[Bioc-devel] Package Classifications via BiocViews

Wed Oct 5 14:56:02 CEST 2022

I believe this should all be taken care of now.  Please let us know if anything does not seem correct but gemma.R should now be a software package and not have an association with data/experiment

Cheers,

Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Burak Ogan Mancarci <ogan.mancarcii using gmail.com>
Sent: Thursday, September 29, 2022 2:55 AM
To: Herv� Pag�s <hpages.on.github using gmail.com>
Cc: Kern, Lori <Lori.Shepherd using RoswellPark.org>; bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Package Classifications via BiocViews

I have switched out the terms. Thanks a lot and sorry about the mess.

Cheers,
Ogan

On Wed, Sep 28, 2022 at 4:36 PM Herv� Pag�s <hpages.on.github using gmail.com<mailto:hpages.on.github using gmail.com>> wrote:
On 28/09/2022 16:03, Herv� Pag�s 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<https://secure-web.cisco.com/1HsI4_qyxulTiGwT330qZq188MAh-YTIB-1RpQwM0annyTzCK_dwcGjFfGvDLCe3-Es2wOrZHcm8_oAvh8KzNTBpPLP1bwAH864RCohx4VONiwmJFKyStEMlMpJRFqbTvgWL-Ia9Ma1uLdgafCIUEaZOTDEBjC2IgTU4VeV3m07ze2ohtkeXgo5QtO6qfBULFu1rGGGibgomjLs5Jhgzqih2kGyYmQ3gDr_8b0Ue81jSe_gsJtzceJs3YGQs_466B-SmT1onTu4wpVdcVsBgHgJdqAztZ1c7y1BSSosZFzJkNFLJWKOQhsehJS6kA8vrq/https%3A%2F%2Fgithub.com%2FBioconductor%2FbiocViews%2Fblob%2Fmaster%2Finst%2Fdot%2FbiocViewsVocab.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<http://secure-web.cisco.com/1N0hpaKBlyOErRP8gXSzCl8XM0Gh7FhTTBlyVJnwkVjzFWM0wlTlsT7CSE1yt20J5XssU6zgnTN0h8ZgOe06BOpK58p6NFnTuDoTMHx4LEh2WSKvFlM_u2dLoMPwBS7cr4rtxLZFKHSaaK3dxhFA2NwTPUTLpar8VO_4QWi4zj7UQh3GMlOsb8LlzkSsIfQ77GG02bp-RDpOCE1obmYxClU78AB5TkwFLgxuF1I98y9dI46qy97GZv7P_kqaFiH1Aq4aoG_5nrJ7i4AetRCNYLQHIFJxT4NMhb3cDF7k94YD-8hzqUezh0O7zSqs4KZDb/http%3A%2F%2Fgit.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<mailto: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<mailto:bioc-devel-bounces using r-project.org>> on behalf of
>>> Burak
>>> Ogan Mancarci <ogan.mancarcii using gmail.com<mailto:ogan.mancarcii using gmail.com>>
>>> *Sent:* Wednesday, September 28, 2022 9:17 AM
>>> *To:* bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org<mailto: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]]
>>>
>>> _______________________________________________
>>> Bioc-devel using r-project.org<mailto:Bioc-devel using r-project.org> mailing list
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>>>
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>>
>> _______________________________________________
>> Bioc-devel using r-project.org<mailto:Bioc-devel using r-project.org> mailing list
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--
Herv� Pag�s

Bioconductor Core Team
hpages.on.github using gmail.com<mailto:hpages.on.github using gmail.com>

This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
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