[Bioc-devel] Acceptable dataset origins besides ExperimentHub

Tue Nov 10 13:34:09 CET 2020

Including this data should be okay.  The benefit of the ExperimentHub package would be to allow broader use of the data beyond your package to the Bioconductor community at large.    If you include the data from the site,  I would strongly, strongly suggest implementing a caching mechanism (ExperimentHub does this already in the backend)  so that if the public server goes down or has connectivity issues, any previously cached version could be utilized  (I'm bias but see BiocFileCache)

Lori Shepherd

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 Sean Davis <seandavi using gmail.com>
Sent: Tuesday, November 10, 2020 7:29 AM
To: Hector Gracia <hgracia using ibecbarcelona.eu>
Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Acceptable dataset origins besides ExperimentHub

Hi, Hector.

While an "unofficial" answer, there are many packages that access data from
public repositories, so using an EBI-supported repository and FTP site
seems perfectly acceptable to me.

Sean

ᐧ

On Tue, Nov 10, 2020 at 5:54 AM Hector Gracia <hgracia using ibecbarcelona.eu>
wrote:

> Recently our package AlpsNMR was accepted in Bioconductor
> https://secure-web.cisco.com/1QVyrCOoYojsO56K9awpCpiKlq4s6e6G9Ge_d2An_SuDgWlzM-MlYzxEysc-Y7SuG5Udcl6X2SKaZpUe9Z9D3S36GdqsSexPj2VVXSG9UoIvIzyHGV1C4gmIsQ2OyggbYCLelhaW5Vhk_tOZqQg1t_OLQCIOwM7k05edN1JtOMDMObKi0JG8SRt66UgRyG_urIe_hcCt17o6dwDheJBapQQLY6zEtlcij57JGzGB6CtgnKsuPzV7vBxNUbl85mCu83TbmuFPOWJRTm2Otyw2BeeWgZapUluBSXDYnNSe_iJ_3sqY815LFDgEFuZ1Ry1yZyw98GWjzUy7S1rEl4_bMuQ/https%3A%2F%2Fbioconductor.org%2Fpackages%2Fdevel%2Fbioc%2Fhtml%2FAlpsNMR.html
>
> For pass the review process we had to remove a dataset that was stored in
> Dropbox and that was used in one long tutorial about the package.
>
> Besides create an ExperimentHub package with this data, is there other
> ways to include this data in the package tutorial?
>
> I ask it because the dataset is public available in metabolights ftp and i
> like to know if this ftp can be considered as dedicated server that ensure
> logevity of the data
> ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS242/
>
> Or if the only way to do this is create a data package in ExperimentHub
>
> Thanks
>
> Enviado desde Correo<https://secure-web.cisco.com/1t5lpRsDmmRl-UbsUQFQ7DOM21FbgmkgZzwxGYdyfF5SRxrcVfxJlXqWxYWh3_WRoyy-NdPEKRE-zdJlEg4d5txDJLEra279O45g0wgQ5Nf00Iihh2s_xAOfBkmFHtAGu4THRshFQntMsO4eH8wV5FeYsUowQgfZVmVKfwUxIBdnrL2Go-eJeUUV2IyyycGieQdJT4oWO90NfkugTD5AJMiIs-gQU6KF5rIZMgqmEFZV-PvECRUni7qQFsL9x9mRjrn6sQ901POibI0kdTi-n-qLmhQwI8X4bBt0Ux-91sb0lRhxPeNk7N3cpYIVi7wTvOuaV1S-xz2exABKjAN5EyQ/https%3A%2F%2Fgo.microsoft.com%2Ffwlink%2F%3FLinkId%3D550986> para
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--
Sean Davis, MD, PhD
Center for Cancer Research
National Cancer Institute
National Institutes of Health
Bethesda, MD 20892
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