Re: [Gmod-schema] Cvterms shared between multiple cvs (ontologies)

[Chris M. <cjm...@lb...>]

For now you would have to fix the ontology - the developers (cc'd) may 
be able to do this. Or you could hack something ugly into your workflow. 
But note this may indicative of worse problems to come. What happens if 
the 'MIREOT'ed copy of a subset of GO merged into MIRO is out of date to 
the extent that you have terms obsolete in one and live in the other? 
You might want to invest some effort evaluating your set of required 
ontologies, how they connect and if any pre-processing is required.

Pantelis you can contact me off list if you want help fixing the 
workflow for MIRO

On 24 Feb 2015, at 9:01, Bob MacCallum wrote:

> Hello all,
>
> This follows on from a discussion more than a year ago:
>
> http://gmod.827538.n3.nabble.com/stag-storenode-pl-overwrites-existing-cvterms-in-vocabularies-different-from-the-one-being-loaded-td4031069.html
>
> First things first, in the below, when I say "load" I mean the 
> following:
>
> cat file.obo | go2fmt.pl -p obo_text -w xml - | go-apply-xslt
> oboxml_to_chadoxml > file.chado-xml
> stag-storenode.pl -d "dbi:Pg:dbname=$CHADO_DB_NAME" --user $USER 
> file.chado-xml
>
>
>
> If I load GO the term "nuclear chromosome" ends up in the cvterm table
> belonging to the "cellular_component" cv - which is fine.
>
> Then I load MIRO via the same process
>
> And the row in cvterm is updated so that cv_id is now pointing to 
> MIRO.
>
> Here's the MIRO nuclear chromosome term for reference:
> http://bioportal.bioontology.org/ontologies/MIRO?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGO_0000228
>
>
> This hasn't been a problem for us until now.  Now we want to write a 
> script
> which "gets all terms from MIRO and ... [dumps them to Solr JSON 
> FWIW]".
> And because of the fragile nature of the cvterm.cv_id column (and its
> one-to-one-ness) we can't do this.
>
> Has anyone else tackled this issue?
>
> many thanks,
> Bob.
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