* zotero (or mendeley) integration with org
@ 2011-03-26 15:47 Stephen Eglen
2011-03-26 21:04 ` Cian
` (3 more replies)
0 siblings, 4 replies; 21+ messages in thread
From: Stephen Eglen @ 2011-03-26 15:47 UTC (permalink / raw)
To: emacs-orgmode; +Cc: Stephen Eglen
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.)
Stephen
^ permalink raw reply [flat|nested] 21+ messages in thread* Re: zotero (or mendeley) integration with org 2011-03-26 15:47 zotero (or mendeley) integration with org Stephen Eglen @ 2011-03-26 21:04 ` Cian 2011-03-26 21:06 ` Ramon Diaz-Uriarte ` (2 subsequent siblings) 3 siblings, 0 replies; 21+ messages in thread From: Cian @ 2011-03-26 21:04 UTC (permalink / raw) To: emacs-orgmode I use Mendeley and just set it up to export bibtex files. Then you can just reference those in org-mode using reftex. I think you can do something similar using zotero. It works okay. I don't annotate PDFs using Mendeley (I just write my notes in org-mode), so I'm not sure if you can access those somehow? But as a system for managing PDFs it's adequate. On Sat, Mar 26, 2011 at 3:47 PM, Stephen Eglen <S.J.Eglen@damtp.cam.ac.uk> 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.) > > Stephen > > ^ permalink raw reply [flat|nested] 21+ messages in thread
* Re: zotero (or mendeley) integration with org 2011-03-26 15:47 zotero (or mendeley) integration with org Stephen Eglen 2011-03-26 21:04 ` Cian @ 2011-03-26 21:06 ` Ramon Diaz-Uriarte 2011-03-28 9:14 ` Stephen Eglen 2011-03-28 17:06 ` Erik Hetzner 2011-03-29 3:32 ` Matt Lundin 3 siblings, 1 reply; 21+ messages in thread From: Ramon Diaz-Uriarte @ 2011-03-26 21:06 UTC (permalink / raw) To: Stephen Eglen; +Cc: emacs-orgmode Dear Stephen, [My ---long--- comments refer only to Mendeley, not org, so maybe this should be off-list]. On Sat, Mar 26, 2011 at 4:47 PM, Stephen Eglen <S.J.Eglen@damtp.cam.ac.uk> 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.) > I've been using Mendeley for about 9 months now, after spending a few weeks examining how Mendeley, Zotero, and some other options, fitted into my habits. Here are some comments about your questions: 1. Syncing: the "orthodox" Mendeley way allows for two options: a) you sync the database of the refs (not pdfs) via their servers; b) you also sync the pdfs, which will most likely require you to pay for storage in their servers if you have a decent number of pdfs. However, I do the syncing myself. I've used rsync, then Dropbox, and for the last four months Wuala. I sync the directory where the dbs are (~/.local/share/data/Mendeley Ltd./Mendeley Desktop) and the directory where I store my pdfs. I have had this set up for the 9 months, shared between four machines, and it works fine (I try not to have Mendeley open in more than one machine at the same time, to prevent problems, but have never run into any). 2. All pdfs into a folder with a few subfolders. In Mendeley you can have each reference under its own subdirectory with some limited flexibility for the naming of the subdirectories (author, date, title, etc). Its not ideal (e.g., I dislike spaces in directory names), but I like it better than Zotero's (names of subdirectories are a random string). Keeping each ref in its own directory allows me to store other stuff (e.g., code, suppl. mat, etc) in the same place as the pdf. Now, that said, I am not all that happy with Mendeley. To begin with, Mendeley is not free software. Zotero is, but the naming of directories and the lack of a built-in pdf editor were a no-go for me. Mendeley's pdf editor allows me to underline and add notes to pdfs. At least in Linux, adding comments and underlining pdfs is not yet well solved: evince currently allows comments in the devel. version, but no underlining. Okular allows comments and underlining, but stores them in ~/.kde/share/apps/okular, which I dislike (it seems very fragile), and in okular you cannot underline a single column in papers with multi-column setup (another no-go for me). However, with Mendeley's pdf editor/viewer you can only display one pdf at a time, which is a pain if you want to compare two or more papers side by side. In fact, Mendely's pdf viewer is rather under-powered compared to, say, okular (e.g., lack of keyboard shortcuts for viewing to page or width size, difference between scrolling and moving to next page, fast searching, etc). If I only need read-only access to the pdf, even from within Mendeley, I use another pdf viewer. I thought about going back to JabRef, and using recoll for searching over all of my pdf collection (I like recoll's search much more than Mendeley's one). But that leaves unsolved the pdf commenting issue. Also, I like the ease of adding papers with Mendeley (e.g., when searching in the web, or its generally successful extraction of metadata from a paper's pdf); in fact, I find adding papers is even easier with Zotero (and friendlier also if you add things like web pages, etc). I also looked into paperpile, but I find it to be much more beta than Mendeley, and so far less flexible in almost everything. So I'd also like to know how others are dealing with pdfs. Anyway, and in spite of my complaints, since about 9 months ago I have not printed a single paper. It is great to have all those pdfs synced among my machines, be able to search them quickly, and not carry around kilograms of dead trees. Best, R. > Stephen > > -- Ramon Diaz-Uriarte Structural Biology and Biocomputing Programme Spanish National Cancer Centre (CNIO) http://ligarto.org/rdiaz Phone: +34-91-732-8000 ext. 3019 Fax: +-34-91-224-6972 ^ permalink raw reply [flat|nested] 21+ messages in thread
* Re: zotero (or mendeley) integration with org 2011-03-26 21:06 ` Ramon Diaz-Uriarte @ 2011-03-28 9:14 ` Stephen Eglen 2011-03-28 14:07 ` brian powell 0 siblings, 1 reply; 21+ messages in thread From: Stephen Eglen @ 2011-03-28 9:14 UTC (permalink / raw) To: Ramon Diaz-Uriarte; +Cc: emacs-orgmode, Stephen Eglen Dear all, Thanks for the informative replies. I gave zotero a short-test yesterday,and in general liked what I found, although as it uses sql databases, it is moves away from my preference for plain text files to see everything in. I appreciate that sql may scale better, but I don't have huge databases. I think I'll continue to watch how the zotero standalone develops. In the meantime, it made me think a bit more about looking after pdf collections. I'll try out using org mode for annotating my pdfs, to see how that works. I had not seen recoll before, that certainly looks nice. Will feedback to the list if I have anything useful to add. Stephen ^ permalink raw reply [flat|nested] 21+ messages in thread
* Re: zotero (or mendeley) integration with org 2011-03-28 9:14 ` Stephen Eglen @ 2011-03-28 14:07 ` brian powell 0 siblings, 0 replies; 21+ messages in thread From: brian powell @ 2011-03-28 14:07 UTC (permalink / raw) To: Stephen Eglen; +Cc: emacs-orgmode It uses SQLite--Stephen: I'd consider myself a plaintext-whenever-possible sort of dude too; but, SQLite (used in ZOTERO) is a simple/short C program and its (last time I checked) extremely simple--for example there is only "left outer join". SQLite "databases" are very easy to work with and are often 1 simple, small, very portable file. I was reading some article yesterday: SQLite was ranked #1 in the top ten best/most useful software of all time. I understand your concern; and, often an SQL database is overkill and "NOSQL" seems in vogue right now--but SQLite is something you might really like--you can manipulate SQLite databases easily, like plaintext. I just tried ZOTERO too--very impressive. I'm a lot more used to using BibTeX though--which is purely plaintext; but, BibTeX can be a typing chore! On Mon, Mar 28, 2011 at 5:14 AM, Stephen Eglen <S.J.Eglen@damtp.cam.ac.uk> wrote: > Dear all, > > Thanks for the informative replies. I gave zotero a short-test > yesterday,and in general liked what I found, although as it uses sql > databases, it is moves away from my preference for plain text files to > see everything in. I appreciate that sql may scale better, but I don't > have huge databases. I think I'll continue to watch how the zotero > standalone develops. ^ permalink raw reply [flat|nested] 21+ messages in thread
* Re: zotero (or mendeley) integration with org 2011-03-26 15:47 zotero (or mendeley) integration with org Stephen Eglen 2011-03-26 21:04 ` Cian 2011-03-26 21:06 ` Ramon Diaz-Uriarte @ 2011-03-28 17:06 ` Erik Hetzner 2011-03-29 3:32 ` Matt Lundin 3 siblings, 0 replies; 21+ messages in thread From: Erik Hetzner @ 2011-03-28 17:06 UTC (permalink / raw) To: emacs-orgmode; +Cc: Stephen Eglen [-- Attachment #1: Type: text/plain, Size: 1294 bytes --] At Sat, 26 Mar 2011 15:47:44 +0000, 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/ [-- Attachment #2: Type: text/plain, Size: 53 bytes --] Sent from my free software system <http://fsf.org/>. ^ permalink raw reply [flat|nested] 21+ messages in thread
* Re: zotero (or mendeley) integration with org 2011-03-26 15:47 zotero (or mendeley) integration with org Stephen Eglen ` (2 preceding siblings ...) 2011-03-28 17:06 ` Erik Hetzner @ 2011-03-29 3:32 ` Matt Lundin 2011-03-29 7:21 ` William Gardella 2011-03-30 0:54 ` Alan E. Davis 3 siblings, 2 replies; 21+ messages in thread From: Matt Lundin @ 2011-03-29 3:32 UTC (permalink / raw) To: Stephen Eglen; +Cc: emacs-orgmode Stephen Eglen <S.J.Eglen@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 ^ permalink raw reply [flat|nested] 21+ messages in thread
* Re: zotero (or mendeley) integration with org 2011-03-29 3:32 ` Matt Lundin @ 2011-03-29 7:21 ` William Gardella 2011-03-29 10:55 ` Rasmus 2011-03-30 0:54 ` Alan E. Davis 1 sibling, 1 reply; 21+ messages in thread From: William Gardella @ 2011-03-29 7:21 UTC (permalink / raw) To: emacs-orgmode; +Cc: S.J.Eglen Matt Lundin <mdl@imapmail.org> writes: > Stephen Eglen <S.J.Eglen@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 ^ permalink raw reply [flat|nested] 21+ messages in thread
* Re: zotero (or mendeley) integration with org 2011-03-29 7:21 ` William Gardella @ 2011-03-29 10:55 ` Rasmus 2011-03-29 11:42 ` William Gardella 2011-03-29 13:14 ` Matt Lundin 0 siblings, 2 replies; 21+ messages in thread From: Rasmus @ 2011-03-29 10:55 UTC (permalink / raw) To: emacs-orgmode > [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/ ^ permalink raw reply [flat|nested] 21+ messages in thread
* Re: zotero (or mendeley) integration with org 2011-03-29 10:55 ` Rasmus @ 2011-03-29 11:42 ` William Gardella 2011-03-29 13:14 ` Matt Lundin 1 sibling, 0 replies; 21+ messages in thread From: William Gardella @ 2011-03-29 11:42 UTC (permalink / raw) To: emacs-orgmode Rasmus <rasmus.pank@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 ^ permalink raw reply [flat|nested] 21+ messages in thread
* Re: zotero (or mendeley) integration with org 2011-03-29 10:55 ` Rasmus 2011-03-29 11:42 ` William Gardella @ 2011-03-29 13:14 ` Matt Lundin 2011-03-31 11:39 ` Stephen Eglen 1 sibling, 1 reply; 21+ messages in thread From: Matt Lundin @ 2011-03-29 13:14 UTC (permalink / raw) To: Rasmus; +Cc: emacs-orgmode Rasmus <rasmus.pank@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 ^ permalink raw reply [flat|nested] 21+ messages in thread
* Re: zotero (or mendeley) integration with org 2011-03-29 13:14 ` Matt Lundin @ 2011-03-31 11:39 ` Stephen Eglen 2011-03-31 20:13 ` Matt Lundin 0 siblings, 1 reply; 21+ messages in thread From: Stephen Eglen @ 2011-03-31 11:39 UTC (permalink / raw) To: emacs-orgmode > 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 ^ permalink raw reply [flat|nested] 21+ messages in thread
* Re: zotero (or mendeley) integration with org 2011-03-31 11:39 ` Stephen Eglen @ 2011-03-31 20:13 ` Matt Lundin 2011-04-02 1:40 ` Alan E. Davis 0 siblings, 1 reply; 21+ messages in thread From: Matt Lundin @ 2011-03-31 20:13 UTC (permalink / raw) To: Stephen Eglen; +Cc: emacs-orgmode Stephen Eglen <S.J.Eglen@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 ^ permalink raw reply [flat|nested] 21+ messages in thread
* Re: Re: zotero (or mendeley) integration with org 2011-03-31 20:13 ` Matt Lundin @ 2011-04-02 1:40 ` Alan E. Davis 2011-04-02 13:19 ` Matt Lundin 2011-04-02 13:37 ` Eric S Fraga 0 siblings, 2 replies; 21+ messages in thread From: Alan E. Davis @ 2011-04-02 1:40 UTC (permalink / raw) To: Matt Lundin; +Cc: emacs-orgmode, Stephen Eglen [-- Attachment #1: Type: text/plain, Size: 2158 bytes --] 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 <mdl@imapmail.org> wrote: > Stephen Eglen <S.J.Eglen@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 > > [-- Attachment #2: Type: text/html, Size: 2882 bytes --] ^ permalink raw reply [flat|nested] 21+ messages in thread
* Re: zotero (or mendeley) integration with org 2011-04-02 1:40 ` Alan E. Davis @ 2011-04-02 13:19 ` Matt Lundin 2011-04-02 13:37 ` Eric S Fraga 1 sibling, 0 replies; 21+ messages in thread From: Matt Lundin @ 2011-04-02 13:19 UTC (permalink / raw) To: Alan E. Davis; +Cc: Stephen Eglen, emacs-orgmode "Alan E. Davis" <lngndvs@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 ^ permalink raw reply [flat|nested] 21+ messages in thread
* Re: Re: zotero (or mendeley) integration with org 2011-04-02 1:40 ` Alan E. Davis 2011-04-02 13:19 ` Matt Lundin @ 2011-04-02 13:37 ` Eric S Fraga 2011-04-02 14:13 ` Alan E. Davis 1 sibling, 1 reply; 21+ messages in thread From: Eric S Fraga @ 2011-04-02 13:37 UTC (permalink / raw) To: Alan E. Davis; +Cc: emacs-orgmode "Alan E. Davis" <lngndvs@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) ^ permalink raw reply [flat|nested] 21+ messages in thread
* Re: Re: zotero (or mendeley) integration with org 2011-04-02 13:37 ` Eric S Fraga @ 2011-04-02 14:13 ` Alan E. Davis 0 siblings, 0 replies; 21+ messages in thread From: Alan E. Davis @ 2011-04-02 14:13 UTC (permalink / raw) To: org-mode; +Cc: Matt Lundin [-- Attachment #1: Type: text/plain, Size: 99 bytes --] I have been enlightened. This closes a loop for my handling of literature. Thank you both. alan [-- Attachment #2: Type: text/html, Size: 116 bytes --] ^ permalink raw reply [flat|nested] 21+ messages in thread
* Re: Re: zotero (or mendeley) integration with org 2011-03-29 3:32 ` Matt Lundin 2011-03-29 7:21 ` William Gardella @ 2011-03-30 0:54 ` Alan E. Davis 2011-03-30 8:26 ` Cian 2011-03-30 14:34 ` Joost Kremers 1 sibling, 2 replies; 21+ messages in thread From: Alan E. Davis @ 2011-03-30 0:54 UTC (permalink / raw) To: Matt Lundin; +Cc: emacs-orgmode, Stephen Eglen [-- Attachment #1: Type: text/plain, Size: 631 bytes --] 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 > > > [-- Attachment #2: Type: text/html, Size: 892 bytes --] ^ permalink raw reply [flat|nested] 21+ messages in thread
* Re: Re: zotero (or mendeley) integration with org 2011-03-30 0:54 ` Alan E. Davis @ 2011-03-30 8:26 ` Cian 2011-03-30 14:34 ` Joost Kremers 1 sibling, 0 replies; 21+ messages in thread From: Cian @ 2011-03-30 8:26 UTC (permalink / raw) To: emacs-orgmode 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 <lngndvs@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 > > > ^ permalink raw reply [flat|nested] 21+ messages in thread
* Re: Re: zotero (or mendeley) integration with org 2011-03-30 0:54 ` Alan E. Davis 2011-03-30 8:26 ` Cian @ 2011-03-30 14:34 ` Joost Kremers 1 sibling, 0 replies; 21+ messages in thread From: Joost Kremers @ 2011-03-30 14:34 UTC (permalink / raw) To: emacs-orgmode 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 ^ permalink raw reply [flat|nested] 21+ messages in thread
* Re: zotero (or mendeley) integration with org
@ 2011-03-27 3:12 Rustom Mody
0 siblings, 0 replies; 21+ messages in thread
From: Rustom Mody @ 2011-03-27 3:12 UTC (permalink / raw)
To: emacs-orgmode
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
^ permalink raw reply [flat|nested] 21+ messages in threadend of thread, other threads:[~2011-04-02 14:13 UTC | newest] Thread overview: 21+ messages (download: mbox.gz / follow: Atom feed) -- links below jump to the message on this page -- 2011-03-26 15:47 zotero (or mendeley) integration with org Stephen Eglen 2011-03-26 21:04 ` Cian 2011-03-26 21:06 ` Ramon Diaz-Uriarte 2011-03-28 9:14 ` Stephen Eglen 2011-03-28 14:07 ` brian powell 2011-03-28 17:06 ` Erik Hetzner 2011-03-29 3:32 ` Matt Lundin 2011-03-29 7:21 ` William Gardella 2011-03-29 10:55 ` Rasmus 2011-03-29 11:42 ` William Gardella 2011-03-29 13:14 ` Matt Lundin 2011-03-31 11:39 ` Stephen Eglen 2011-03-31 20:13 ` Matt Lundin 2011-04-02 1:40 ` Alan E. Davis 2011-04-02 13:19 ` Matt Lundin 2011-04-02 13:37 ` Eric S Fraga 2011-04-02 14:13 ` Alan E. Davis 2011-03-30 0:54 ` Alan E. Davis 2011-03-30 8:26 ` Cian 2011-03-30 14:34 ` Joost Kremers -- strict thread matches above, loose matches on Subject: below -- 2011-03-27 3:12 Rustom Mody
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