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eagle-i software is predicated upon the principle of ontology layering. Applications are driven by an application layer ontology that complements and annotates a domain ontology. An application layer ontology encapsulates the specifics of the software behavior and is not meant to be reusable in and of itself, in contrast to a domain ontology. The The domain ontology used in the current eagle-i deployment stack is the ERO (eagle-i resource ontology). The layering principle is applicable to other domain ontologies.
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The runtime memory model that represents the ontology to the applications is built by successively loading the domain ontology and application ontologies and applying the application ontologies into one aggregate modelfilters described in the application ontology.
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Summary of app ontology
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owl classes:
ClassGroup
PropertyGroup
owl object properties:
inClassGroup - range: ClassGroup
inPropertyGroup - range: PropertyGroup
Individuals of type ClassGroup:
(eagle-i-app-def.owl)
Namespace
all of the classes and properties below have the namespace:
http://eagle-i.org/ont/app/1.0/ClassGroup_DataModelExclude
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http://eagle-i.org/ont/app/1.0/ClassGroup_DataModelExclude
http://eagle-i.org/ont/app/1.0/ClassGroup_PrimaryResourceType
http://eagle-i.org/ont/app/1.0/ClassGroup_EmbeddedResourceType
http://eagle-i.org/ont/app/1.0/ClassGroup_NoAssertedInstances
http://eagle-i.org/ont/app/1.0/ClassGroup_ReferencedTaxonomy
http://eagle-i.org/ont/app/1.0/ClassGroup_InstanceCreate
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http://eagle-i.org/ont/app/1.0/ClassGroup_InstanceCreate
Individuals of type PropertyGroup:
http://eagle-i.org/ont/app/1.0/PropertyGroup_AdminData
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http://eagle-i.org/ont/app/1.0/PropertyGroup_AdminData
http://eagle-i.org/ont/app/1.0/PropertyGroup_ContactInformation
http://eagle-i.org/ont/app/1.0/PropertyGroup_DataModelExclude
http://eagle-i.org/ont/app/1.0/PropertyGroup_SearchFacet
http://eagle-i.org/ont/app/1.0/PropertyGroup_PrimaryProperty
http://eagle-i.org/ont/app/1.0/PropertyGroup_ResourceProvider
http://eagle-i.org/ont/app/1.0/PropertyGroup_SecondaryProperty
http://eagle-i.org/ont/app/1.0/PropertyGroup_TertiaryProperty
http://eagle-i.org/ont/app/1.0/PropertyGroup_AdminData
http://eagle-i.org/ont/app/1.0/PropertyGroup_ContactInformation
http://eagle-i.org/ont/app/1.0/PropertyGroup_DataModelExclude
http://eagle-i.org/ont/app/1.0/PropertyGroup_SearchFacet
http://eagle-i.org/ont/app/1.0/PropertyGroup_PrimaryProperty
http://eagle-i.org/ont/app/1.0/PropertyGroup_ResourceProvider
http://eagle-i.org/ont/app/1.0/PropertyGroup_SecondaryProperty
http://eagle-i.org/ont/app/1.0/PropertyGroup_TertiaryProperty
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http://eagle-i.org/ont/app/1.0/PropertyGroup_TertiaryProperty
Examples of usage:
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Classes
ClassGroup
PropertyGroup
Object properties
These behave as annotation properties, i.e. they appear in triples where the subject is an owl class or an owl property. However their predicate is always an individual of type ClassGroup or PropertyGroup, hence they are declared as object properties.
inClassGroup => range is ClassGroup
inPropertyGroup => range is PropertyGroup
Individuals of type ClassGroup
| Description | Usage in software |
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ClassGroup_DataModelExclude | classes that are not to be included in the eagle-i model. For example, upper ontology classes. | When the memory model is built, these classes are ignored |
ClassGroup_InstanceCreate | classes of which instances are created in the eagle-i repository. In other words, the only asserted types in the eagle-i repository are classes that belong to this group. | Appear under "Resource Types" in the ontology browser. |
ClassGroup_PrimaryResourceType | classes that are considered an eagle-i primary type - they represent biomedical research resources (as opposed to ancillary types needed for describing biomedical research resources). Note that all primary types must be in the InstanceCreate group, but some classes in the instanceCreate group are not considered primary by the eagle-i software because they do not represent research resources (e.g. Document, Person, Organization) | Drives the SWEET left bar |
ClassGroup_EmbeddedResourceType | classes whose instances only have significance when associated to an instance of another "containing"class (e.g. construct insert -> construct). In an eagle-i repository, instances of embedded classes are never shared among instances of containing classes there exist a one to one correspondance embedded instance -> containing instance | Appear under "Embedded Types" in the glossary. |
ClassGroup_NoAssertedInstances | If a class belongs to this group, it will never have asserted instances in the eagle-i repository - these are typically logical definitions that should only be inferred | The SWEET prevents users from directly assigning a one of these types when creating a resource |
ClassGroup_ReferencedTaxonomy | Classes that are only used for annotating a resource (as opposed to having instances created). Note that the data is produced with these classes used as instances - in other words, triples exist that have the class URI as a predicate (punning) | Appear under "Referenced Taxonomies" in the ontology browser. |
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Individuals of type PropertyGroup
PropertyGroup_AdminData
PropertyGroup_ContactInformation
PropertyGroup_DataModelExclude
PropertyGroup_SearchFacet
PropertyGroup_ResourceProvider
PropertyGroup_PrimaryProperty
PropertyGroup_SecondaryProperty
PropertyGroup_TertiaryProperty
Annotation properties
domainConstraint
preferredDefinition
preferredLabel
rangeConstraint
referencedTaxonomyIRI
Usage
Overview
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