Semantic SQL OBO module

Abstractions for working with OBO ontologies. Assumes usage of OMO. Currently this module contains mostly checks/reports, similar to ROBOT report

URI: https://w3id.org/semsql/obo Name: semsql_obo

Classes

Class	Description
AllProblems
AnnotationPropertyNode	A node representing an OWL annotation property
AnonymousClassExpression	An OWL anonymous class expression, such as for example `SomeValuesFrom(partOf...
AnonymousExpression	An OWL expression, such as a class expression
AnonymousIndividualExpression
AnonymousPropertyExpression
AsymmetricPropertyNode
AxiomDbxrefAnnotation
BlankNode	A node with an ID that is not preserved between databases
ClassNode	A node that represents an RDFS/OWL class
ClassTrait
CountOfInstantiatedClasses	Number of distinct instantiations of a class
CountOfPredicates	Number of distinct usages of a predicate
CountOfSubclasses	Number of subclasses for a given class
DeprecatedNode
HasBroadMatchStatement
HasBroadSynonymStatement
HasDbxrefStatement
HasExactMatchStatement
HasExactSynonymStatement
HasMappingStatement
HasMatchStatement
HasNarrowMatchStatement
HasNarrowSynonymStatement
HasOioSynonymStatement
HasRelatedMatchStatement
HasRelatedSynonymStatement
HasSynonymStatement
HasTextDefinitionStatement
IndividualTrait
IriNode
IrreflexivePropertyNode	A node representing an OWL irreflexive object property
IsReport	Used to describe classes/views that have a reporting function
LexicalProblem	a problem with the textual value of an annotation property
NamedIndividualNode	A node that represents an OWL Named Individual
Node	The basic unit of representation in an RDF or OWL graph
NodeToNodeStatement	A statement where object is non-null and value is not populated
NodeToValueStatement	A statement where value is non-null and object is not populated
NodeTrait	abstract groupings/properties for different aspects of the model
NodeWithTwoLabelsProblem
ObjectPropertyNode	A node representing an OWL object property
OntologyNode	A node representing an ontology
OntologyStatusStatement
OwlAllValuesFrom
OwlAxiom
OwlAxiomAnnotation
OwlComplementOfStatement
OwlComplexAxiom	An axiom that is composed of two or more statements
OwlDisjointClassStatement
OwlEquivalentClassStatement	A statement that connects two class_nodes where both classes are equivalent
OwlEquivalentToIntersectionMember	Composition of OwlEquivalentClass, OwlIntersectionOf, and RdfListMember...
OwlHasSelf
OwlHasValue
OwlImportsStatement
OwlInverseOfStatement
OwlReifiedAxiom	An OWL axiom that has been reified - i
OwlRestriction	An OWL restriction, such as SomeValuesFrom(partOf Hand)
OwlSameAsStatement	A statement that connects two individual nodes where both individual are equi...
OwlSomeValuesFrom	An OWL SomeValuesFrom restriction
OwlSubclassOfSomeValuesFrom	Composition of subClassOf and SomeValuesFrom
Prefix	Maps CURIEs to URIs
Problem	Represents an instance of a problem pertaining to conformance to OBO guidelin...
PropertyNode	Note this only directly classifies nodes asserted to be rdf:Properties
PropertyTrait
PropertyUsedWithDatatypeValuesAndObjects	A problem in which the same property is used two two different ways, one in w...
RdfFirstStatement	A statement that connects a list to its first element
RdfLevelSummaryStatistic	Abstract grouping for views/classes that provide some kind of count summary a...
RdfListMemberStatement
RdfListNode	A node representing an RDF list
RdfListStatement	A statement that is used to represent aspects of RDF lists
RdfRestStatement	A statement that connects a list to its remaining elements
RdfRestTransitiveStatement
RdfTypeStatement	A statement that indicates the asserted type of the subject entity
RdfsDomainStatement
RdfsLabelStatement
RdfsRangeStatement
RdfsSubclassOfNamedStatement
RdfsSubclassOfStatement
RdfsSubpropertyOfStatement
ReflexivePropertyNode	A node representing an OWL reflexive object property
RepairAction	Represents an action that needs to be taken to repair a problem
Statements	Represents an RDF triple
SymmetricPropertyNode	A node representing an OWL symmetric object property
TrailingWhitespaceProblem
TransitivePropertyNode	A node representing an OWL transitive object property

Slots

Slot	Description
annotation_datatype
annotation_language
annotation_object
annotation_predicate
annotation_subject
annotation_value
axiom_datatype
axiom_language
axiom_object
axiom_predicate
axiom_value
base	The base URI a prefix will expand to
count_value
datatype	the rdf datatype of the value, for example, xsd:string
description
element
evidence_type
filler
id	An identifier for an element
label1
label2
language	the human language in which the value is encoded, e
object	Note the range of this slot is always a node
on_property
predicate	The predicate of the statement
prefix	A standardized prefix such as 'GO' or 'rdf' or 'FlyBase'
publication
restriction
source
stanza	the term which this statement is about
subject	The subject of the statement
value	Note the range of this slot is always a string

Enumerations

Enumeration	Description

Types

Type	Description
xsd:boolean	A binary (true or false) value
xsd:date	a date (year, month and day) in an idealized calendar
linkml:DateOrDatetime	Either a date or a datetime
xsd:dateTime	The combination of a date and time
xsd:decimal	A real number with arbitrary precision that conforms to the xsd:decimal speci...
xsd:double	A real number that conforms to the xsd:double specification
xsd:float	A real number that conforms to the xsd:float specification
xsd:integer	An integer
LiteralAsStringType
xsd:string	Prefix part of CURIE
NodeIdType	IDs are either CURIEs, IRI, or blank nodes
shex:nonLiteral	A URI, CURIE or BNODE that represents a node in a model
shex:iri	A URI or CURIE that represents an object in the model
xsd:string	A character string
xsd:dateTime	A time object represents a (local) time of day, independent of any particular...
xsd:anyURI	a complete URI
xsd:anyURI	a URI or a CURIE

Subsets

Subset	Description
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...