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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 domain ontology used in the current eagle-i stack is the ERO (eagle-i resource ontology). The layering principle is applicable to other domain ontologies.
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The runtime model that represents the ontology to the applications is built by loading the domain and application ontologies 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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| Description | Usage in software |
|---|---|---|
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
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