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:
- Bookmark: NCBO BioPortal
- Bookmark: NEMO Sourceforge Ontology Request Tracker
- Download: Protégé
- Bookmark: NEMO Sourceforge Ontology Version Control
- Annotation Properties Guide Sheet: Please see http://nemo.nic.uoregon.edu/wiki/File:NEMO-TR2010-002_PropertyAnnotations_20100305.doc.
- The most current OWL version of NEMO Annotation Properties is available on Sourceforge.
- See Data_Annotation.
- See Database.
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:
- Deprecated ontology using OBO format in Word, especially focused on NEMO_spatial (10/2008 to 06/2009): File:Nemolex.doc
- The OWLDoc archive of the ontology, which provides an HTML browser view (01/2009): File:OWLdoc ERP 01 05 09.rar
- The OWLDoc archive of the ontology, which provides an HTML browser view (04/2009): File:OWLDoc NEMO 040409.rar
- Deprecated version of NEMO_spatial, generated automatically from the above deprecated OBO-Word format (06/2009): File:NEMO spatial OBO to OWL 06022009 pl v3.owl. Newer versions are on Sourceforge: NEMO_spatial.owl.
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.