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 Hervé Pagès <hpages.on.git...@gmail.com> wrote: > 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.sheph...@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-boun...@r-project.org> on behalf of > >>> Burak > >>> Ogan Mancarci <ogan.mancar...@gmail.com> > >>> *Sent:* Wednesday, September 28, 2022 9:17 AM > >>> *To:* bioc-devel@r-project.org <bioc-devel@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@r-project.org mailing list > >>> > >>> > https://secure-web.cisco.com/1T5fXNWrq0wVkhsBGGZem_PrfqZL4JVbxk93lJB7cvCmSzN0HQXSMpdqsrdB-M-09zasav4vj733ww5BnQASs1jdsouSO0jb4woXH7k0uksmqx3BhiCXJy0Mwx7Lm3Y-CZdMcl-wRht_iwp5HSLm92GQ0X9FlCbqajgbnLRL79fA6nWZAIFiGim4shu4ZdLRn1HpNCM-UApMLDl1YReeF_UVn6EWI1QphpP--G8sq4j0nYkOefHddWPyHlTNwCg-f2aZd94WzVyCs9rzrmaF54N8FmJ-RTYeRHbVsmsWez047xQCe1sEkuv5HUjkC8Wqy/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel > >>> > >>> > >>> > >>> 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. > >> [[alternative HTML version deleted]] > >> > >> _______________________________________________ > >> Bioc-devel@r-project.org mailing list > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > -- > Hervé Pagès > > Bioconductor Core Team > hpages.on.git...@gmail.com > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
