[DAS2] modification to /type request & response

Suzanna Lewis suzi at fruitfly.org
Mon Apr 11 21:57:17 UTC 2005

You also might want to check the FMA
for human anatomical terms:


I think we will be using it for phenotypes one day
(some day...)

It would be, like SO, structured and something
that could be referenced as the ontology.


On Apr 11, 2005, at 2:49 PM, Allen Day wrote:

> On Mon, 11 Apr 2005, Suzanna Lewis wrote:
>> On Apr 11, 2005, at 1:33 PM, Allen Day wrote:
>>>>> I'd like to remove the constraint that all types inherit from a 
>>>>> type.
>>>>>  It
>>>>> makes sense to keep a constraint like this in place for genome
>>>>> sequence
>>>>> features, but not any other record type.
>>> [...]
>>>>> Regarding protein feature types, I think the SO team plans to put
>>>>> them
>>>>> in
>>>>> SO/SOFA since they summarize it as, "a set of terms used to 
>>>>> describe
>>>>> features on a nucleotide or protein sequence." But there is no
>>>>> support
>>>>> for
>>>>> proteins in SO/SOFA yet. Suzi?
>>>> Yes, that is pretty much where it stands. There is the intention of
>>>> doing this, but we have not yet gotten to that point. Including the
>>>> basic structural descriptions of a protein (alpha helices, beta
>>>> sheets...)
>>>> seems an obvious new addition and easy enough to do.
>>>> I strongly agree with Steve here that we absolutely must stay
>>>> away from ad hoc types. They are the sirens on the rocks:
>>>> alluring, but lethal.
>>> Regarding ad hoc types, I agree as well.  What I meant to say is that
>>> we
>>> ought to allow non-sequence feature types be served up by DAS/2, and 
>>> to
>>> allow extensions to those types.  Basically I'm proposing to have 
>>> DAS/2
>>> handle non-sequence feature ontologies in the same way that it 
>>> handles
>>> the
>>> sequence feature ontology.
>> Hi Allen,
>> I don't understand, but maybe I'm muddling GFF3 with DAS/2.
>> In GFF3 clearly everything is sequence-based in one way or
>> another.
>> Perhaps you could provide some scenarios/examples where
>> this would apply in DAS/2?
> I can't think of anything in genome-DAS that should not have its 
> primary
> type be a sequence feature type, or some derivative of an existing
> sequence feature type.
> An example of where I need to do this is outside the genome service -- 
> in
> the array-DAS service.  I need to be able to attach types to biological
> source materials that participate in experiments.  For example, I might
> want to annotate a skeletal muscle sample from a morbidly obese human 
> from
> the mouse anatomical ontology as "skeletal muscle".  I'd also attach 
> the
> type "morbidly obese", which is an extension to the mammalian phenotype
> ontology type "obese".
> -Allen

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