OAK Association Data Model

A data model for representing generic associations and changes of these associations.

The core data model is broad, encompassing the W3 Open Annotation data model as well as common ontology annotation data models using in the biosciences, such as the GAF data model used by the Gene Ontology, and the HPOA association model used by the Human Phenotype Ontology.

The core elements of the data model are the subject (the entity being described) and the object (the term, descriptor, or other entity that describes some aspect of the subject).

A subject might be a biological entity such as gene, drug, disease, person, or chemical. The object is typically a class from an ontology such as a term from GO.

URI: https://w3id.org/oak/association

Name: association

Classes

Class	Description
AssociationChange	A change object describing a change between two associations.
PairwiseCoAssociation	A collection of subjects co-associated with two objects
ParserConfiguration	Settings that determine behavior when parsing associations.
PositiveOrNegativeAssociation	None
Association	A generic association between a thing (subject) and another thing (object).
NegatedAssociation	A negated association between a thing (subject) and another thing (object).
PropertyValue	A generic tag-value that can be associated with an association.
RollupGroup	None

Slots

Slot	Description
aggregator_knowledge_source	The knowledge source that aggregated the association
associations	A collection of associations
associations_for_subjects_in_common
closure_delta
closure_information_content_delta
closure_predicates	The set of predicates used to determine if the new association object is a sp…
comments	Comments about the association
core_triple	A grouping slot for the core subject-predicate-object triple
creation_date	The date the association was created
date	The date the association was created or last updated
denormalized_slot	denormalized slots are for models that follow a denormalized data model
diff_slot	A mixin for any paired slot that pertains to an association diff
evidence_type	The type of evidence supporting the association
group_object	An ontology entity that is the ancestor of the objects in the group’s
include_association_attributes	If true, then the parser will include non S/P/O properties as additional attr…
is_creation
is_deletion
is_generalization	True if the association was inferred to become more general (based on closure…
is_migration	if the object (e
is_specialization	True if the association was inferred to become more specific (based on closur…
modification_date	The date the association was last modified
negated	True if the association is negated - i
new_date	The date of the new association
new_object	The object (e
new_predicate	If the association diff is a change in predicate, this is the predicate on th…
number_subject_unique_to_entity1
number_subject_unique_to_entity2
number_subjects_in_common
number_subjects_in_union
object	An ontology entity that is associated with the subject
object1
object1_label
object2
object2_label
object_closure	The set of objects that are related to the object of the association via the …
object_closure_label	The set of objects that are related to the object of the association via the …
object_label	The label of the ontology entity that is associated with the subject
old_date	The date of the old association
old_object	The object (e
old_object_obsolete	if the object (e
old_predicate	If the association diff is a change in predicate, this is the predicate on th…
original_object	The original object of the association prior to normalization
original_predicate	The original subject of the association prior to normalization
original_subject	The original subject of the association prior to normalization
predicate	The type of relationship between the subject and object
predicate_label	The label of the type of relationship between the subject and object
preserve_negated_associations	If true, then the parser will keep negated associations in the output
primary_knowledge_source	The primary knowledge source for the association
property_values	Arbitrary key-value pairs with additional information about the association
proportion_entity1_subjects_in_entity2
proportion_entity2_subjects_in_entity1
proportion_subjects_in_common
publication_is_added	True if the publication was not present in the old association set (and prese…
publication_is_deleted	True if the publication is not present in the new association set (and presen…
publications	The publications that support the association
sub_groups	Container for groups within a rollup group
subject	The thing which the association is about
subject_closure	The set of subjects that are related to the subject of the association via th…
subject_closure_label	The set of subjects that are related to the subject of the association via th…
subject_label	The label of the thing which the association is about
subjects_in_common
summary_group	The field used to group an association diff summary
supporting_objects	The objects that support the association

Enumerations

Enumeration	Description

Types

Type	Description
Boolean	A binary (true or false) value
Curie	a compact URI
Date	a date (year, month and day) in an idealized calendar
DateOrDatetime	Either a date or a datetime
Datetime	The combination of a date and time
Decimal	A real number with arbitrary precision that conforms to the xsd:decimal speci…
Double	A real number that conforms to the xsd:double specification
Float	A real number that conforms to the xsd:float specification
Integer	An integer
Jsonpath	A string encoding a JSON Path
Jsonpointer	A string encoding a JSON Pointer
Ncname	Prefix part of CURIE
Nodeidentifier	A URI, CURIE or BNODE that represents a node in a model
Objectidentifier	A URI or CURIE that represents an object in the model
Sparqlpath	A string encoding a SPARQL Property Path
String	A character string
Time	A time object represents a (local) time of day, independent of any particular…
Uri	a complete URI
Uriorcurie	a URI or a CURIE

Subsets

Subset	Description