[Bioc-devel] Package Classifications via BiocViews
hp@ge@@on@g|thub @end|ng |rom gm@||@com
Thu Sep 29 01:36:56 CEST 2022
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:
> 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!
> 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.
>> 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
>>> end to change the manifest the package belongs to and to clear the
>>> products from the data repositories so it is only found in one
>>> Are you sure you want to proceed with switching? It is not trivial
>>> on our
>>> 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
>>> 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
>>> I am a developer working on the bioconductor package gemma.R
>>> 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?
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