[InterMine Dev] important of sequence ontology additions

Julie Sullivan julie at flymine.org
Thu Mar 7 11:07:24 GMT 2013


Fantastic!! :)

Sorry about that, I'll add something about sequence ontology in the docs so you 
won't have to guess how this all works!

On 06/03/13 16:08, JD Wong wrote:
> 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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