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.sheph...@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-boun...@r-project.org> on behalf of
Burak
Ogan Mancarci <ogan.mancar...@gmail.com>
*Sent:* Wednesday, September 28, 2022 9:17 AM
*To:* bioc-devel@r-project.org <bioc-devel@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
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Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
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