[InterMine Dev] important of sequence ontology additions

JD Wong jdmswong at gmail.com
Wed Mar 6 16:08:40 GMT 2013


Hi Julie,

This completely solves my issue.

Thank you!
-JD

On Wed, Mar 6, 2013 at 10:49 AM, Julie Sullivan <julie at flymine.org> wrote:

> 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
>>>>
>>>>
>>>>
>>>>
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>>>>
>>>>
>>>
>>
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