Ontology Curation Tools & Onto-Centric Viewers

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Construction and Maintenance Tools Oriented Toward the Ontology Curator

Please send your comments and suggestions to Dr. Maryann Martone or Bill Bug.

[Listing In Progress]

Most of these are not for the faint of heart - tools such as:

• Protege
• DAGEdit
• COBrA
• Chimaera
• OilEd
• OntoLingua
• WebOnto
• OntoSaurus
• Ontology-based Software Development Environment (ODE)
• KADS22
• OntoEdit
• OBO-Edit
• etc..

There is also an excellent onto-centric tool list maintained GO Consortium containing mostly, though not exclusively, tools for maniupulating & mapping with the GO. We will provide a description of the formal ontological format(s) supported by a tool, and our evaluation of the relative utility & ease-of-use of each tool we've used to meet the ontological curation efforts required across the Mouse BIRN Projects.

See also:

• Patrick Lambrix, Manal Habbouche and Marta Perez. (2003) Evaluation of ontology development tools for bioinformatics. Bioinformatics, v19, n12, p1564–1571.
• A. J. Duineveld, A.J., Stoter, R., Weiden, M.R., Kenepa, B. and Benjamins, V.R. (2000) WonderTools? A comparative study of ontological engineering tools.Int. J. Human-Computer Studies, v52, p1111-1133.

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Ontology-Centric Viewers Oriented Toward the End-User/Investigator

[Listing In Progress]
Some for browsing the ontological framework alone (e.g., AmiGO, the Mammalian Phenotype Browser, etc.), and others for browsing knowledge maps built by mapping instance data into the conceptual nodes in the ontology(s). Examples of the later are relatively rare. In fact, one of the overall objectives of the Mouse BIRN Project is to create such an end-user oriented onto-centric query client. Investigators will use this interface to pose novel scientific questions, specifying via ontological aids (including a canonical spatial brain atlas) the domains & modalities of biological data they would like to inter-relate. Results will also be presented using a cogent, layered organization via the use of ontological frameworks.

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