From mboxrd@z Thu Jan 1 00:00:00 1970 From: "Doyley, Marvin M." Subject: Re: Using org-ref to automatically download articles from Pubmed that satisfies a given search term Date: Mon, 8 Jan 2018 22:52:32 +0000 Message-ID: <34208F18-F727-4EC7-A657-62A96AE87FD0@ur.rochester.edu> References: <410D0E64-1A87-4EE8-AB9F-990292C3209A@ur.rochester.edu> Mime-Version: 1.0 Content-Type: multipart/signed; boundary="Apple-Mail=_F1904BC5-7A7C-404A-A52E-0F5343297AF9"; protocol="application/pgp-signature"; micalg=pgp-sha512 Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:50349) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1eYgHZ-0000WU-62 for emacs-orgmode@gnu.org; Mon, 08 Jan 2018 17:52:42 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1eYgHV-0001nx-2r for emacs-orgmode@gnu.org; Mon, 08 Jan 2018 17:52:41 -0500 Received: from mail-by2nam01on0131.outbound.protection.outlook.com ([104.47.34.131]:50195 helo=NAM01-BY2-obe.outbound.protection.outlook.com) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1eYgHU-0001mr-JE for emacs-orgmode@gnu.org; Mon, 08 Jan 2018 17:52:36 -0500 In-Reply-To: Content-Language: en-US List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Sender: "Emacs-orgmode" To: John Kitchin Cc: "emacs-orgmode@gnu.org" , "Doyley, Marvin M." --Apple-Mail=_F1904BC5-7A7C-404A-A52E-0F5343297AF9 Content-Type: multipart/alternative; boundary="Apple-Mail=_413F87DA-BBA8-4F91-80FD-828707012498" --Apple-Mail=_413F87DA-BBA8-4F91-80FD-828707012498 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Thanks John, I really appreciate this. Cheers, M > On Jan 8, 2018, at 5:37 PM, John Kitchin = wrote: >=20 > 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. >=20 > 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. >=20 > John >=20 > ----------------------------------- > 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 = >=20 >=20 > On Mon, Jan 8, 2018 at 3:32 PM, Doyley, Marvin M. = > wrote: > Hi there, >=20 > 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) ? >=20 > Thanks, >=20 > M >=20 >=20 >=20 >=20 >=20 >=20 --Apple-Mail=_413F87DA-BBA8-4F91-80FD-828707012498 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-ascii 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


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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