[Bioc-devel] Experiment Data biocViews updates

Vincent Carey stvjc at channing.harvard.edu
Mon Dec 8 17:44:03 CET 2014

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


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

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