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

[Nathan Sheffield]

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}}

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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