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The tasks described below assume that the relevant domain content has already been created in the ontology according to the workflows and conventions outlined in Annotation Properties and Individuals for driving the Application. Here we describe the addition of axioms that facilitate the interaction of the eagle-i SWEET application with this content, in order to dynamically populate the user interface and support data collection.

In the list below, the ontology task is the primary title of each item in bold, and is followed in parentheses with the application feature or function that this action supports.

1) Assigning Application-Specific Labels and Definition (Drives tool tips in SWEET)

Create an annotation on the class or property of interest using the eagle-i preferred definition and eagle-i preferred label annotation properties, and enter desired text.

  • These axioms should live in the application file that is paired with the domain layer file where the class or property of interest lives (e.g. ero-core-app.owl for ero.owl terms not from extended taxonomies, uberon-import-app.owl for uberon classes)
  • Preferred labels should be capitalized.
  • Preferred definitions are applied primarily on properties, and they are used to drive tool tips in the application. But preferred definitions can also be given to classes, and will show up in the eagle-i Ontology Browser web application (https://search.eagle-i.net/model/).

2) Flagging a Class as a Resource Type (Enables instances to be created in the SWEET)

All resources for which instances are created need an InClassGroup annotation axiom on the class itself (or an asserted or inferred ancestor) with the value Class Instance Create (http://eagle-i.org/ont/app/1.0/ClassGroup_InstanceCreate). These annotation axioms should live in the app layer file that is paired with the class being annotated.

Primary Resource Types need a second InClassGroup annotation axiom with the value Class Primary Resource Type (http://eagle-i.org/ont/app/1.0/ClassGroup_PrimaryResourceType).
Examples include 'reagent', 'software', 'instrument'.
 
Embedded Resource Types need a second InClassGroup annotation axiom with the value Class Embedded Resource Type (http://eagle-i.org/ont/app/1.0/ClassGroup_EmbeddedResourceType)
Examples include 'construct insert', 'phenotype annotation'.
 
Stubbed Resource Types need no additional annotation axiom. Classes with only a Class Instance Create annotation will be treated as stubbed resources
Examples include 'genetic alteration', 'human subject'.

Note that these InClassGroup annotations are inherited by descendent classes, so they are not needed on a given class if an asserted or inferred ancestor has one. For example, the ero class 'reagent' is directly annotated with InClassGroup Class Instance Create and InClassGroup Class Primary Resource Type annotations in ero-app.owl, and its inferred child 'cell line' inherits this annotation axiom and thus requires no InClassGroup annotations to inform the application that 'cell line' instances can be created and are primary resource types.

  • No labels