From: Jane L. <ja...@eb...> - 2011-10-26 13:00:50
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It's working okay now! Not sure what changed...deleting my config didn't seem to fix it. Perhaps I did the edit in a different order. Jane On 25/10/2011 22:11, Nomi Harris wrote: > On Oct 25, 2011, at 3:08 AM, Jane Lomax wrote: > >> Hi Nomi - sorry, I only work part-time… > So do I. :-) > >> unfortunately I'm still seeing >> the same problem BUT if it's specific to my set-up and only seems to >> affect these terms let's not let it hold up the release. > It's not clear to me whether it's specific to your setup or whether I'm just not doing the same sequence of operations as you. Can someone else try this (merge GO:0019282 into GO:0003961) and see if anything (synonyms etc.) gets lost? > >> I'll try deleting my config. > Yes, good idea--actually, you could start by just removing/renaming your ~/oboedit_config/perspectives -- usually that's the component of the config directory that causes the weird behavior. Let me know if that helps! > > Nomi > >> cheers, >> >> Jane >> >> On 24/10/2011 18:59, Nomi Harris wrote: >>> Hi Jane, >>> >>> Did the new version fix the merge problem? >>> >>> Nomi >>> >>> On Oct 21, 2011, at 10:31 AM, Nomi Harris wrote: >>> >>>> I am not able to reproduce this problem--I tried it in OE 2.1-rc1 and rc2 and I can merge the terms in question (GO:0019282 into GO:0003961) without losing synonyms etc. (see screenshot). >>>> >>>> However, I did notice (as I mentioned yesterday) an exception flying when I did the merge, so it's possible that that's causing problems. I will send you a link to try a new version with the exception fixed--please try it and tell me if it fixes your merge problem. >>>> >>>> Nomi >>>> >>>> <Screen shot 2011-10-21 at 10.30.10 AM.png> >>>> >>>> On Oct 20, 2011, at 2:37 PM, Jane Lomax wrote: >>>> >>>>> Sorry! I meant of course: >>>>> >>>>> http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology_ext.obo >>>>> >>>>> >>>>> On 20/10/2011 21:29, Nomi Harris wrote: >>>>>> On Oct 20, 2011, at 1:08 PM, Jane Lomax wrote: >>>>>> >>>>>>> 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 >>>>>> That seems wrong; that just has relations, not terms. >>>>>> >>>>>>> and the ids are GO:0019282 into GO:0003961. Just tried it again and the >>>>>>> same happened. >>>>>> I am investigating. >>>>>> >>>>>>>>> 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'm not sure when it used to list the term name; I tried version 2.0 and it doesn't. So maybe this was something in OE 1? You can submit a Feature Request for this. >>>>>> >>>>>> Nomi >>>>>> >>>>>> >>>>>>> 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 |