • BlankNode - A node with an ID that is not preserved between databases
  • IriNode
  • NamedIndividualNode - A node that represents an OWL Named Individual
  • NestedNodeObject
  • NodeObject
  • TypedNode
    • ClassNode - A node that represents an RDFS/OWL class
      • GraphClassNode
        • OboClass
          • AnatomicalEntity
          • BloodVessel
          • CellType
          • ChemicalEntity
          • OboClassWithCategory
      • OboClassFiltered
      • TaxonApplicableClass
      • TaxonClass
        • UbergraphTaxonClass - all classes representing a taxon in ubergraph
    • PropertyNode - Note this only directly classifies nodes asserted to be rdf:Properties
• NodeOrLiteral - A grouping for nodes or literals, maps to Any type
• OwlAnnotation
• PairwiseCommonAncestor - Common ancestor in relation graph over any relations between two nodes
  • PairwiseCommonSubClassAncestor
• PairwiseCommonDescendant - Common descendant in relation graph over any relations between two nodes
  • PairwiseCommonSubClassDescendant
• PairwiseCommonDescendantMatrix - Common descendant in relation graph over any relations between two nodes from two axes
  • PairwiseCommonSubClassDescendantMatrix
• PairwiseMostRecentCommonSubClassAncestor - Common non-redundant SubClass ancestor between two nodes
• PairwiseMostRecentCommonAncestor - Common non-redundant ancestor in relation graph over any relations between two nodes
• Prefix - Maps CURIEs to URIs
• SetwiseCommonSubClassAncestor - Common superclass ancestor to a set of nodes
• SetwiseMostRecentCommonSubClassAncestor - Most recent common superclass ancestor to a set of nodes
• SomeValuesFromRestriction
• SubclassOfSomeValuesFrom
  • ConjugateBase
    • ConjugateBaseWithCharge
• TraversalBasedPairwiseDisjointnessViolation
• Triple - Represents a single unadorned RDF triple
  • SubClassCountTriple
  • ClassTaxonExclusion
  • ClassTaxonExclusionViaNeverIn - An inferred never-in between a subject term and an object taxon, which holds
  • ClassTaxonExclusionViaOnlyIn
  • InTaxonTriple - In ubergraph, an in-taxon triple is pre-inferred
  • NestedTriple
  • NeverInTaxonTriple
  • NodeToNodeTriple - A triple where object is a node (isIRI)
    • BiolinkCategoryTriple - A triple that connects any node to its biolink category
    • ConformsToTriple
    • NamedNodeToNamedNodeTriple - A triple where subject and object are both nodes (isIRI)
      • OwlNamedEquivalentClassTriple - An equivalence triple between two named classes
    • OwlEquivalentClassTriple - A statement that connects two class nodes where both classes are equivalent
    • RdfTypeTriple - A triple that indicates the asserted type of the subject entity
    • RdfsDomainTriple
    • RdfsRangeTriple
    • RdfsSubclassOfTriple
      • RdfsSubclassOfNamedTriple
      • RedundantRdfsSubclassOfTriple
    • RdfsSubpropertyOfTriple
  • NodeToValueTriple - A triple where object is a literal
    • DefinitionTriple
    • RdfsLabelTriple
  • NormalizedInformationContentTriple
  • OwlTripleAnnotation
  • OwlTripleWithAnnotationsTODO
  • Quad - Represents an RDF triple plus named graph to which the triple belongs
    • RelationGraphQuad
      • NonRedundantQuad - A triple that indicates the asserted type of the subject entity
      • UbergraphQuad - a quad in an ubergraph endpoint
        • IsAOrPartOf
    • Statement - A quad that is optionally adorned with statements about it
      • Association
        • GeneToGeneAssociation
      • AssociationWithInferredCategories
      • NodeToNodeStatement - A statement where object is a node (isIRI)
        • ConformsToStatement
        • RdfTypeStatement - A statement that indicates the asserted type of the subject entity
      • NodeToValueStatement - A statement where object is a literal

Mixins

• GenericResult
• ClassTrait
• EquivalenceTripleMixin
• IndividualTrait
• NodeTrait - abstract groupings/properties for different aspects of the model
  • ClassTrait
  • IndividualTrait
  • PropertyTrait
• PropertyTrait
• TaxonApplicable

Slots

• ancestor
• annotations
• axiom_identifier
• axiom_object
• axiom_predicate
• base - The base URI a prefix will expand to
• ➞subClassOf
• binding_key
• binding_value
• bindings
• branching_part_of
• category
  • object_category
  • object_category_inferred
  • subject_category
  • subject_category_inferred
• charge
• class1
• class2
• class_with_constraint
• ➞object_charge
• ➞subject_charge
• datatype
• definition
• descendant
• descendant_class
• description
• direct_taxon
• drains
• exact_synonyms
• filler
• graph - Graph to which the triple belongs
  • relation graph quad➞graph - Indicates inference/redundancy status
    • non redundant quad➞graph - Source of
• id - An identifier for an element. Note blank node ids are not unique across databases
  • iri node➞id
• is_direction_canonical
• label
• label_regex
• label_starts_with
• language
• ➞xobject
• node1
• node1_candidates
• node2
• node2_candidates
• nodes
• object - a literal or node representing the object of the triple
  • class taxon exclusion via never in➞object - The taxon that cannot have the subject class.
  • class taxon exclusion via only in➞object - The taxon that cannot have the subject class.
  • class taxon exclusion➞object - The taxon that cannot have the subject class.
  • equivalence triple mixin➞object - One of the two classes that are equivalent. No significance to subject vs object
    • owl named equivalent class triple➞object
  • nested triple➞object
  • node to node statement➞object
    • rdf type statement➞object - The entity type
  • node to node triple➞object
    • rdf type triple➞object - The entity type
    • rdfs subclass of triple➞object - The superclass element of the triple
    • rdfs subproperty of triple➞object - The superproperty element of the triple
  • node to value statement➞object
  • node to value triple➞object
  • node_object
  • taxon applicable➞object
  • value_object
• predicate
  • predicate1
  • predicate2
• prefix - A standardized prefix such as 'GO' or 'rdf' or 'FlyBase'
• query_has_subclass_ancestor
• query_template
• regex_slot
• results
  • deprecated obo class query➞results
  • describe equivalent expression➞results
  • obo class query➞results
• statements
  • node_statements
    • statement➞node_statements - statements about the quad where the object is a node
  • value_statements
    • statement➞value_statements - statements about the quad where the object is a literal
• subcategory
  • blood vessel➞subcategory
• subject
  • class taxon exclusion via never in➞subject - The class inferred to have the constraint
  • class taxon exclusion via only in➞subject - The class inferred to have the constraint
  • class taxon exclusion➞subject - The class inferred to have the constraint
  • equivalence triple mixin➞subject - One of the two classes that are equivalent. No significance to subject vs object
    • owl named equivalent class triple➞subject
  • nested triple➞subject
  • rdfs subclass of triple➞subject - The subclass element of the triple
  • rdfs subproperty of triple➞subject - The subproperty element of the triple
  • taxon applicable➞subject
• subject_predicate
• supplies
• type
• value - Note the range of this slot is always a string. Only used the triple represents a literal assertion
  • rdfs label triple➞value - The label value
• xxresults

Enums

• BloodVesselSubcategory
• UberGraphSourceEnum

Subsets

• BaseTable - Indicates the class/table is typically not constructed from a view
• Export - Used to indicate a table/class that should be dumped as part of the export of a db

Types

Built in

• Bool
• Decimal
• ElementIdentifier
• NCName
• NodeIdentifier
• URI
• URIorCURIE
• XSDDate
• XSDDateTime
• XSDTime
• float
• int
• str

Defined

• Boolean (Bool) - A binary (true or false) value
• Date (XSDDate) - a date (year, month and day) in an idealized calendar
• Datetime (XSDDateTime) - The combination of a date and time
• Decimal (Decimal) - A real number with arbitrary precision that conforms to the xsd:decimal specification
• Double (float) - A real number that conforms to the xsd:double specification
• Float (float) - A real number that conforms to the xsd:float specification
• Integer (int) - An integer
• LiteralAsStringType (String)
• Ncname (NCName) - Prefix part of CURIE
• NodeIdType (Uriorcurie) - IDs are either CURIEs, IRI, or blank nodes. IRIs are wrapped in <>s to distinguish them from CURIEs, but in general it is good practice to populate the [prefixes][Prefixes.md] table such that they are shortened to CURIEs. Blank nodes are ids starting with _:.
• Nodeidentifier (NodeIdentifier) - A URI, CURIE or BNODE that represents a node in a model.
• Objectidentifier (ElementIdentifier) - A URI or CURIE that represents an object in the model.
• String (str) - A character string
• Time (XSDTime) - A time object represents a (local) time of day, independent of any particular day
• Uri (URI) - a complete URI
• Uriorcurie (URIorCURIE) - a URI or a CURIE