[Bioc-devel] EXTERNAL: Accessing package citation info programmatically without running R?

[Ryan Thompson]

Hi again,

I just had a thought. Would it be possible to extend the citation pages
that you linked to also provide the bibtex source at a similar URL, e.g.
http://bioconductor.org/packages/3.7/bioc/citations/BiocFileCache/bibtex.html
<http://bioconductor.org/packages/3.7/bioc/citations/BiocFileCache/citation.html>
 ?

Regards,

Ryan Thompson

On Tue, Apr 17, 2018 at 12:23 PM Ryan Thompson <rct at thompsonclan.org> wrote:

> I wasn't specific about what I meant by "structured" because I'm not
> certain what kind of citation data types CiteAs can handle, though I'd
> assume bibtex would probably be fine. It's possible that the unprocessed
> CITATION file might also be good enough (I'm not familiar with the format).
>
> On Tue, Apr 17, 2018 at 11:57 AM Marcel Ramos <
> Marcel.Ramos at roswellpark.org> wrote:
>
>> Hi Ryan,
>>
>> Thanks for pointing this out.
>>
>> I'm not sure what you mean by "structured" or "format". We do have
>> public facing citations
>> which can be found at:
>>
>> http://bioconductor.org/packages/3.7/bioc/citations/BiocFileCache/citation.html
>>
>> (Thanks Lori for locating these pages!)
>>
>>
>> And even with a web-browsable git repository (as you mentioned), one
>> would still only be able
>> to get the "unprocessed" CITATION file. The best way to programmatically
>> get these at the moment
>> is through the git repository via:
>>
>> git archive
>> --remote=git at git.bioconductor.org:packages/MultiAssayExperiment.git \
>>    HEAD inst/CITATION | tar -xO inst/CITATION > citation.txt
>>
>> although, we would have to provide the CiteAs service with a key for
>> read-only access.
>>
>> Best regards,
>>
>> Marcel
>>
>>
>> On 04/17/2018 12:44 PM, Ryan Thompson wrote:
>> > There's a nice online tool called CiteAs which tries to figure out the
>> > proper citation for a given URL. I've recently helped the author to add
>> > support for extracting the DOI from Bioconductor package information
>> pages:
>> > https://github.com/Impactstory/citeas-api/issues/12
>> >
>> > This is a good start, but is suboptimal, since some many packages have
>> > actual published articles which should be used as the canonical citation
>> > instead of the package's URL. However, I'm not sure how to get this
>> > citation information in a structured format short of running R and
>> > installing the package, which isn't really an option for a web service
>> like
>> > this, which wants to return a result quickly. Does anyone know a good
>> way
>> > to access this info?
>> >
>> > Thanks,
>> >
>> > Ryan Thompson
>> >
>> >       [[alternative HTML version deleted]]
>> >
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>>
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