[Bioc-devel] Experiment Data biocViews updates
sarora at fredhutch.org
Thu Dec 11 20:36:59 CET 2014
As an initial cut,
a) I have removed "WholeGenomeData" from under TechnologyData ->
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,
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
>> 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
> 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,
>>> On Mon, Dec 8, 2014 at 10:28 AM, Sonali Arora <sarora at fredhutch.org>
>>> Hi everyone,
>>>> We have revised the Experiment Data biocViews and have updated most of
>>>> 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 :
>>>> 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,
>> Thanks and Regards,
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