Using org-ref to automatically download articles from Pubmed that satisfies a given search term

Using org-ref to automatically download articles from Pubmed that satisfies a given search term

[Doyley, Marvin M.]

Hi there,

I am in the process of writing a broad literature review and was wondering if there is a way to get org-ref to search Pubmed and automatically pull (pdf, abstracts, etc) all the papers that satisfy a given  search terms (year range, keyword, authors) ?

Thanks,

M

Re: Using org-ref to automatically download articles from Pubmed that satisfies a given search term

[John Kitchin]

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There is a command in org-ref-pubmed that will download a bibtex entry from
a pmid: pubmed-insert-bibtex-from-pmid. There is also the commands:
pubmed-simple-search which will prompt for a query and open the search in
pubmed, the command "pubmed" which just opens the pubmed site, and
"pubmed-advanced" which opens the advances search page.

There isn't however, anything as sophisticated as you want for pubmed. You
would have to use it to get the DOIs, and then use the doi-add-bibtex-entry
function to get the bibtex entry and (if it knows how) the pdf.

John

-----------------------------------
Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu


On Mon, Jan 8, 2018 at 3:32 PM, Doyley, Marvin M. <m.doyley@rochester.edu>
wrote:

> Hi there,
>
> I am in the process of writing a broad literature review and was wondering
> if there is a way to get org-ref to search Pubmed and automatically pull
> (pdf, abstracts, etc) all the papers that satisfy a given  search terms
> (year range, keyword, authors) ?
>
> Thanks,
>
> M
>
>
>
>
>
>

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Re: Using org-ref to automatically download articles from Pubmed that satisfies a given search term

[Doyley, Marvin M.]

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Thanks John,
I really appreciate this.

Cheers,
M
> On Jan 8, 2018, at 5:37 PM, John Kitchin <jkitchin@andrew.cmu.edu> wrote:
> 
> There is a command in org-ref-pubmed that will download a bibtex entry from a pmid: pubmed-insert-bibtex-from-pmid. There is also the commands: pubmed-simple-search which will prompt for a query and open the search in pubmed, the command "pubmed" which just opens the pubmed site, and "pubmed-advanced" which opens the advances search page.
> 
> There isn't however, anything as sophisticated as you want for pubmed. You would have to use it to get the DOIs, and then use the doi-add-bibtex-entry function to get the bibtex entry and (if it knows how) the pdf.
> 
> John
> 
> -----------------------------------
> Professor John Kitchin
> Doherty Hall A207F
> Department of Chemical Engineering
> Carnegie Mellon University
> Pittsburgh, PA 15213
> 412-268-7803
> @johnkitchin
> http://kitchingroup.cheme.cmu.edu <https://urldefense.proofpoint.com/v2/url?u=http-3A__kitchingroup.cheme.cmu.edu&d=DwMFaQ&c=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU&r=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU&m=H6YoFReSxOsGNCWFjFOb7BY7fkgnr_5tlTfCQEW7ck8&s=xak0y049_VKcjFA7_x91GoPfe7gxb85PFs6tKYiZrfI&e=>
> 
> 
> On Mon, Jan 8, 2018 at 3:32 PM, Doyley, Marvin M. <m.doyley@rochester.edu <mailto:m.doyley@rochester.edu>> wrote:
> Hi there,
> 
> I am in the process of writing a broad literature review and was wondering if there is a way to get org-ref to search Pubmed and automatically pull (pdf, abstracts, etc) all the papers that satisfy a given  search terms (year range, keyword, authors) ?
> 
> Thanks,
> 
> M
> 
> 
> 
> 
> 
> 


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Re: Using org-ref to automatically download articles from Pubmed that satisfies a given search term

[John Kitchin]

You might also consider the crossref search.

M-x crossref-add-bibtex-entry

It will download a bibtex and pdf (if it knows how to). I doubt you can
do year range query, but certainly authors and keywords. It really
excels at freeform citations as the query.

Doyley, Marvin M. writes:

> Hi there,
>
> I am in the process of writing a broad literature review and was wondering if there is a way to get org-ref to search Pubmed and automatically pull (pdf, abstracts, etc) all the papers that satisfy a given  search terms (year range, keyword, authors) ?
>
> Thanks,
>
> M


-- 
Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu

Re: Using org-ref to automatically download articles from Pubmed that satisfies a given search term

[Doyley, Marvin M.]

Crossref-add-bibtex-entry is awesome. One quick question, how do you select multiple references ?

Cheers,
M

> On Jan 8, 2018, at 10:11 PM, John Kitchin <jkitchin@andrew.cmu.edu> wrote:
> 
> You might also consider the crossref search.
> 
> M-x crossref-add-bibtex-entry
> 
> It will download a bibtex and pdf (if it knows how to). I doubt you can
> do year range query, but certainly authors and keywords. It really
> excels at freeform citations as the query.
> 
> Doyley, Marvin M. writes:
> 
>> Hi there,
>> 
>> I am in the process of writing a broad literature review and was wondering if there is a way to get org-ref to search Pubmed and automatically pull (pdf, abstracts, etc) all the papers that satisfy a given  search terms (year range, keyword, authors) ?
>> 
>> Thanks,
>> 
>> M
> 
> 
> -- 
> Professor John Kitchin
> Doherty Hall A207F
> Department of Chemical Engineering
> Carnegie Mellon University
> Pittsburgh, PA 15213
> 412-268-7803
> @johnkitchin
> https://urldefense.proofpoint.com/v2/url?u=http-3A__kitchingroup.cheme.cmu.edu&d=DwIBAg&c=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU&r=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU&m=SvHYbzQWmnb9yyFa_ZsCzhc0a0UZZ2QycfE978DTDG8&s=_8S7VQ_YkQIojPf7ecqFGLP_cOZ0Fja9CqdHzFp9AQM&e= 

Re: Using org-ref to automatically download articles from Pubmed that satisfies a given search term

[John Kitchin]

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I think you can do that with C-spc.

John

-----------------------------------
Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu


On Tue, Jan 9, 2018 at 9:40 AM, Doyley, Marvin M. <m.doyley@rochester.edu>
wrote:

> Crossref-add-bibtex-entry is awesome. One quick question, how do you
> select multiple references ?
>
> Cheers,
> M
>
> > On Jan 8, 2018, at 10:11 PM, John Kitchin <jkitchin@andrew.cmu.edu>
> wrote:
> >
> > You might also consider the crossref search.
> >
> > M-x crossref-add-bibtex-entry
> >
> > It will download a bibtex and pdf (if it knows how to). I doubt you can
> > do year range query, but certainly authors and keywords. It really
> > excels at freeform citations as the query.
> >
> > Doyley, Marvin M. writes:
> >
> >> Hi there,
> >>
> >> I am in the process of writing a broad literature review and was
> wondering if there is a way to get org-ref to search Pubmed and
> automatically pull (pdf, abstracts, etc) all the papers that satisfy a
> given  search terms (year range, keyword, authors) ?
> >>
> >> Thanks,
> >>
> >> M
> >
> >
> > --
> > Professor John Kitchin
> > Doherty Hall A207F
> > Department of Chemical Engineering
> > Carnegie Mellon University
> > Pittsburgh, PA 15213
> > 412-268-7803
> > @johnkitchin
> > https://urldefense.proofpoint.com/v2/url?u=http-3A__
> kitchingroup.cheme.cmu.edu&d=DwIBAg&c=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9
> EI2eaqQZhHbOU&r=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BN
> Cy_RylYdxU&m=SvHYbzQWmnb9yyFa_ZsCzhc0a0UZZ2QycfE978DTDG8&s=_
> 8S7VQ_YkQIojPf7ecqFGLP_cOZ0Fja9CqdHzFp9AQM&e=
>
>

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Re: Using org-ref to automatically download articles from Pubmed that satisfies a given search term

[myglc2]

On 01/08/2018 at 20:32 Doyley, Marvin M. writes:
> I am in the process of writing a broad literature review and was
> wondering if there is a way to get org-ref to search Pubmed and
> automatically pull (pdf, abstracts, etc) all the papers that satisfy a
> given search terms (year range, keyword, authors) ?

Dunno/haven't used org-ref. FWIW a couple years ago I used
https://github.com/wash/pubmode to search pubmed. It works well.

HTH - George