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

[Alexander Diehl]

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