On Fri, Jan 5, 2018 at 10:02 AM, Nathan Sheffield <nat...@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 <lg...@cam.ac.uk> > > Sent: Thursday, October 19, 2017 3:10:52 PM > > To: bioc-devel@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 > >> > >> > >> 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 > > > > -- > > Laurent Gatto | @lgatt0 > > http://cpu.sysbiol.cam.ac.uk/ > > http://lgatto.github.io/ > > > > > > 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 > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel -- 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 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
