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seandavi / BiocPkgTools

Computable build reports, package metadata, and download stats from the Bioconductor project
https://seandavi.github.io/BiocPkgTools/
MIT License
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Fix DOI to bib #12

Open seandavi opened 6 years ago

seandavi commented 6 years ago

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

seandavi commented 6 years ago

This issue, as well as #6, #7, and #9 may get some refactoring when the DOI system we are using changes. NCI let me know of the change, but we don't have a date just yet.