[O] Re: zotero (or mendeley) integration with org
Alan E. Davis lngn...@gmail.com writes:
Is it possible to use org babel to extract bibtex entries from file of
notes to a *.bib file?
Yes, you can use babel's tangling facilities to extract bibtex entries
enclosed in source blocks.
#+begin_src bibtex :tangle history.bib
@InCollection{levi2001_microhistory,
author = {Levi, Giovanni},
title ={On Microhistory},
editor = {Peter Burke},
booktitle ={New Perspectives on Historical Writing},
address = {University Park, PA},
publisher ={Penn State Press},
year = 2001,
}
#+end_src
Calling org-babel-tangle-file will put this entry in the file
history.bib.
The stumbling point for me in saving bibtex sources is I don't see a
way to use the file as a bibtex *.bib file so as to use that as the
direct source for the publication. Perhaps this could be automated
with babel?
There are a few other routes.
1. Bibtex discards anything outside of an entry so you could symlink
your org file to something with a bib extension (e.g., notes.org -
notes.bib) and simply point latex/bibtex to that file.
2. You could instruct emacs to edit bib files with orgmode and use babel
and source blocks to enter items
(add-to-list 'auto-mode-alist
'(\\.\\(org\\|bib\\)$ . org-mode))
3. AFAICT, reftex is blissfully indifferent to non-bibtex data, so you
could use reftex to query your org files for citation keys. Then, you
could use reftex to generate a proper bib file with all entries cited
in your paper.
Best,
Matt
Re: [O] Re: zotero (or mendeley) integration with org
Alan E. Davis lngn...@gmail.com writes:
Is it possible to use org babel to extract bibtex entries from file of notes
to a *.bib file?
The stumbling point for me in saving bibtex sources is I don't see a way to
use the file as a bibtex *.bib file so as to use that as the direct source
for the publication. Perhaps this could be automated with babel?
Would tangling do what you want? Seems to work for me:
--8---cut here---start-8---
#+babel: :tangle hens.bib
* heat exchanger network synthesis
*** Rewriting grammar for HENS with splitting (Fraga, 2009)
#+begin_src bib
@article{fraga-2009a,
title = {A rewriting grammar for heat exchanger network structure
evolution with stream splitting},
volume = 41,
issn = {{0305-215X}},
doi = {10.1080/03052150903070153},
number = 9,
journal = {Engineering Optimization},
author = {Eric S. Fraga},
year = 2009,
pages = {813-831}
}
#+end_src
--8---cut here---end---8---
Put this in a file, t.org say, and hit =C-c C-v t= (=org-babel-tangle=)
and it should create =hens.bib=. Sorry for the self-citation here ;-)
You could also put the actual tangle destination on each src block, in
case you want to tangle to more than one file from the same org file.
--
: Eric S Fraga (GnuPG: 0xC89193D8FFFCF67D) in Emacs 24.0.50.1
: using Org-mode version 7.5 (release_7.5.128.ga9e6)
Re: [O] Re: zotero (or mendeley) integration with org
I have been enlightened. This closes a loop for my handling of literature. Thank you both. alan
Re: [O] Re: zotero (or mendeley) integration with org
Is it possible to use org babel to extract bibtex entries from file of notes to a *.bib file? The stumbling point for me in saving bibtex sources is I don't see a way to use the file as a bibtex *.bib file so as to use that as the direct source for the publication. Perhaps this could be automated with babel? Alan On Fri, Apr 1, 2011 at 6:13 AM, Matt Lundin m...@imapmail.org wrote: Stephen Eglen s.j.eg...@damtp.cam.ac.uk writes: Agreed. Google Scholar citations need very close proofreading, as they can be erroneous or poorly formatted. Thanks Matt - I'd agree with this, having seen oddities from google scholar. I emailed them ages ago about one problem (formatting of initials in author names), but never heard back... it is a pity that there is no mechanism for tidying up their references, as it seems to be the best thing out there that covers all the fields. Having said that, if google scholar can save me some typing, I'll happilyuse it as a starting point for a bibtex entry. I've just started using pdfmeat -- this is nice, as given a pdf, it outputs the corresponding bibtex entry from google scholar. Probably works similar to the way zotero does it, but can be used straight from the command line: http://code.google.com/p/pdfmeat/ Thanks for the link! That looks like a useful tool. accessed by bibsnarf are limited to math and sciences. Since I use biblatex together with the Chicago Manual of Style, any bibtex entry I clip has to be edited and tweaked substantially. (Indeed, manual editing is unavoidable when using biblatex.) If its not too tangential, why do you use biblatex -- is it the future for bibtex? I use biblatex because I use citation styles in the humanities (especially the Chicago Manual of Style). Biblatex and the chicago-notes package (both now part of TeXLive) handle Chicago Style footnotes and bibliographies beautifully, with an astounding number of options and flawless formatting -- but the bibtex entries are a bit fussier than standard bibtex. Best, Matt
[O] Re: zotero (or mendeley) integration with org
Agreed. Google Scholar citations need very close proofreading, as they can be erroneous or poorly formatted. Thanks Matt - I'd agree with this, having seen oddities from google scholar. I emailed them ages ago about one problem (formatting of initials in author names), but never heard back... it is a pity that there is no mechanism for tidying up their references, as it seems to be the best thing out there that covers all the fields. Having said that, if google scholar can save me some typing, I'll happilyuse it as a starting point for a bibtex entry. I've just started using pdfmeat -- this is nice, as given a pdf, it outputs the corresponding bibtex entry from google scholar. Probably works similar to the way zotero does it, but can be used straight from the command line: http://code.google.com/p/pdfmeat/ (Warning: I couldn't get one of the python dependencies, unidecode, to work on mac, but it does work on ubuntu for me.) accessed by bibsnarf are limited to math and sciences. Since I use biblatex together with the Chicago Manual of Style, any bibtex entry I clip has to be edited and tweaked substantially. (Indeed, manual editing is unavoidable when using biblatex.) If its not too tangential, why do you use biblatex -- is it the future for bibtex? Thanks for summarising your workflow, very helpful. Stephen
[O] Re: zotero (or mendeley) integration with org
Stephen Eglen s.j.eg...@damtp.cam.ac.uk writes: Agreed. Google Scholar citations need very close proofreading, as they can be erroneous or poorly formatted. Thanks Matt - I'd agree with this, having seen oddities from google scholar. I emailed them ages ago about one problem (formatting of initials in author names), but never heard back... it is a pity that there is no mechanism for tidying up their references, as it seems to be the best thing out there that covers all the fields. Having said that, if google scholar can save me some typing, I'll happilyuse it as a starting point for a bibtex entry. I've just started using pdfmeat -- this is nice, as given a pdf, it outputs the corresponding bibtex entry from google scholar. Probably works similar to the way zotero does it, but can be used straight from the command line: http://code.google.com/p/pdfmeat/ Thanks for the link! That looks like a useful tool. accessed by bibsnarf are limited to math and sciences. Since I use biblatex together with the Chicago Manual of Style, any bibtex entry I clip has to be edited and tweaked substantially. (Indeed, manual editing is unavoidable when using biblatex.) If its not too tangential, why do you use biblatex -- is it the future for bibtex? I use biblatex because I use citation styles in the humanities (especially the Chicago Manual of Style). Biblatex and the chicago-notes package (both now part of TeXLive) handle Chicago Style footnotes and bibliographies beautifully, with an astounding number of options and flawless formatting -- but the bibtex entries are a bit fussier than standard bibtex. Best, Matt
Re: [O] Re: zotero (or mendeley) integration with org
I just use refmode to insert bib citations into my org-files. Both Zotero and Mendeley can export bibtex files, so that's one method of semi-automating the process (Mendeley will automatically update the file for you - not sure about Zotero). On Wed, Mar 30, 2011 at 1:54 AM, Alan E. Davis lngn...@gmail.com wrote: It's in my mind to find a way to use orgmode for organizing pdfs and BibTex data. I haven't untangled storage of PDFs and linking to BibTeX, and I haven't found a solution to organizing it all through orgmode. An important piece of the puzzle, though, needs mention: cb2bib helps semi-automate making a BibTeX entry from a citation, or Google Scholar BibTeX output. I wonder if it would help to use orgmode for bibtex *.bib files. I think comments can be included in those files. Or does it also work the other way around, that any file can be used as a bibtex source database? Matt's workflow makes sense. Alan Davis
Re: [O] Re: zotero (or mendeley) integration with org
On Wed, Mar 30, 2011 at 10:54:58AM +1000, Alan E. Davis wrote: I wonder if it would help to use orgmode for bibtex *.bib files. I think comments can be included in those files. yes. there is a @comment command, but bibtex ignores everything that's not inside an @entry, @string or @preamble command, so that you could create an org file that contains bibtex entries and use that as your bibliography file. however, i don't know if biblatex+biber is equally forgiving. Or does it also work the other way around, that any file can be used as a bibtex source database? in essence yes, as long as it's a text file and contains valid bibtex entries. (note that bibtex isn't unicode-aware; i have no idea how bibtex reacts to files containing unicode characters in text it's ignoring.) -- Joost Kremers Life has its moments
[O] Re: zotero (or mendeley) integration with org
Matt Lundin m...@imapmail.org writes: Stephen Eglen s.j.eg...@damtp.cam.ac.uk writes: There was a mail-thread lastyear about zotero and integration with org. Now that there is an alpha release of 'org-standalone' http://www.zotero.org/blog/2011/02/ has anyone looked at whether this helps integrate org and zotero? I've not yet switched to a pdf manager (they're all stuffed into a folder, with a few subfolders, and the only meta-data is in the filename!), so I'd appreciate hearing what others to do to look after their pdfs. Mendeley is a possibility too (although syncing between machines is a must, and Mendeley doesn't offer that yet.) One option is to manage metadata in org-mode itself, relying on org-attach to store and preserve links to the pdf files. Bibtex source blocks can used to store bibliographical data for each pdf. I find the combination of emacs-w3m, google scholar, and org-mode to be an easier and more transparent way to manage bibtex data than an indirect route via Zotero or Mendeley. But I also prefer to edit all my bibtex data by hand. :) Recoll is great for indexing. I have a mess of spaghetti code I use to pull recoll results into a temporary org outline. I can then open the relevant files using org links. I'd be happy to share it if anyone is interested. Best, Matt I use something like the setup Matt describes as well (except I haven't played with Recoll). I use org-attach to keep documents organized; usually they're attached to a :noexport: top-level heading creatively called Documents, which contains the citation info and keeps my research/reading notes distinct from the paper I'm writing. Since my org files are themselves indexed and easily searchable, I've not felt the need for any collection management software beyond that. (For legal research it's particularly good, because I can get LEXIS to email me most legal texts as plaintext, which I then just add inline as subheadings to the Documents heading.) For bibliography generation, I use RefTeX to do my BibTeXing for me, and I use a pretty crude one bibliography database to one paper kind of system. Best, Will -- William Gardella J.D. Candidate Class of 2011, University of Pittsburgh School of Law
[O] Re: zotero (or mendeley) integration with org
[Matt and William's setup] I have looked for a good way to keep track of academic papers (pdfs) and Bibtex for a long time. I'd love to see a worg page on this topic. Meanwhile, I have found some sweet Bibtex-search interfaces for Emacs. These will query a academic search engine and can copy Bibtex entries directly to a .bib file. I found bibsnarfl[fn:1] being the most interesting, but a similar code is available for PubMed[fn:2]. Unfortunately, being limited to certain fields, I am personally not able to adopt either. It would be great to have an interface to a general academic search engine (Google Scholar, ugh?). Imagine the combination of a Emacs-powered interface to some search engine, a university network and some magic snip that would download a pdf, add it to a .bib-file (removing annoying entries and adding a sensible key), and making a nice, easy-to-browse Org-file. One day, maybe... –Rasmus Footnotes: [fn:1] http://www.emacswiki.org/emacs/bibsnarf.el [fn:2] http://www.bioinformatics.org/texmed/
[O] Re: zotero (or mendeley) integration with org
Rasmus rasmus.p...@gmail.com writes: [Matt and William's setup] I have looked for a good way to keep track of academic papers (pdfs) and Bibtex for a long time. I'd love to see a worg page on this topic. Meanwhile, I have found some sweet Bibtex-search interfaces for Emacs. These will query a academic search engine and can copy Bibtex entries directly to a .bib file. I found bibsnarfl[fn:1] being the most interesting, but a similar code is available for PubMed[fn:2]. Unfortunately, being limited to certain fields, I am personally not able to adopt either. It would be great to have an interface to a general academic search engine (Google Scholar, ugh?). Imagine the combination of a Emacs-powered interface to some search engine, a university network and some magic snip that would download a pdf, add it to a .bib-file (removing annoying entries and adding a sensible key), and making a nice, easy-to-browse Org-file. One day, maybe... –Rasmus Footnotes: [fn:1] http://www.emacswiki.org/emacs/bibsnarf.el [fn:2] http://www.bioinformatics.org/texmed/ That'd be a glorious way to do research. I can see it happening if a few of these academic database search engines and library websites decide to use some kind of free software infrastructure, or at least a relatively open and consistent API...alas, I don't know if library science is really evolving in that direction yet. -- William Gardella J.D. Candidate Class of 2011, University of Pittsburgh School of Law
[O] Re: zotero (or mendeley) integration with org
Rasmus rasmus.p...@gmail.com writes: [Matt and William's setup] I have looked for a good way to keep track of academic papers (pdfs) and Bibtex for a long time. I'd love to see a worg page on this topic. Meanwhile, I have found some sweet Bibtex-search interfaces for Emacs. These will query a academic search engine and can copy Bibtex entries directly to a .bib file. I found bibsnarfl[fn:1] being the most interesting, but a similar code is available for PubMed[fn:2]. Unfortunately, being limited to certain fields, I am personally not able to adopt either. It would be great to have an interface to a general academic search engine (Google Scholar, ugh?). Agreed. Google Scholar citations need very close proofreading, as they can be erroneous or poorly formatted. I would submit that one should never use a Google Scholar citation without checking it carefully against the article or book to which it refers. An advantage of Google Scholar, however, is that it offers skeletal bibtex entries for books and articles in a wide variety of fields, whereas many of the databases accessed by bibsnarf are limited to math and sciences. Since I use biblatex together with the Chicago Manual of Style, any bibtex entry I clip has to be edited and tweaked substantially. (Indeed, manual editing is unavoidable when using biblatex.) FWIW, here's my workflow: 1. Clip a bibtex citation or unformatted bibliographical data using org-capture and conkeror or emacs. (This generates a timestamp and a link to where I first found the reference --- very useful data for reviewing one's own research habits and sources.) 2. Download the pdf, if possible (or make a todo to get/read it later). 3. While in the capture buffer, use org-attach to move the pdf quickly from ~/Downloads to the attachments directory (this is much faster than it sounds). 4. Create or correct a bibtex source block within the org entry. 5. Make a TODO to read the pdf. :) Later, when I read the document, I proofread the bibtex entry once again and call a function that moves it to a centralized bibtex file, leaving a link in its place. As a rule, any citation that goes into my official bibtex file *must* be correct and complete. Reftex, another of Carsten's ingenious creations, is very handy for creating links to the citation while taking notes. For my own purposes, there would be little point in automating this process, as any pdf I download needs to be inspected manually and any bibtex entry I clip needs to be proofread and tweaked. The process itself forces me to check every citation for accuracy. Best, Matt
Re: [O] Re: zotero (or mendeley) integration with org
It's in my mind to find a way to use orgmode for organizing pdfs and BibTex data. I haven't untangled storage of PDFs and linking to BibTeX, and I haven't found a solution to organizing it all through orgmode. An important piece of the puzzle, though, needs mention: cb2bib helps semi-automate making a BibTeX entry from a citation, or Google Scholar BibTeX output. I wonder if it would help to use orgmode for bibtex *.bib files. I think comments can be included in those files. Or does it also work the other way around, that any file can be used as a bibtex source database? Matt's workflow makes sense. Alan Davis
[O] Re: zotero (or mendeley) integration with org
At Sat, 26 Mar 2011 15:47:44 +, Stephen Eglen wrote: There was a mail-thread lastyear about zotero and integration with org. Now that there is an alpha release of 'org-standalone' http://www.zotero.org/blog/2011/02/ has anyone looked at whether this helps integrate org and zotero? I've not yet switched to a pdf manager (they're all stuffed into a folder, with a few subfolders, and the only meta-data is in the filename!), so I'd appreciate hearing what others to do to look after their pdfs. Mendeley is a possibility too (although syncing between machines is a must, and Mendeley doesn't offer that yet.) Hi Stephen, Re. zotero-plain [1] integration with Zotero standalone, it would depend on what external interface Zotero standalone is presenting for integration with external programs (e.g. the Chrome or Safari extensions), which is not at all clear to me. zotero-plain currently depends on mozrepl, which I do not think would distributed with Zotero standalone. However, with a few modifications it should be possible to get zotero-plain to work with the zotero.org web API, which would provide most of the benefits of Zotero standalone, although you would be relying on a 3rd party service. best, Erik 1. http://e6h.org/~egh/hg/zotero-plain/ Sent from my free software system http://fsf.org/.
[O] Re: zotero (or mendeley) integration with org
Stephen Eglen s.j.eg...@damtp.cam.ac.uk writes: There was a mail-thread lastyear about zotero and integration with org. Now that there is an alpha release of 'org-standalone' http://www.zotero.org/blog/2011/02/ has anyone looked at whether this helps integrate org and zotero? I've not yet switched to a pdf manager (they're all stuffed into a folder, with a few subfolders, and the only meta-data is in the filename!), so I'd appreciate hearing what others to do to look after their pdfs. Mendeley is a possibility too (although syncing between machines is a must, and Mendeley doesn't offer that yet.) One option is to manage metadata in org-mode itself, relying on org-attach to store and preserve links to the pdf files. Bibtex source blocks can used to store bibliographical data for each pdf. I find the combination of emacs-w3m, google scholar, and org-mode to be an easier and more transparent way to manage bibtex data than an indirect route via Zotero or Mendeley. But I also prefer to edit all my bibtex data by hand. :) Recoll is great for indexing. I have a mess of spaghetti code I use to pull recoll results into a temporary org outline. I can then open the relevant files using org links. I'd be happy to share it if anyone is interested. Best, Matt
[O] Re: zotero (or mendeley) integration with org
Stephen Eglen wrote: I've not yet switched to a pdf manager (they're all stuffed into a folder, with a few subfolders, and the only meta-data is in the filename!), so I'd appreciate hearing what others to do to look after their pdfs. Maybe look at tracker [assuming linux] http://projects.gnome.org/tracker/ ? More generally http://www.wikinfo.org/index.php/Comparison_of_desktop_search_software
Re: [O] Re: zotero (or mendeley) integration with org
On Sun, 27 Mar 2011 08:42:19 +0530 Rustom Mody rustompm...@gmail.com wrote: Stephen Eglen wrote: I've not yet switched to a pdf manager (they're all stuffed into a folder, with a few subfolders, and the only meta-data is in the filename!), so I'd appreciate hearing what others to do to look after their pdfs. Maybe look at tracker [assuming linux] http://projects.gnome.org/tracker/ ? More generally http://www.wikinfo.org/index.php/Comparison_of_desktop_search_software or Recoll (on GNU/Linux) -- Suvayu Open source is the future. It sets us free.
