[InterMine Dev] important of sequence ontology additions

JD Wong jdmswong at gmail.com
Wed Mar 6 15:45:36 GMT 2013

Hi Julie,

Your points are well taken.  My root issue is the modelling of
cds.transcript.  In the so_additions.xml this relationship is stored as a
reference, which precludes the possibility of multiple parenthood.  This is
a problem with CDS's which exist within more than one transcript.  I don't
want to create another field for this special case, just replace the
existing one with something more appropriate.  Modifying the so_terms file
will probably be held as a last resort.

Thank you!

On Wed, Mar 6, 2013 at 4:24 AM, Julie Sullivan <julie at flymine.org> wrote:

> 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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