[Bioc-devel] Experiment Data biocViews updates
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