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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.

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^{Image Added}).

Downloading and Configuring Protégé

Information in this guide is written specifically for eagle-i data curators. Curators will find instructions and guidelines for:

• 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.
  

  Contents

  Table of Contents
  maxLevel 2

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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