[Bioc-devel] Package Classifications via BiocViews

[Burak Ogan Mancarci]

I have switched out the terms. Thanks a lot and sorry about the mess.

Cheers,
Ogan

On Wed, Sep 28, 2022 at 4:36 PM Hervé Pagès <hpages.on.github using gmail.com>
wrote:

> On 28/09/2022 16:03, Hervé Pagès wrote:
>
> > Hi Burak,
> >
> > Based on your description of what the package does, this is really a
> > software package in nature, so is in the wrong repository. We need to
> > fix this.
> >
> > In 4 steps:
> >
> > 1. Please remove the ExperimentData term from the biocViews field as
> > well as any term that belongs to the ExperimentData ontology, that is:
> > DiseaseModel, OrganismData, Homo_sapiens_Data, Mus_musculus_Data,
> > Rattus_norvegicus_Data, TechnologyData, MicroarrayData,
> > SequencingData, and RNASeqData. Yep, most of your terms will go away.
>
> After taking a second look I realize that **all** your current terms are
> from the ExperimentData ontology, instead of being a mix of Software and
> ExperimentData terms as I thought initially. So they should all be removed.
>
> >
> > 2. Add the Software term, in first position. You're welcome to add new
> > terms if you want, from the following vocabulary:
> >
> https://github.com/Bioconductor/biocViews/blob/master/inst/dot/biocViewsVocab.dot.
>
> > Please make sure to pick terms that belong to the Software ontology
> > (i.e. are offsprings of the Software term).
>
> You should definitely add new terms from the Software ontology!
>
> Thanks,
>
> H.
>
> >
> > 3. Bump the package version (only the z part in x.y.z), and push your
> > changes to git.bioconductor.org.
> >
> > 4. Let us know when you're done. We'll make the required adjustments
> > on our side.
> >
> > Thanks,
> >
> > H.
> >
> > On 28/09/2022 09:37, Burak Ogan Mancarci wrote:
> >> Apologies for the inconvenience.
> >>
> >> The change isn't essential on our end and can be avoided or delayed
> >> if you
> >> think the ExperimentData label can be applied to a package
> >> responsible for
> >> accessing data from a database rather than storing static data. We were
> >> only worried about misleading use of biocviews terms.
> >>
> >> Cheers,
> >> Ogan
> >>
> >> On Wed., Sep. 28, 2022, 14:26 Kern, Lori,
> >> <Lori.Shepherd using roswellpark.org>
> >> wrote:
> >>
> >>> Changing the biocviews is not sufficient.  There needs to be work on
> >>> our
> >>> end to change the manifest the package belongs to and to clear the
> >>> build
> >>> products from the data repositories so it is only found in one
> >>> location.
> >>>
> >>> Are you sure you want to proceed with switching?  It is not trivial
> >>> on our
> >>> end.
> >>>
> >>> Lori Shepherd - Kern
> >>>
> >>> Bioconductor Core Team
> >>>
> >>> Roswell Park Comprehensive Cancer Center
> >>>
> >>> Department of Biostatistics & Bioinformatics
> >>>
> >>> Elm & Carlton Streets
> >>>
> >>> Buffalo, New York 14263
> >>> ------------------------------
> >>> *From:* Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of
> >>> Burak
> >>> Ogan Mancarci <ogan.mancarcii using gmail.com>
> >>> *Sent:* Wednesday, September 28, 2022 9:17 AM
> >>> *To:* bioc-devel using r-project.org <bioc-devel using r-project.org>
> >>> *Subject:* [Bioc-devel] Package Classifications via BiocViews
> >>>
> >>> Hi,
> >>>
> >>> I am a developer working on the bioconductor package gemma.R
> >>> <
> >>>
> https://secure-web.cisco.com/1wIQY41Mq8CRYqLq1luoPm43XSj6Icl27w6udr35y-BxPHgEP6B5pApAAeBdBeWsydixV0CSwBVIVl2C7mJykPI3ESX7qtp-xJOSvJAu4T1yzHr3CWRc7s6LY_WtIcrnzfyw3MI7z0oqv1hzA1x5oRN1kFZ-KF6tttbi86SwIwZhYADSMaK1xXJxmlZ0Oe8CtJ6jKBrSjnn6fnDONMFHadvspGk8Gxc7N15gdoVzcbADiR0q1V7O973S1e0Fu6CFPAayqcCBKIOs4_xfp6nm1HNupK82P0Bawyi3Bc4Fu2vcDQKLcgU-gyiBMkego3WW4/https%3A%2F%2Fbioconductor.org%2Fpackages%2F3.16%2Fdata%2Fexperiment%2Fhtml%2Fgemma.R.html
> >>>
> >>>> .
> >>> On publication we have used the ExperimentData biocview to classify the
> >>> package but we believe this was not the correct decision since the
> >>> package's function is to access a database much like geoquery. I was
> >>> wondering if it was safe to change the classification on our end by
> >>> changing biocviews directly or if it would cause issues with the
> >>> bioconductor infrastructure?
> >>>
> >>> Cheers,
> >>> Ogan
> >>>
> >>>          [[alternative HTML version deleted]]
> >>>
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> --
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.github using gmail.com
>
>

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