[Bioc-devel] Package Classifications via BiocViews

[Hervé Pagès]

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
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