Question: Please Recommend A *Good* Ontology Editor For Biomedical Ontologies
3
gravatar for Michael Dondrup
6.6 years ago by
Bergen, Norway
Michael Dondrup45k wrote:

I am currently implementing an ontology of the developmental stages of an organism (Sea Lice in this case, but it doesn't really matter). I would like to have your recommendation on a good and user friendly editor for biological or biomedical ontologies (written in OBO or OWL). It should include syntax support for the language of choice, best with graph representation and node editing. In principle it should be like OBOedit but with a usable interface (the UI of oboedit is utterly horrible imho and sometimes it seems to mess with my obo graphs). So don't recommend OBOedit unless you have written it, or can confirm that you use it on a daily basis to write ontologies xD

Currently I have the impression that any text editor would be more efficient, but could there be an editor with syntax highlighting at least? I promise to seriously spend time on each of your suggestions and that I will use the highest ranked answer in my project (or at least try hard)

ontology • 2.0k views
ADD COMMENTlink modified 6.6 years ago by iw9oel_ad6.0k • written 6.6 years ago by Michael Dondrup45k
6
gravatar for iw9oel_ad
6.6 years ago by
iw9oel_ad6.0k
iw9oel_ad6.0k wrote:

I use Protege for OWL ontologies because I find OBOedit's UI, shall we say, idiosyncratic. Protege has nice features like reasoner plugins that can spot errors and make inferences. However, it is complex and takes some time to learn. The documentation is quite good, which helps. I'm certainly not a "power user", having not invested the necessary effort, but it's still my first choice when I need this kind of tool.

ADD COMMENTlink written 6.6 years ago by iw9oel_ad6.0k

Thank you Keith, I have started to work with Protege and you are right the user interface is much more usable then OBOedit; therefore and for the lack of alternatives, I will validate this answer. However, while working with Protege, I noticed that the expressive power of different ontology languages (OWL vs OBO) has a larger impact than I though. I have the impression, that OWL forces a way of thinking on me I am very uncomfortable with, I think I am too much used to the UML way of thinking. Examples, please correct me if I am wrong:

  • Classes can't have properties, only individuals can (correct?)
  • So, there is no way to "inherit" properties via the class hierarchy(?), e.g. all LifeCycleEvents depend on an "age" and "temperature" property, but I couldn't define these properties for LifeCycleEvent. Do I have to define them for any individual event (there are about 25), or is there some kind of inverse logic?
  • Only instances can be used in the annotation, sometimes 2 specific state are indistinguishable, so the super state should be used.
    Example: I might say: This animal is either in "Larva 1" or "Larva2" stage (both subclass of "Larva"), so I might annotate as "Larva".

I will read a bit more....

Btw, here is a quickly drafted model in protege's graph visualizer image

ADD REPLYlink modified 6.6 years ago • written 6.6 years ago by Michael Dondrup45k
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