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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 guides and instructions in the pages below will help you configure Protégé, edit the core ontology module, and add annotations to drive the user interfaces.

Goals

Our modeling approach had three main drivers. The first was to represent real data collected about resources. The second was to have the ontology control the userinterface (UI) and the logic of the data collection tool and search application. The third was a commitment to build a set of ontologies that could be reusable and interoperable with other ontologies and existing efforts for representing biomedical entities. This latter requirement translated into decisions to a) follow OBO Foundry principles and best practices for biomedical ontology development and b) engage in active discussions within the bio-ontology community in order to provide context for eagle-i interoperability and align with domain-wide standards for resource representation (http://bit.ly/rrcoord).

Ontology structure

Viewing the ontology using Protégé

The following instructions will help you configure Protégé, edit the core ontology module, and add annotations to drive the user interfaces. 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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Open the Excel file, IDS.xlsx, which is typically located here: SVN ---> src -> ontology. This file consists of five columns of information labeled as follows: column (A) ERO ID #, column (B) Mireot, (C) Label, (D) Class and column (E) URI.

1. Enter the following information in each column:

   Column A ERO ID #	Column B Mireot	Column C Label	Column D Type	Column E URI
   Choose the next consecutive number	Nothing	Enter the name of the term	Typ Class	Choose the next consecutive number

2. Save the file, but leave the spreadsheet open, you'll come back to retrieve the ERO ID#.
3. Open Protégé. Open the OWL ontology. Choose the file, eagle-app.owl from your directory. For example: /Users/JaneCurator/eagle-i-datamodel/trunk/src/ontology/eagle-i-app.owl.
4. From the Active Ontology tab, click Classes.

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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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