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), as derived from the ISF (Integrated Semantic Framework). The layering principle is shown in the figure below, and 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 the application ontologies into one aggregate model.

General app ontology

owl classes:

ClassGroup

PropertyGroup

owl object properties:

inClassGroup - range: ClassGroup

inPropertyGroup - range: PropertyGroup

Individuals of type ClassGroup:

http://eagle-i.org/ont/app/1.0/ClassGroup_DataModelExclude

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

http://eagle-i.org/ont/app/1.0/ClassGroup_InstanceCreate

Individuals of type PropertyGroup:

http://eagle-i.org/ont/app/1.0/PropertyGroup_AdminData

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

http://eagle-i.org/ont/app/1.0/PropertyGroup_TertiaryProperty

Examples of usage:

and interpreting the annotations in different ways. The memory model is organized as a core model fully stored in memory and a collection of referenced taxonomy models stored in Solr indexes for rapid access.

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Important files

• eagle-i-app-def.owl contains axioms that define the basic annotation vocabulary (classes and properties). 
• ero-app.owl serves as a root for the software loading mechanism. It provides the chain of imports - if an owl file is reachable directly or indirectly from this file via an owl:import statement, it will be loaded as part of the core model. It is a configurable parameter in the software.
• Files named *-app.owl contain the axioms that annotate the domain ontologies. There is typically one app file per domain owl file (e.g. disease-imports-app.owl, disease-imports.owl)
  • Note that ero-app.owl serves this purpose for the ero.owl file. 
  • (describe mechanism for loading referenced taxonomy files into solr)

Requirements of *-app.owl files

• Every app file must declare an ontology IRI
• Every app file must declare an ontology version
• Every app file must import its corresponding domain owl file

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