[Ontology-editors] marking xp terms

[Alexander Diehl]

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
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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