Re: [OBO-Edit Working Group] Problems with OE merge?

[Jane L. <ja...@eb...>]

Hi Nomi -
> Weird. This doesn't happen with previous OEs? Can you send me the two terms you were trying to merge, a screenshot showing the lost information, and an URL for the full GO file? (Don't try to email the whole file, it's too big.)
>
> I tried this with the version of gene_ontology.obo I have around, and the merge resulted in an exception, which could be the source of the problems you saw (though I didn't seem to lose the synonyms etc. when I tried it).
Not sure - it's the first time I've seen this bug. The file is here:

http://www.geneontology.org/scratch/xps/go_annotation_extension_relations.obo

and the ids are GO:0019282 into GO:0003961. Just tried it again and the 
same happened.

This is the output from the history browser, which shows which fields 
were deleted:

Changed definition of GO:0003961 from "MERGED DEFINITION: TARGET 
DEFINITION: Catalysis of the reaction: O-acetyl-L-homoserine + 
methanethiol = L-methionine + acetate. -------------------- SOURCE 
DEFINITION: The direct chemical reactions and pathways resulting in the 
formation of L-methionine from other compounds, including 
O-acetyl-L-homoserine." to "Catalysis of the reaction: 
O-acetyl-L-homoserine + methanethiol = L-methionine + acetate.", Changed 
synonym scope of GO:0003961 from "Exact" to "Related", Deleted general 
dbxref GOC:mah from synonym L-methionine anabolism, direct, from 
O-acetyl-L-homoserine of GO:0003961, Deleted synonym "L-methionine 
anabolism, direct, from O-acetyl-L-homoserine" from GO:0003961, Changed 
synonym scope of GO:0003961 from "Exact" to "Related", Deleted general 
dbxref GOC:mah from synonym L-methionine formation, direct, from 
O-acetyl-L-homoserine of GO:0003961, Deleted synonym "L-methionine 
formation, direct, from O-acetyl-L-homoserine" from GO:0003961, Changed 
synonym scope of GO:0003961 from "Exact" to "Related", Deleted general 
dbxref GOC:mah from synonym L-methionine synthesis, direct, from 
O-acetyl-L-homoserine of GO:0003961, Deleted synonym "L-methionine 
synthesis, direct, from O-acetyl-L-homoserine" from GO:0003961, Changed 
synonym scope of GO:0003961 from "Exact" to "Related", Deleted general 
dbxref GOC:mah from synonym methionine biosynthetic process, direct, 
from O-acetyl-L-homoserine of GO:0003961, Deleted synonym "methionine 
biosynthetic process, direct, from O-acetyl-L-homoserine" from 
GO:0003961, Changed synonym scope of GO:0003961 from "Exact" to 
"Related", Deleted synonym "L-methionine biosynthetic process, direct, 
from O-acetyl-L-homoserine" from GO:0003961]

cheers,

Jane
>
>> GO:0019282 is a process and GO:0003961 is a function if that makes any difference. I'm able to get other processes to merge into functions successfully though, so I don't think that's the problem.
>>
>> On a more minor note, the history browser used to list the term name as well as term id in its output, which was extremely useful, but now only seems to give id.
> I will look at that. I didn't make that change, as far as I know.
>
> Thanks for testing!
>
> 	Nomi
>
>> thanks,
>>
>> Jane
>
>
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