[InterMine Dev] important of sequence ontology additions

Julie Sullivan julie at flymine.org
Wed Mar 6 09:24:51 GMT 2013


JD

The Sequence Ontology is the basis for the InterMine biological model, so no you 
should not remove so_additions.xml.

To modify which SO terms are included in your model, you can update your 
so_terms file in `dbmodel/resources`. That's the file that generates 
so_additions.xml. Maybe that's what you need?

However, as part of the InterMOD project you want your model to be as close to 
SO as possible, therefore you want to add as many terms as you can to the 
so_terms file.

In general, you want to keep WormMine as close to InterMine as is feasible. e.g. 
not removing files needed for the build. We've had trouble in the past when 
mines have custom core InterMine code. Upgrading can be problematic / 
impossible, we have a hard time debugging etc etc.

A different approach would be to tell us what sort of problem you are trying to 
solve. It's likely that others may have (had) a similar problem, in which case 
the problem has been addressed, or maybe the solution means a change to the core 
InterMine code.

But I think in this case, editing the `so_terms` file will get you what you 
need. Let me know if it doesn't!

Julie

On 05/03/13 22:56, JD Wong wrote:
> Hello InterMine developers,
>
> I understand that InterMine is loosely based off of Sequence Ontology, but
> I'm wondering how essential this feature is to the application.  Is it
> possible to modify or remove so_additions.xml without consequence?
>
> All the best,
> -JD
>
>
>
>
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