[Bioc-devel] Package Classifications via BiocViews

Burak Ogan Mancarci og@n@m@nc@rc|| @end|ng |rom gm@||@com
Wed Sep 28 18:37:08 CEST 2022

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.


On Wed., Sep. 28, 2022, 14:26 Kern, Lori, <Lori.Shepherd using roswellpark.org>

> 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
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