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Consistency Checking

Attention! GraphDB is not supported anymore, therefore parts related to it in this document are redundant.

Requirements

Knora is designed to prevent inconsistencies in RDF data, as far as is practical, in a triplestore-independent way (see Triplestore Updates). However, it is also useful to enforce consistency constraints in the triplestore itself, for two reasons:

  1. To prevent inconsistencies resulting from bugs in the DSP-API server.
  2. To prevent users from inserting inconsistent data directly into the triplestore, bypassing Knora.

The design of the knora-base ontology supports two ways of specifying constraints on data (see knora-base: Consistency Checking for details):

  1. A property definition should specify the types that are allowed as subjects and objects of the property, using knora-base:subjectClassConstraint and (if it is an object property) knora-base:objectClassConstraint. Every subproperty of knora-base:hasValue or a knora-base:hasLinkTo (i.e. every property of a resource that points to a knora-base:Value or to another resource) is required have this constraint, because the DSP-API server relies on it to know what type of object to expect for the property. Use of knora-base:subjectClassConstraint is recommended but not required.
  2. A class definition should use OWL cardinalities (see OWL 2 Quick Reference Guide) to indicate the properties that instances of the class are allowed to have, and to constrain the number of objects that each property can have. Subclasses of knora-base:Resource are required to have a cardinality for each subproperty of knora-base:hasValue or a knora-base:hasLinkTo that resources of that class can have.

Specifically, consistency checking should prevent the following:

  • An object property or datatype property has a subject of the wrong class, or an object property has an object of the wrong class (GraphDB's consistency checke cannot check the types of literals).
  • An object property has an object that does not exist (i.e. the object is an IRI that is not used as the subject of any statements in the repository). This can be treated as if the object is of the wrong type (i.e. it can cause a violation of knora-base:objectClassConstraint, because there is no compatible rdf:type statement for the object).
  • A class has owl:cardinality 1 or owl:minCardinality 1 on an object property or datatype property, and an instance of the class does not have that property.
  • A class has owl:cardinality 1 or owl:maxCardinality 1 on an object property or datatype property, and an instance of the class has more than one object for that property.
  • An instance of knora-base:Resource has an object property pointing to a knora-base:Value or to another Resource, and its class has no cardinality for that property.
  • An instance of knora-base:Value has a subproperty of knora-base:valueHas, and its class has no cardinality for that property.
  • A datatype property has an empty string as an object.

Cardinalities in base classes are inherited by derived classes. Derived classes can override inherited cardinalities by making them more restrictive, i.e. by specifying a subproperty of the one specified in the original cardinality.

Instances of Resource and Value can be marked as deleted, using the property isDeleted. This must be taken into account as follows:

  • With owl:cardinality 1 or owl:maxCardinality 1, if the object of the property can be marked as deleted, the property must not have more than one object that has not been marked as deleted. In other words, it's OK if there is more than one object, as long only one of them has knora-base:isDeleted false.
  • With owl:cardinality 1 or owl:minCardinality 1, the property must have an object, but it's OK if the property's only object is marked as deleted. We allow this because the subject and object may have different owners, and it may not be feasible for them to coordinate their work. The owner of the object should always be able to mark it as deleted. (It could be useful to notify the owner of the subject when this happens, but that is beyond the scope of consistency checking.)

Design

Ontotext GraphDB provides a mechanism for checking the consistency of data in a repository each time an update transaction is committed. Knora provides GraphDB-specific consistency rules that take advantage of this feature to provide an extra layer of consistency checks, in addition to the checks that are implemented in Knora.

When a repository is created in GraphDB, a set of consistency rules can be provided, and GraphDB's consistency checker can be turned on to ensure that each update transaction respects these rules, as described in the section Reasoning of the GraphDB documentation. Like custom inference rules, consistency rules are defined in files with the .pie filename extension, in a GraphDB-specific syntax.

We have added rules to the standard RDFS inference rules file builtin_RdfsRules.pie, to create the file KnoraRules.pie. The .ttl configuration file that is used to create the repository must contain these settings:

owlim:ruleset "/path/to/KnoraRules.pie" ;
owlim:check-for-inconsistencies "true" ;

The path to KnoraRules.pie must be an absolute path. The scripts provided with Knora to create test repositories set this path automatically.

Consistency checking in GraphDB relies on reasoning. GraphDB's reasoning is Forward-chaining, which means that reasoning is applied to the contents of each update, before the update transaction is committed, and the inferred statements are added to the repository.

A GraphDB rules file can contain two types of rules: inference rules and consistency rules. Before committing an update transaction, GraphDB applies inference rules, then consistency rules. If any of the consistency rules are violated, the transaction is rolled back.

An inference rule has this form:

Id: <rule_name>
    <premises> <optional_constraints>
    -------------------------------
    <consequences> <optional_constraints>

The premises are a pattern that tries to match statements found in the data. Optional constraints, which are enclosed in square brackets, make it possible to specify the premises more precisely, or to specify a named graph (see examples below). Consequences are the statements that will be inferred if the premises match. A line of hyphens separates premises from consequences.

A GraphDB consistency rule has a similar form:

Consistency: <rule_name>
    <premises> <optional_constraints>
    -------------------------------
    <consequences> <optional_constraints>

The differences between inference rules and consistency rules are:

  • A consistency rule begins with Consistency instead of Id.
  • In a consistency rule, the consequences are optional. Instead of representing statements to be inferred, they represent statements that must exist if the premises are satisfied. In other words, if the premises are satisfied and the consequences are not found, the rule is violated.
  • If a consistency rule doesn't specify any consequences, and the premises are satisfied, the rule is violated.

Rules use variable names for subjects, predicates, and objects, and they can use actual property names.

Empty string as object

If subject i has a predicate p whose object is an empty string, the constraint is violated:

Consistency: empty_string
    i p ""
    ------------------------------------

Subject and object class constraints

If subject i has a predicate p that requires a subject of type t, and i is not a t, the constraint is violated:

Consistency: subject_class_constraint
    p <knora-base:subjectClassConstraint> t
    i p j
    ------------------------------------
    i <rdf:type> t

If subject i has a predicate p that requires an object of type t, and the object of p is not a t, the constraint is violated:

Consistency: object_class_constraint
    p <knora-base:objectClassConstraint> t
    i p j
    ------------------------------------
    j <rdf:type> t

Cardinality constraints

A simple implementation of a consistency rule to check owl:maxCardinality 1, for objects that can be marked as deleted, could look like this:

Consistency: max_cardinality_1_with_deletion_flag
    i <rdf:type> r
    r <owl:maxCardinality> "1"^^xsd:nonNegativeInteger
    r <owl:onProperty> p
    i p j
    i p k [Constraint j != k]
    j <knora-base:isDeleted> "false"^^xsd:boolean
    k <knora-base:isDeleted> "false"^^xsd:boolean
    ------------------------------------

This means: if resource i is a subclass of an owl:Restriction r with owl:maxCardinality 1 on property p, and the resource has two different objects for that property, neither of which is marked as deleted, the rule is violated. Note that this takes advantage of the fact that Resource and Value have owl:cardinality 1 on isDeleted (isDeleted must be present even if false), so we do not need to check whether i is actually something that can be marked as deleted.

However, this implementation would be much too slow. We therefore use two optimisations suggested by Ontotext:

  1. Add custom inference rules to make tables (i.e. named graphs) of pre-calculated information about the cardinalities on properties of subjects, and use those tables to simplify the consistency rules.
  2. Use the [Cut] constraint to avoid generating certain redundant compiled rules (see Entailment rules).

For example, to construct a table of subjects belonging to classes that have owl:maxCardinality 1 on some property p, we use the following custom inference rule:

Id: maxCardinality_1_table
    i <rdf:type> r
    r <owl:maxCardinality> "1"^^xsd:nonNegativeInteger
    r <owl:onProperty> p
    ------------------------------------
    i p r [Context <onto:_maxCardinality_1_table>]

The constraint [Context <onto:_maxCardinality_1_table>] means that the inferred triples are added to the context (i.e. the named graph) http://www.ontotext.com/_maxCardinality_1_table. (Note that we have defined the prefix onto as http://www.ontotext.com/ in the Prefices section of the rules file.) As the GraphDB documentation on Rules explains:

If the context is provided, the statements produced as rule consequences are not ‘visible’ during normal query answering. Instead, they can only be used as input to this or other rules and only when the rule premise explicitly uses the given context.

Now, to find out whether a subject belongs to a class with that cardinality on a given property, we only need to match one triple. The revised implementation of the rule max_cardinality_1_with_deletion_flag is as follows:

Consistency: max_cardinality_1_with_deletion_flag
    i p r [Context <onto:_maxCardinality_1_table>]
    i p j [Constraint j != k]
    i p k [Cut]
    j <knora-base:isDeleted> "false"^^xsd:boolean
    k <knora-base:isDeleted> "false"^^xsd:boolean
    ------------------------------------

The constraint [Constraint j != k] means that the premises will be satisfied only if the variables j and k do not refer to the same thing.

With these optimisations, the rule is faster by several orders of magnitude.

Since properties whose objects can be marked as deleted must be handled differently to properties whose objects cannot be marked as deleted, the knora-base ontology provides a property called objectCannotBeMarkedAsDeleted. All properties in knora-base whose objects cannot take the isDeleted flag (including datatype properties) should be derived from this property. This is how it is used to check owl:maxCardinality 1 for objects that cannot be marked as deleted:

Consistency: max_cardinality_1_without_deletion_flag
    i p r [Context <onto:_maxCardinality_1_table>]
    p <rdfs:subPropertyOf> <knora-base:objectCannotBeMarkedAsDeleted>
    i p j [Constraint j != k]
    i p k [Cut]
    ------------------------------------

To check owl:minCardinality 1, we do not care whether the object can be marked as deleted, so we can use this simple rule:

Consistency: min_cardinality_1_any_object
    i p r [Context <onto:_minCardinality_1_table>]
    ------------------------------------
    i p j

This means: if a subject i belongs to a class that has owl:minCardinality 1 on property p, and i has no object for p, the rule is violated.

To check owl:cardinality 1, we need two rules: one that checks whether there are too few objects, and one that checks whether there are too many. To check whether there are too few objects, we don't care whether the objects can be marked as deleted, so the rule is the same as min_cardinality_1_any_object, except for the cardinality:

Consistency: cardinality_1_not_less_any_object
    i p r [Context <onto:_cardinality_1_table>]
    ------------------------------------
    i p j

To check whether there are too many objects, we need to know whether the objects can be marked as deleted or not. In the case where the objects can be marked as deleted, the rule is the same as max_cardinality_1_with_deletion_flag, except for the cardinality:

Consistency: cardinality_1_not_greater_with_deletion_flag
    i p r [Context <onto:_cardinality_1_table>]
    i p j [Constraint j != k]
    i p k [Cut]
    j <knora-base:isDeleted> "false"^^xsd:boolean
    k <knora-base:isDeleted> "false"^^xsd:boolean
    ------------------------------------

In the case where the objects cannot be marked as deleted, the rule is the same as max_cardinality_1_without_deletion_flag, except for the cardinality:

Consistency: cardinality_1_not_less_any_object
    i p r [Context <onto:_cardinality_1_table>]
    ------------------------------------
    i p j

Knora allows a subproperty of knora-base:hasValue or knora-base:hasLinkTo to be a predicate of a resource only if the resource's class has some cardinality for the property. For convenience, knora-base:hasValue and knora-base:hasLinkTo are subproperties of knora-base:resourceProperty, which is used to check this constraint in the following rule:

Consistency: resource_prop_cardinality_any
    i <knora-base:resourceProperty> j
    ------------------------------------
    i p j
    i <rdf:type> r
    r <owl:onProperty> p

If resource i has a subproperty of knora-base:resourceProperty, and i is not a member of a subclass of an owl:Restriction r with a cardinality on that property (or on one of its base properties), the rule is violated.

A similar rule, value_prop_cardinality_any, ensures that if a value has a subproperty of knora-base:valueHas, the value's class has some cardinality for that property.

Last update: January 19, 2023