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 <sar...@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 <sar...@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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