[Ontology-editors] XP file

[Chris Mungall]

OK, here's what I did with Midori's:

obo-subtract.pl obo-subtract.pl --comment  
biological_process_xp_cellular_component-unvetted.obo   
biological_process_xp_cellular_component.obo > nu
mv nu biological_process_xp_cellular_component-unvetted.obo

obo-subtract.pl is in go-perl cvs, it's standalone

Now, any stanza that is in the vetted file is commented out in the  
unvetted file. This means the vetted and unvetted are non-redundant,  
and the union provides the full set.

I chose to comment out rather than remove altogether; this way we keep  
around additional comments that may not have made it into the vetted  
file (remember, those comments will eventually be ditched as soon as  
we do our first OE roundtrip). For example:

!!   [Term]
!!   id: GO:0001325 ! formation of extrachromosomal circular DNA
!!   intersection_of: GO:0048646 ! anatomical structure formation
!!   intersection_of: OBO_REL:results_in_formation_of GO:0005727 !  
extrachromosomal circular DNA
!!   !! unexpected, and not reflected in existing graph, but actually  
looks ok

I'm looking at yours Jen and I'm not 100% sure what the different  
files are - is biological_process_xp_self_with_defs.obo used for  
anything?

I think this is the one I want to use:
	biological_process_xp_self_edit.obo

I would just strip this down to the bare xp defs and use this as the  
vetted file to replace biological_process_xp_self.obo

But I see 606 xps in there, you say 650 - do you need to commit?

On Mar 5, 2009, at 8:45 AM, Jennifer Deegan (nee Clark) wrote:

> Thanks. I don't have neatly commented sanzas like Midori, so if it  
> could just pick up on "id: GO:xxxxxxx" in the file of problem  
> stanzas that would be awfully helpful.
>
> Jen
>
> Chris Mungall wrote:
>> On Mar 5, 2009, at 2:42 AM, Midori Harris wrote:
>>> Hi Jen,
>>>
>>> What Chris did with my BP-CC xps is create a new file for the ones  
>>> that *haven't* passed muster as fully checked. (I'll find the  
>>> relevant email and forward it.) His plan is to convert the file  
>>> with the original name into the file for fully vetted xps, but  
>>> that hasn't been done yet. At the moment they're still in the go/ 
>>> scratch/xps/ directory, and I'm inclined to leave all the xp file  
>>> there at least until we have another chat with Chris (mhich maybe  
>>> we should do soon).
>>>
>>> Specifically, in go/scratch/xps/ Chris added  
>>> biological_process_xp_cellular_component-unvetted.obo, and intends  
>>> to strip anything that appears in that file from  
>>> biological_process_xp_cellular_component.obo; I presume you can  
>>> copy your difficult stanzas into a new file with an '- 
>>> unvetted.obo' name.
>>>
>>> Chris - are you still planning to eliminate duplication between  
>>> whatever-xps-.obo and whatever-xps-unvetted.obo, or should we work  
>>> on that?
>> Yes. I will knock together a quick 'obo-subtract' script to do this
>>>
>>> m
>>>
>>> On Thu, 5 Mar 2009, Jennifer Deegan (nee Clark) wrote:
>>>
>>>> Hi,
>>>>
>>>> The majority (about 650) of my XP stanzas in the bp-self file are  
>>>> nearly good to go. There are a bunch of others (about 100) that  
>>>> are going to be really difficult to fix and will need extensive  
>>>> rearrangements of the live structure.
>>>>
>>>> I would like to start to move my good stanzas to a file that is  
>>>> marked in some way as 'fully checked stanzas'. I feel as if the  
>>>> current policy of trying to fix all stanzas in a file before  
>>>> passing on the file is stopping the good stanzas from being used.  
>>>> The difficult terms that need work may take a *long* time, just  
>>>> because of the difficulty of the rearrangements and the current  
>>>> lack of support in OBO-Edit.
>>>>
>>>> I believe the current policy is that finished files will be moved  
>>>> to somewhere in go/ontology/. Would you be happy for me to make a  
>>>> bp-self file there and start to trickle-feed my fully checked  
>>>> stanzas into it? If so, then is there any preference for the  
>>>> location and naming scheme?
>>>>
>>>> Thanks,
>>>>
>>>> Jennifer
>>>>
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>