[Ontology-editors] regulation term requests

[Chris Mungall]

On Sep 11, 2008, at 3:59 PM, Tanya Berardini wrote:

> Hi Chris,
>
> I've just added a couple terms to the new-term-queue.txt file and  
> checked it into cvs.  I wasn't quite sure about the appropriate use  
> of the new-terms.obo and new-terms-full.obo files.  It seems that if  
> I'm going to type out a new term suggestion in obo format, then I  
> have all the info necessary to do it in OE and OE is less likely to  
> make mistakes in the format than I am.

you did the right thing. The only reason you would add to new-terms- 
full.obo is if you have new core BP terms that you want to use in a  
regulation term composition. This scenario would most likely arise if  
you are already working with a branch of the main ontology. In this  
case you may just want to run the wrapper script yourself..

> I'm excited to see what will turn up in go_reglive_withNew-reasoned- 
> filtered.obo in the morning.  Following on Jane's question below,  
> what would you suggest the best step to integrate the new terms into  
> the ontology would be?
>
> Just take the new obo stanzas and then plop them into a fresh copy  
> of the gene_ontology_write.obo?
>
> Obomerge?

yep. you could paste in, but we don't really want to be hand editing;  
and there may be subtle cases where other parts of the ontology change  
(for example, if your reg terms occupy intermediate positions in the  
reg graph)

>
> Thanks,
>
> Tanya
>
> On Thu, Sep 11, 2008 at 4:55 AM, Jane Lomax <jane at ebi.ac.uk> wrote:
> How does this system work wrt merges with the live file, Chris? Do  
> we need to use obomerge to merge go_reglive_withNew-reasoned- 
> filtered.obo with the live file?
>
> cheers,
>
> Jane
>
>
> On Fri, 5 Sep 2008, Chris Mungall wrote:
>
> If anyone wants to try out the regulation term request system, it's  
> ready for action. Get a fresh copy of go/scratch/regulates_xp_live,  
> modify and commit new-term-queue.txt and/or new-terms.obo, then  
> check go_reglive_withNew-reasoned-filtered.obo the next day!
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> Dr Jane Lomax
> GO Editorial Office
> EMBL-EBI
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> -- 
> Tanya Berardini
> TAIR Curator
> www.arabidopsis.org