[InterMine Dev] important of sequence ontology additions

Julie Sullivan julie at flymine.org
Wed Mar 6 15:49:09 GMT 2013


You can force a many to many relationship by putting that in the so_terms file.

This is what FlyMine has:

	# many-to-many part_of relationships (default is many-to-one)
	exon.transcript
	intron.transcript
	UTR.transcript
	EST.overlapping_EST_set

I think that's what you need?

On 06/03/13 15:45, JD Wong wrote:
> 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!
> -JD
>
> 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
>>>
>>>
>>>
>>>
>>> ______________________________**_________________
>>> dev mailing list
>>> dev at intermine.org
>>> http://mail.intermine.org/cgi-**bin/mailman/listinfo/dev<http://mail.intermine.org/cgi-bin/mailman/listinfo/dev>
>>>
>>
>



More information about the dev mailing list