[Ontology-editors] [OBO-Edit Working Group] marking xp terms

[Chris Mungall]

obof allows one comment per term. If you load two files each having  
distinct comments per term, then a parser should croak. I believe the  
current OE behavior would be to silently drop one (bug)

On Apr 9, 2009, at 8:29 AM, Alexander Diehl wrote:

> Why not just use the regular comment field then, since OBO-Edit can
> search comments, although apparently not unknown fields.
>
> Midori Harris wrote:
>> OBO-Editt does roundtrip unrecognized tags, but Jen's talking about  
>> the
>> pared-down OBO files containing cross-product tags  -- the ones in  
>> the
>> go/scratch/xps/ directory. Those are generated by some procedure that
>> preserves only the ID and intersection_of tags, plus term names as
>> exclamation-point comments.
>>
>> m
>>
>> On Thu, 9 Apr 2009, Alexander Diehl wrote:
>>
>>
>>> This points to the problem that comments in OBO files set off by  
>>> exclamation
>>> points are not preserved upon loading and saving an OBO file.  The  
>>> comments
>>> that show term names in stanza lines for relationships to other  
>>> terms are
>>> regenerated upon every save (keeps term names updated).
>>>
>>> It would be nice to have a tag for term specific comments that  
>>> roundtrips
>>> within a term stanza, but is not part of the official term data  
>>> associated
>>> with the term, and is not the same as the "comment:" field.  Does  
>>> OBO-edit 2
>>> automatically roundtrip unrecognized tags and their values?  If  
>>> so, you could
>>> just use your own made up tag.
>>>
>>> -- Alex
>>>
>>>
>>> Jennifer Deegan (nee Clark) wrote:
>>>
>>>> Hi,
>>>>
>>>> Has anybody come up with any cunning schemes for marking which  
>>>> terms they
>>>> have checked in the cross product file?
>>>>
>>>> I am working through bp-self in OE2 just now, checking the graph  
>>>> above the
>>>> term that has a logical definition in the xp file. I started by  
>>>> putting
>>>> '!!' on the end of the term name in the xp text file to mark the  
>>>> terms I
>>>> had checked. I planned then to reload all the files and do a  
>>>> search on 'has
>>>> is_intersection' AND NOT 'has name ends_with !!'. However, when I  
>>>> load the
>>>> files, the version of the term names in the live file overwrites  
>>>> the
>>>> version in the xp file and the !! is lost. If I load the files in  
>>>> the
>>>> opposite order then it should solve this problem, but then I  
>>>> would have no
>>>> way of noticing those terms in the live file that have changed  
>>>> their name
>>>> since my xp file was made (quite a lot of them going by  
>>>> experience so far.)
>>>>
>>>> It's hard to mark these even if I mark with dbxrefs in OBO-Edit  
>>>> and then
>>>> save out and filter to regenerate my xp file, as the dbxrefs to  
>>>> not go in
>>>> there.
>>>>
>>>> Is there any other way to mark a term name that would not be  
>>>> overwritten by
>>>> the live file version of the term name?
>>>>
>>>> Thanks,
>>>>
>>>> Jen
>>>> _______________________________________________
>>>> Ontology-editors mailing list
>>>> Ontology-editors at geneontology.org
>>>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
>>>>
>>>
>>>
>>
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>
>
> -- 
> Alexander D. Diehl, Ph.D.
> Senior Scientific Curator
> Mouse Genome Informatics
> The Jackson Laboratory
> 600 Main Street
> Bar Harbor, ME  04609
>
> email:  adiehl at informatics.jax.org
> work:  +1 (207) 288-6427
> fax:  +1 (207) 288-6131
>
>
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