[Taxacom] A question about tools for building morphology ontologies.

Jerry Cooper CooperJ at landcareresearch.co.nz
Wed Nov 26 19:08:23 CST 2008

A question about tools for building morphology ontologies.

I  have a small new project to develop an interactive Lucid key to a group of fungi.  The group isn't my main interest so I'll be 'learning on the job' about some of the morphological nuances of the group. I know I could develop my character/state matrix in Lucid. However, it won't necessarily be the platform we use to capture the character/state data. And I see the Lucid key as just one specific  use of the resulting data-set. I'd much prefer to use another tool to define an ontology that describes the potential intricacies of the morphological character/states and their relationships. That way it becomes re-usable and expandable in other contexts. But my main reason for going this route is it gives me an excuse to get my head around the basics of this ontology stuff.

So what tool development and what format should I be using?

I've played with OBO-EDIT for a couple of hours. The interface looks intuitive  but I've struggled to get it to work the way I think it should work! And I haven't found a decent tutorial . They seem either trivial or very heavy.  And a nice example morphology ontology would be nice. They must be out there somewhere?

I've played with Protégé in the past. But now I see Protégé 4 is a 'frames editor' rather than an OWL editor. That doesn't mean much to me.
Should I be using that instead?

I haven't played with Altova's Semantic Works but could throw some valuable grant dollars in that direction if convinced to do so.

I don't want this to turn into a one year exercise in becoming an ontology expert. I just want a tool that will capture the semantics of organisms macro/micro morphology with least possible hassle.

Thanks - for any online or offline answers.

Jerry Cooper
Landcare Research
Phone +64 3 321 9641
P.O. Box 40, Lincoln 7640, New Zealand

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