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• Adding terms to the eagle-i ontology. Ontology terms are added, edited and obsoleted using an open source ontology editor. This section contains instructions for downloading and configuring the ontology editor as well as guidelines for adding new terms, obsoleting terms and the use of annotation properties.
• Adding resources to the eagle-i repository using the bulk loading process, ETL (extract, transfer, load). Resources such as instruments, laboratories, reagents and more, can be added using eagle-i's data tool. Large data sets can be added using the ETL process explained in this page.
• Adding Harvard Catalyst-compliant data. The eagle-i repository now supplies all of the core facility data that is displayed in the Harvard Catalyst database of core facilities at Harvard University. Guidelines in this section explain how curators should enter catalyst-compliant data.
  

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The eagle-i Ontology

A unique feature of eagle-i is that the data collection and search tools are completely driven by ontologies. These ontologies are a set of modules that are written in the OWL language and edited and managed using Protégé. The following instructions will help you configure Protégé, edit the core ontology module, and add annotations to drive the user interfaces.

Downloading and Configuring Protégé

eagle-i curators use Protégé OBI (Ontology for Biomedical Investigations) to manage and view the eagle-i ontology. Protégé is a free, open source ontology editor and knowledge-base framework.

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https://sites.google.com/a/eagle-i.org/workspace/data-curators-workspace/configuring-and-editing-with-protege-4/onto_lib.tiff?attredirects=0

1. Close Protégé.

Adding a New Term to the eagle-i Ontology

It is important to note that the following steps assume that you have a basic understanding of Protégé, and the revision control software Subversion as well as an understanding of an ontology.

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This is the last step.  Notify the curators that the file has been unlocked using an e-mail that looks similar to: {{\[UNLOCKING\] ero.owl and eagle-i-app.owl.}}

Obsoleting a Term in the Ontology

Before obsoleting a term it is best practice to check the usage of the terms across the repositories. You can do this using either SPARQL queries or ECDT tools.

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1. Open SmartSVN.
2. Click Update to check for any changes.
3. Write a detailed list of the changes that have been made.
4. Commit.

Annotation Properties

Application-specific properties and annotations are kept in the eagle-i app file. https://sites.google.com/a/eagle-i.org/workspace/build-team-workspace/data-model-integration/applicationspecificannotations for most current values) The purpose of these annotation properties and their values is to allow curators to "flag" classes and properties to "tell" the eagle-i, for example, to which class is a resource is connected or which property connects a resource to a lab.

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