Re: [GUSDEV] InsertSequenceFeatures plugin

[Deborah P. <pi...@pc...>]

Wouldn't it be better to avoid using dots.SequenceType, a table for 
which there is no controlled vocabulary, and instead use the 
sres.sequenceontology.term_name to get a 
sequenceontology.sequence_ontology_id? Especially since the SO file will 
have been loaded. It seems as if that would be a minor change to the plugin.
                           
                                                                                                                                                                                              
Debbie
                                                                                                                                                                                  


Steve Fischer wrote:

> for those of you who are using the beta version of the ISF plugin:
>  1. i will improve its documentation to indicate what it expects to 
> already be in the database:
>         - SequenceOntology   (InsertSequenceOntology plugin)
>         - NCBI Taxon   (LoadTaxon plugin)
>         - External database and release (InsertExternalDatabase and 
> InsertExternalDatabaseRls plugins)
>         - at least one row in SequenceType so you can say what type of 
> sequence you are loading (you can use LoadRow plugin for this)
>
>  2.  i will improve the error messages so that it better detects the 
> absence of these, and makes it more clear what to do.
>
> About loading SO:
>   1. can you send the SO term with definition that is too big?
>
>   2. i understand about the rollback.  we have been discussing how to 
> undo a plugin.   for now, you need to do it with sql.
>
> Thanks for helping us make this plugin better.
>
> steve
>
>
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