From mboxrd@z Thu Jan 1 00:00:00 1970 From: John Kitchin Subject: Re: Managing bibtex database using org-mode? Date: Mon, 2 Jun 2014 13:31:35 -0400 Message-ID: References: <5369F4E8.3020807@gmail.com> <587A9279-A389-4A3F-808D-1E090741DD98@agrarianresearch.org> <538C600E.1000706@gmail.com> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary=e89a8ff2537858d10004faddc4f4 Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:37361) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1WrW5D-0004yK-Ks for emacs-orgmode@gnu.org; Mon, 02 Jun 2014 13:31:41 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1WrW5B-0001TC-7u for emacs-orgmode@gnu.org; Mon, 02 Jun 2014 13:31:39 -0400 Received: from mail-pa0-x235.google.com ([2607:f8b0:400e:c03::235]:52349) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1WrW5A-0001Sv-TW for emacs-orgmode@gnu.org; Mon, 02 Jun 2014 13:31:37 -0400 Received: by mail-pa0-f53.google.com with SMTP id lj1so3367823pab.12 for ; Mon, 02 Jun 2014 10:31:35 -0700 (PDT) In-Reply-To: <538C600E.1000706@gmail.com> 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-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: Leonard Avery Randall Cc: Richard Lawrence , org-mode mailing list , Vikas Rawal --e89a8ff2537858d10004faddc4f4 Content-Type: text/plain; charset=UTF-8 those look pretty useful. I have been working on some utilities to download bibtex entries from a doi in emacs, and also the pdf if you have permission, and the module knows how to do it. The code can be seen here: https://github.com/jkitchin/jmax/blob/master/user/doi-utils.el It is still a work in progress, but if you are lisp savvy it is hopefully readable. It still needs some documentation, and the function names may still change. I will probably integrate this code into an org-file to be tangled to create the el file and provide the documentation. The idea is to run M-x insert-bibtex-entry-from-doi RET some-doi and you will get a new cleaned bibtex entry at your cursor, the pdf will be downloaded and saved as bibtex-key.pdf, and an entry in a notes.org file. feedback would be welcomed! John ----------------------------------- John Kitchin Associate Professor Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803 http://kitchingroup.cheme.cmu.edu On Mon, Jun 2, 2014 at 7:29 AM, Leonard Avery Randall < leonard.a.randall@gmail.com> wrote: > Hi Vikas, > Sorry I did not reply earlier. Your original email prompted me to develop > a more functional workflow. > > I have developed a few functions that make organizing research much > easier. I have functions that reorganize, rename, and add links to pdfs, > search for and add links to pdfs that have been organized by other programs > (Papers2), import notes from Skim, rename org-bibtex headlines to a format > I find more useful (e.g. Author (year) Title), and do a few other things > that I find convenient. The renaming functions also look up crossrefs, and > the headline renaming function lets you know if they are missing. The > functions are partially documented and have a few customizable functions so > they can be set up for different systems. Also note that the pdf organizing > system uses the conventions of my old research organizing tool (Papers2) > but this can be modified without too much work. I have attached a file with > the functions. The bottom of the file also contains the variables that I > have set and hooks that I have added to make the functions integrate more > smoothly into my set up. They may serve as a guide if you choose to use > them. > > > Additionally, here is the capture template I use for bibtex entries, it is > based largely on Richard's but it has you import more bibtex info during > the main capture process, and uses a function to help you find crossrefs. > > ("r" "Reading" entry > (file+olp "~/Google-Drive/Personal-Projects/Bib/Readinglist.org" > "RLIST Inbox") > "** %^{Todo state|READ|FIND|PRINT|NOTES} [#%^{Priority|A|B|C}] > New Reading Entry %? %^{BIB_TITLE}p %^{BIB_AUTHOR}p %^{BIB_EDITOR}p > %^{BIB_YEAR}p %^{CUSTOM_ID}p %^g > :PROPERTIES: > :BIB_BTYPE: %^{Entry > type|book|article|inbook|bookinbook|incollection|suppbook|phdthesis|proceedings|inproceedings|booklet} > :ENTERED_ON: %U %(my-org-bibtex-crossref) > :END:" :prepend t) > > > When I have some time I will follow up to explain how the functions work > in more detail. In the mean time let me know if you have any questions. > > All best, > Leonard > > --e89a8ff2537858d10004faddc4f4 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
those look pretty useful. I have been = working on some utilities to download bibtex entries from a doi in emacs, a= nd also the pdf if you have permission, and the module knows how to do it. = The code can be seen here: https://github.com/jkitchin/jmax/blob/master/use= r/doi-utils.el

It is still a work in progress, but if you are lisp savvy it is h= opefully readable. It still needs some documentation, and the function name= s may still change. I will probably integrate this code into an org-file to= be tangled to create the el file and provide the documentation.

The idea is to run

M-x insert-bibtex-entry-from-doi RET so= me-doi

and you will get a new cleaned bibtex entry at your cur= sor, the pdf will be downloaded and saved as bibtex-key.pdf, and an entry i= n a notes.org file.

feedback would be welcomed!



John

---------------------------------= --
John Kitchin
Associate Professor
Doherty Hall A207F
Departme= nt of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
http://kitchingr= oup.cheme.cmu.edu



On Mon, Jun 2, 2014 at 7:29 AM, Leonard = Avery Randall <leonard.a.randall@gmail.com> wrote:=
Hi=20 Vikas,
Sorry I did not reply earlier. Your original email prompted me to develop a more functional workflow.

I have developed a few=20 functions that make organizing research much easier. I have functions=20 that reorganize, rename, and add links to pdfs, search for and add links to pdfs that have been organized by other programs (Papers2), import=20 notes from Skim, rename org-bibtex headlines to a format I find more=20 useful (e.g. Author (year) Title), and do a few other things that I find convenient. The renaming functions also look up crossrefs, and the=20 headline renaming function lets you know if they are missing. The=20 functions are partially documented and have a few customizable functions so they can be set up for different systems. Also note that the pdf=20 organizing system uses the conventions of my old research organizing=20 tool (Papers2) but this can be modified without too much work. I have=20 attached a file with the functions. The bottom of the file also contains the variables that I have set and=20 hooks that I have added to make the functions integrate more smoothly=20 into my set up. They may serve as a guide if you choose to use them.=C2=A0 =


Additionally, here is the capture template I use for bibtex entries, it is based=20 largely on Richard's but it has you import more bibtex info during the= =20 main capture process, and uses a function to help you find crossrefs.

<= span style=3D"font-family:monospace">("r" "Reading" ent= ry
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0 (file+olp "~/Google-Drive/Personal-Projects/Bib/Readinglist.org"= "RLIST Inbox")
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 "*= * %^{Todo=20 state|READ|FIND|PRINT|NOTES} [#%^{Priority|A|B|C}] New Reading Entry %?=20 %^{BIB_TITLE}p %^{BIB_AUTHOR}p %^{BIB_EDITOR}p %^{BIB_YEAR}p=20 %^{CUSTOM_ID}p %^g
:PROPERTIES:
:BIB_BTYPE: %^{Entry=20 type|book|article|inbook|bookinbook|incollection|suppbook|phdthesis|proceed= ings|inproceedings|booklet}
:ENTERED_ON: %U %(my-org-bibtex-crossref)
:END:" :prepend t)


When I have some time I=20 will follow up to explain how the functions work in more detail. In the=20 mean time let me know if you have any questions.=C2=A0

All best,Leonard


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