Re: [OBO-Edit Working Group] New Drafts of OBO-Edit Paper and Editor Responses

On Feb 9, 2007, at 10:53 AM, John Day-Richter wrote:

>
> Trouble is, I haven't used recent versions of other ontology  
> editors much, so I can't say what's truly a unique feature. But  
> here are some possible candidates:
>
> 1) OBO-Edit 1.1 includes a scriptable command-line tool for  
> transforming ontologies (obo2obo).

can in principle be done easily for other tools, but in practice this  
is all set up and ready to go with oboedit; and the others don't do  
obo-format of course

> 2) obomerge can resolve two independently edited files into a  
> single file that contains all the changes.

prompt claims to be able to do this
http://protege.stanford.edu/plugins/prompt/prompt.html

i suspect there are differences; and prompt would not work on obo  
files of course

> 3) The rendering system allows many layers of complex, user-defined  
> term highlighting in the main viewer

probably unique

> 4) OBO-Edit has a ontology correctness checking system that allows  
> users to define their own ontology checks

probably unique

> 5) The reasoner can provide a (relatively) easy-to-understand  
> explanation for any inference it makes

I'm still not convinced this is 100% right; other tools like SWOOP  
have an explanation feature but they are not easy to understand

> 6) The way we retain obsolete terms and allow users to assign  
> "replaced-by" and "consider" terms for updating annotations is a  
> feature I haven't seen elsewhere

definitely unique. this is one of the many benefits of the way  
oboedit builds-in ontology metadata

> 7) I don't know of any other ontology editor that allows synonms to  
> be labeled with user-defined synonym types

ditto

> Can we say with any authority that any of these are unique?
>
>    -John
>
> Chris Mungall wrote:
>
>>
>> Seems good. John - did you have any other suggestions for unique   
>> features?
>>
>> On Feb 9, 2007, at 6:00 AM, Midori Harris wrote:
>>
>>> Hi again,
>>>
>>> In the previous draft of the response document I just edited  
>>> what  was there. Now I've gone and added part of Chris's  
>>> suggestions for  unique features, in the attached. See what you  
>>> think ...
>>>
>>> m
>>>
>>> On Fri, 9 Feb 2007, Midori Harris wrote:
>>>
>>>> Hi John et al.,
>>>>
>>>> I've done my bit -- a few edits to the response, and a couple  
>>>> of  small changes to the manuscript draft, all highlighted with  
>>>> 'track  changes'. (Note that the change tracking makes the  
>>>> manuscript look  too long, but if you use the 'accept changes'  
>>>> thingie, it still  just fits into two pages.)
>>>>
>>>> m
>>>>
>>>> On Thu, 8 Feb 2007, John Day-Richter wrote:
>>>>
>>>>> After talking with Melissa, we've made a few more minor  
>>>>> changes  to the
>>>>> editor responses for consistency, and some minor formatting   
>>>>> changes to
>>>>> the manuscript to comply with their manuscript revision policy  
>>>>> (I  made
>>>>> the changes blue, so they're easy to see).
>>>>>
>>>>>    -John
>>>>> <OBO-Edit_Paper_EditorResponses_draft3a.doc>
>>>>
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>
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