[Bioc-devel] Package Classifications via BiocViews

Hervé Pagès hp@ge@@on@g|thub @end|ng |rom gm@||@com
Thu Sep 29 01:03:46 CEST 2022

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.

2. Add the Software term, in first position. You're welcome to add new 
terms if you want, from the following vocabulary: 
Please make sure to pick terms that belong to the Software ontology 
(i.e. are offsprings of the Software term).

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.



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
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Hervé Pagès

Bioconductor Core Team
hpages.on.github using gmail.com

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