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Re: RRID -> SciCrunch (Was: [libtfbs-perl] 01/01: Update metadata; add SciCrunch ID.)



2017-10-25 14:34 GMT+03:00 Steffen Möller <steffen_moeller@gmx.de>:

On 25.10.17 10:56, Michael Crusoe wrote:
> Sorry, I missed the bit where we are deprecating RRID. Can someone
> explain?

Because of https://arxiv.org/ftp/arxiv/papers/1707/1707.03659.pdf and
some web googling from which I gathered that the "Research Resource
IDentifiers" are not only provided by SciCrunch. Admittedly, I fail to
find that page now that I want to find it :o/

There is no conflict here. scicrunch.org is the post-pilot phase of what is described in that paper. 
 

Personally, I could not care less, let those catalog providers fight
that out among themselves. However, I find that the notion of SciCrunch
clearly identifies the provenance of that information, while "RRID" to
me is more of a concept coined by (https://www.force11.org), not a
provider. And with several initiatives following the same purpose, I
found that by using SciCrunch not RRID, we would be the most
provider-neutral. And then again, it is only something local to the
Debian packaging, not publicly visible, so nobody should truly care and
the use of SciCrunch imho serves us best on a technical level.

RRIDs share a single name space that allow for multiple providers, sci crunch being the current main provider for software tools and databases and other registries responsible for the other types. By referring to RRIDs generically then there is no conflict.

See https://www.ebi.ac.uk/miriam/main/datatypes/MIR:00000558 for an overview

Please rename this field to RRID, or better yet just have a list of URIs like we do in CWL so you don't have to care if it is a RRID, DOI or whatever :-)

http://www.commonwl.org/v1.0/CommandLineTool.html#SoftwarePackage


 

The https://www.force2017.org/ starts today in Berlin which should
gather people who know best - is anybody following this list attending?

Steffen


>
> 2017-10-22 14:34 GMT+03:00 Steffen Möller <steffen_moeller@gmx.de
> <mailto:steffen_moeller@gmx.de>>:
>
>     Args, I have only now updated
>
>     https://wiki.debian.org/UpstreamMetadata
>     <https://wiki.debian.org/UpstreamMetadata>
>
>     to reference SciCrunch by their name.
>
>     Many thanks and sorry
>
>     Steffen
>
>     On 22.10.17 12:20, Andreas Tille wrote:
>     > Hi Charles,
>     >
>     > wasn't Steffen just doing heaps of uploads with
>     >
>     > - - Name: RRID
>     > + - Name: SciCrunch
>     >
>     > As far as I understood we now are deprecating RRID.  Should the
>     > UDD importer warn about this?
>     >
>     > Kind regards
>     >
>     >      ANdreas.
>     >
>     > On Sun, Oct 22, 2017 at 08:20:50AM +0000, Charles Plessy wrote:
>     >> This is an automated email from the git hooks/post-receive script.
>     >>
>     >> plessy pushed a commit to branch master
>     >> in repository libtfbs-perl.
>     >>
>     >> commit b070d2137c24b20e577107ae6b5bda6ef78e9800
>     >> Author: Charles Plessy <plessy@debian.org
>     <mailto:plessy@debian.org>>
>     >> Date:   Sun Oct 22 17:20:06 2017 +0900
>     >>
>     >>     Update metadata; add SciCrunch ID.
>     >> ---
>     >>  debian/upstream/metadata | 8 +++++---
>     >>  1 file changed, 5 insertions(+), 3 deletions(-)
>     >>
>     >> diff --git a/debian/upstream/metadata b/debian/upstream/metadata
>     >> index 5c3740b..900ee5a 100644
>     >> --- a/debian/upstream/metadata
>     >> +++ b/debian/upstream/metadata
>     >> @@ -1,4 +1,4 @@
>     >> -Contact: Boris.Lenhard at bccs.uib.no <http://bccs.uib.no>
>     >> +Contact: b.lenhard at imperial.ac.uk <http://imperial.ac.uk>
>     >>  Homepage: http://tfbs.genereg.net/
>     >>  Name: TFBS
>     >>  Reference:
>     >> @@ -12,6 +12,8 @@ Reference:
>     >>   Number: 8
>     >>   Pages: 1135-1136
>     >>   Year: 2002
>     >> - URL:
>     http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/8/1135
>     <http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/8/1135>
>     >> + URL:
>     https://github.com/ComputationalRegulatoryGenomicsICL/TFBS.git
>     <https://github.com/ComputationalRegulatoryGenomicsICL/TFBS.git>
>     >>  Repository: http://www.ii.uib.no/svn/lenhard/TFBS/
>     <http://www.ii.uib.no/svn/lenhard/TFBS/>
>     >> -Watch: http://tfbs.genereg.net/TFBS-(.*)\.tar\.gz
>     <http://tfbs.genereg.net/TFBS-(.*)\.tar\.gz>
>     >> +Registry:
>     >> + - Name: RRID
>     >> +   Entry: SCR_015774
>     >>
>     >> --
>     >> Alioth's /usr/local/bin/git-commit-notice on
>     /srv/git.debian.org/git/debian-med/libtfbs-perl.git
>     <http://git.debian.org/git/debian-med/libtfbs-perl.git>
>     >>
>     >> _______________________________________________
>     >> debian-med-commit mailing list
>     >> debian-med-commit@lists.alioth.debian.org
>     <mailto:debian-med-commit@lists.alioth.debian.org>
>     >>
>     http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
>     <http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit>
>     >>
>
>
>
>
> --
> Michael R. Crusoe
> Co-founder & Lead,
> Common Workflow Language project <http://www.commonwl.org/>
> https://impactstory.org/u/0000-0002-2961-9670
> mrc@commonwl.org <mailto:mrc@commonwl.org>
> +1 480 627 9108



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