[Bioc-devel] EXTERNAL: Re: DOI for packages

[Sean Davis]

On Fri, Jan 5, 2018 at 10:02 AM, Nathan Sheffield <nathan at code.databio.org>
wrote:

> Hi,
>
> Thanks for the package DOIs. I have a question about citation formats
> from these DOIs.
>
> When using the bioconductor DOIs to programatically pull a citation from
> DOI providers in bibtex format, the author field seems to be formatted
> incorrectly. I don't really know how the information is given to the
> provider, or how that is formatted and parsed, but there seems to be a
> hiccup somewhere. For example, if you take the AnnotationHub DOI:
>
> 10.18129/B9.bioc.AnnotationHub
> <https://doi.org/doi:10.18129/B9.bioc.AnnotationHub>
>
> And paste this into the DOI citation formatter at crosscite
> (https://citation.crosscite.org/), with bibtex formatting style, the
> result is:
>
> @article{Martin Morgan [Cre], Marc Carlson [Ctb], Dan Tenenbaum [Ctb],
> Sonali Arora [Ctb]_2017, title={AnnotationHub},
> DOI={10.18129/b9.bioc.annotationhub}, publisher={Bioconductor},
> author={Martin Morgan [Cre], Marc Carlson [Ctb], Dan Tenenbaum [Ctb],
> Sonali Arora [Ctb]}, year={2017}}
>

We should be able to fix this. The parsing to create DOIs was a first pass,
so it deserves some effort for cleanup. If you have thoughts, the (very
simple) code for producing the DOI entry is here:

https://github.com/seandavi/BiocPkgTools/blob/master/R/newBiocPkgDOI.R#L51

Thanks for the report.

Sean



>
> When using the jabref DOI puller, I get the same bibtex:
>
> @Misc{[Cre]2017,
>    author    = {Martin Morgan [Cre], Marc Carlson [Ctb], Dan Tenenbaum
> [Ctb], Sonali Arora [Ctb]},
>    title     = {AnnotationHub},
>    year      = {2017},
>    doi       = {10.18129/b9.bioc.annotationhub},
>    pages     = {-},
>    publisher = {Bioconductor},
>    timestamp = {2018-01-05},
> }
>
> Jabref doesn't correctly parse this bibtex because the author field is
> not formatted correctly in bibtex format. See this page for an
> explanation: http://www.tex.ac.uk/FAQ-manyauthor.html
>
> This also leads to the really strange default bibtex keys. This
> indicates that however the metadata is getting sent to the provider may
> be incorrect, because it's just treating that author field as a single
> string so it's not getting parsed correctly into alternative citation
> formats. It strikes me that the [Cre]/[Ctb] flags would probably need to
> be passed in a separate field, and the authors seem to be not passed in
> correctly as individuals but rather as a concatenated string, somehow.
>
> This could either be a problem with the way bioconductor is passing
> metadata along, or perhaps it's a problem with crosscite or something?
> I'm not sure. Any thoughts?
>
> Nathan Sheffield, PhD
> Assistant Professor
> Center for Public Health Genomics
> University of Virginia
> www.databio.org
>
> On 10/19/2017 03:19 PM, Shepherd, Lori wrote:
> > Many Thanks to Sean Davis for coming up with how to generate and
> providing the infastructure!
> >
> >
> > Lori Shepherd
> >
> > Bioconductor Core Team
> >
> > Roswell Park Cancer Institute
> >
> > Department of Biostatistics & Bioinformatics
> >
> > Elm & Carlton Streets
> >
> > Buffalo, New York 14263
> >
> > ________________________________
> > From: Laurent Gatto <lg390 at cam.ac.uk>
> > Sent: Thursday, October 19, 2017 3:10:52 PM
> > To: bioc-devel at r-project.org
> > Cc: Shepherd, Lori
> > Subject: EXTERNAL: Re: [Bioc-devel] DOI for packages
> >
> >
> > On 19 October 2017 13:22, Shepherd, Lori wrote:
> >
> >> Hello Bioconductor,
> >>
> >> We have added DOI's for packages on Bioconductor package landing
> >> pages. The DOI will get generated automatically when a package is
> >> accepted to Bioconductor. This is the recommended reference to use for
> >> publication/citations/etc.  The DOI link should automatically redirect
> >> to the current release version of a package (or devel if the package
> >> is not yet in release).
> > Thank you for this.
> >
> > Are there any plans to add the DOI to the DESCRIPTION file and
> > automatically include it to the default citation() output?
> >
> > Laurent
> >
> >> Thank you,
> >>
> >>
> >>
> >> Lori Shepherd
> >>
> >> Bioconductor Core Team
> >>
> >> Roswell Park Cancer Institute
> >>
> >> Department of Biostatistics & Bioinformatics
> >>
> >> Elm & Carlton Streets
> >>
> >> Buffalo, New York 14263
> >>
> >>
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> >
> > --
> > Laurent Gatto | @lgatt0
> > http://cpu.sysbiol.cam.ac.uk/
> > http://lgatto.github.io/
> >
> >
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-- 
Sean Davis, MD, PhD
Center for Cancer Research
National Cancer Institute
National Institutes of Health
Bethesda, MD 20892
https://seandavi.github.io/
https://twitter.com/seandavis12

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