[Ontology-editors] XP file

[Chris Mungall]

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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