Ontology Development

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Below, please find documentation regarding best practices, guidelines, and protocols for development of NEMO ontologies. Technical reports that address specific ontology development issues can be downloaded here.

Some of the attached documents have undergone several revisions. You may click on each file to view its history or download the most current version.

Structure of NEMO Ontologies

NEMO Ontology Editing Practices

The following document provides an overview of instructions for viewing & commenting on NEMO ontologies:

This document provides instructions for editing NEMO owl/rdf files in Protege:

The following list includes links to websites that are frequently accessed during NEMO ontology development:

Annotation Properties

Data Annotation

Data Management

Deprecated Documents and Historical Notes

As a historical note, early on, we used MS Word to document terms, definitions and structure in a rudimentary format using tables. We found this to be an easy way to get started with ontology editing. However, we found it increasingly difficult to maintain, view, browse and extend the structure using Word as our editing tool. We therefore made the format more strict by conforming closely to OBO specifications, which helped with viewing and browsing. However, OBO semantics were too restrictive -- we wanted the ability to import and extend NIF and other ontology terms in OWL format and OBO-OWL inter-operability was simply too nascent for us. We therefore wrote some scripts that completely transformed our ontology into OWL and have not looked back. The following documents constitute a partial history of the early documents we worked with:

Historical Planning Notes

The following legacy documents include historical notes and outlines.  

Most planning and task delegation is currently tracked using the NEMO Sourceforge Milestones Tracker.

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