[Bioc-devel] Experiment Data biocViews updates

[Sonali Arora]

Hi Vince,

As an initial cut,
a) I have removed "WholeGenomeData" from under TechnologyData -> 
SequencingData
b) added "Somatic" and "Germline" under SpecimenSource. ( you need to 
click the checkbox on top to see these two as they are childless biocViews.

Thanks and Regards,
Sonali.

On 12/8/2014 8:44 AM, Vincent Carey wrote:
> On Mon, Dec 8, 2014 at 11:22 AM, Sonali Arora <sarora at fredhutch.org> wrote:
>
>> Hi Vince,
>>
>> On 12/8/2014 7:38 AM, Vincent Carey wrote:
>>
>>> Very nice.  Is "WholeGenomeData" under "SequencingData"  sufficiently
>>> clear?
>>>
>> We mirrored the Technology category under Software biocViews for
>> "TechnologyData", thus "SequencingData" mirrored "Sequencing"
>> what would you suggest instead ?
>
> Well, this is something we should get some consensus on if there will be
> any changes.  It seems
> to me that various assays can be regarded as "whole genome data" whereas I
> think what is intended
> for that term is whole genome dna sequencing, and one might want to
> distinguish germ line and
> tumor sequencing for an initial cut?
>
>
>>
>>> We may also want to have a source tissue terminology in the experimental
>>> data space.
>>>
>> We have :
>> SpecimenSource -> Tissue;
>>
> Again I don't want to introduce pointless complexity.  But my understanding
> is that one can only
> use terms that are in the hierarchy, so if there are informative
> distinctions missing from the hierarchy,
> resources go out with vague labels.
>
> one set of terms for tissues is at
>
> http://www.gtexportal.org/home/
>
> since we might want to repackage some of that data, perhaps a coarse subset
> of those terms would
> be useful to have in the hierarchy
>
>
>> SpecimenSource -> Proteome;
>> SpecimenSource -> Genome;
>> SpecimenSource -> StemCell;
>> SpecimenSource -> CellCulture;
>>
>> I believe you want us to expand Tissue more ? Please suggest the best way
>> to break it up further.
>>
>> Thanks for the quick response,
>> Sonali.
>>
>>
>>> On Mon, Dec 8, 2014 at 10:28 AM, Sonali Arora <sarora at fredhutch.org>
>>> wrote:
>>>
>>>   Hi everyone,
>>>> We have revised the Experiment Data biocViews and have updated most of
>>>> the
>>>> Experiment Data packages using our word lookup function(
>>>> recommendBiocViews() ) .
>>>>
>>>> Package Authors are encouraged to check the new biocViews added to their
>>>> Experiment Data package  and add more relevant ones from the new updated
>>>> Experiment Data biocViews tree.
>>>>
>>>> The new Experiment Data biocView tree can be viewed at :
>>>> http://www.bioconductor.org/packages/devel/BiocViews.html#
>>>> ___ExperimentData
>>>>
>>>> Just a friendly reminder - You are allowed to add biocViews only from the
>>>> category of biocViews that you're package belongs to.
>>>> For example, ExperimentData Packages can contain biocViews only from the
>>>> Experiment Data biocViews category.
>>>>
>>>> We hope that this updated tree will help you find test data  more easily
>>>> and efficiently, for the new software packages that you write.
>>>>
>>>> --
>>>> Thanks and Regards,
>>>> Sonali
>>>>
>>>>
>>>>
>> --
>> Thanks and Regards,
>> Sonali
>>
>>