[DAS2] modification to /type request & response

[Suzanna Lewis]

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

http://sig.biostr.washington.edu/projects/fm/

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.

-S

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