How do people handle bibliographic references for papers managed with DT?
Now that I’ve imported all the papers in my archive in DT, I’d like to link them somehow with the BibTeX reference file I have… (Ideally, of course, each file with the appropriate BibTeX entry.) Anyone out there who has thought about that?
I’ve been wondering about this, too. See my entry under “usage”.
I haven’t concocted a method yet either and it is very important to me. Unfortunately Ulysses doesn’t manage them either, nor does NoteTaker (although I could come up with something in NoteTaker probably).
ChemBob
Since you’re a Mac user, have you tried Sente? Or EndNote? Or Bookends?
I’ve owned EndNote (need to upgrade) and tried Bookends, looked at Sente, but none of this really gives me the means to relate a clipping in DEVONthink to a bibliographic reference in one of these programs, unless I’m missing something. Am I? Have you worked out a good method? If so, please share it.
ChemBob
I don’t have a method; like you I’m looking for one 
However, here’s what I have been thinking about:
I’m wondering whether one could have a group containing one doc per bibliographic reference and link them to individual notes (in, say, another group) via Wiki. But how would one export, say EndNote references in such a way that there would be one per file, and how would one link them easily?
I don’t know if you use SpellCatcher, but I had some success in establishing glossary entries based on EndNote reference numbers that would expand into a full bibliographic reference in a note. However, the disadvantage of this was that the glossary entries were a pain to keep up to date.
What do you think?
I don’t know what to think. I’m trying to reduce the number of steps in my work while organizing and managing the flood of information more efficiently. Currently I think these goals are nearly mutually exclusive, although DT and a few other programs are helping with the info flood anyway.
It’s the details, like managing references, etc., that are getting in the way. Even little things like this: I saved a bunch of websites as RTF files in DT after finding them using DA. Each of these websites had a “chunk” of information related to the topic I was researching. So I began dragging and dropping or copying and pasting all these relevant chunks into a single DT note to begin assembling the info for a report. However, I still needed to reference, at the very least, the websites from which each chunk came. I discovered, to my chagrin, that there seems to be no way to drag and drop or copy and paste the website URL from the DEVONthink page (at the top of the page where you can click to open in your browser) into the body of the new document comprised of the chunks. So now I guess I’ll have to go back to all the originals in Safari and drag them in from there. Seems like that shouldn’t be necessary.
Having said that, all the features we users would like to see in DT would take a team of programmers two years or more to implement, with lots of resources at their disposal. Unless these guys can continue to be miracle workers.
ChemBob
ChemBob:
I don’t have to worry about standards for citations, so I can create my own for my projects.
For the most part, I create end notes to hold citations and notes, and set hyperlinks to them. Example: “[1]” --> “[1] Author, Title, URL”. Sometimes I get a bit more formal, adding journal source and date.
NoteTaker is convenient for laying this out. Example: Create Section/Page(s) to hold my article. Create a Section/Page called References. Within my article text, create a citation cue, e.g. “[14]” and go to the References page and create a cell containing "[14] plus the bibliographic information. Flip back to my article, select the item “[14]” and hyperlink it to the cell containing the corresponding References item. Obviously, this works well in both the original notebook open under Notetaker, and in a corresponding HTML Web notebook. It also works well for printed or PDF output (though, of course, the hyperlinks are no longer functional). (One of these days, AquaMinds will release a version of NoteTaker that will work under both Mac OS X and Windows, with free viewers. That may become better than PDF for document distribution on the Web.)
The URL for an HTML item viewed in DT can be grabbed by showing Info, triple-clicking on the URL field and pressing Command-C.
Circus Ponies NoteBook will offer improved linking in the upcoming version 2.0, though still not as convenient as NoteTaker linking. The techniques noted above would work for NoteBook 2.0, with minor limitations.
Finally, DEVONthink itself will be able to export HTML of an article that will also include linked pages, such as my example of a References section attached to an article. (But better print/PDF output will have to wait for future versions of DT.)
I don’t have to worry about citation styles, so these techniques are good enough for my purposes. 
Any ideas on the best way to incorporate citations into DEVONThink itself?
I didn’t think about being able to get the URL from the Info pane. That should work, thanks!
ChemBob
i’d also like to see some solution for handling bibliographic references, since the major portion of by DT database is now PDF’s of journal articles (>2,000).
Although not helpful for future citation issues, I’ve been trying to name many of my PDF’s as I import them into the DEVONthink database in a consistent way, which is:
FirstAuthorLastname Year AbbrevJournal v### p###
That way, when I do similarity searches, I can see in the search results in a glance the year and journal it came out in, and the author name, which is sometimes enough to jog my memory into remembering whether it’s what I’m looking for.
Someday, I’d love to be able to use DEVONthink in some integrated fashion with EndNote and possibly Pubmed. One nice future feature might be to start with a PDF in your library, find the matching Pubmed reference, and grab all the Pubmed metadata and stick it into the comments section.
The new DEVONthink Pro beta supposedly handles Bibtex format in some way, but I’m not familiar with Bibtex format and how to use it.
Joe
I don’t know anything about Bibtext either, and hope to learn from someone who uses it.
I’d be interested in hearing more about the BibTeX integration with the upcoming Pro. Currently, I just index my bib files and keep the bib file in the root level of my literature group.
Ideally, though, I’d like to see some sort of import/export from bib format so I can create a subgroup per paper, drag a pdf to DT, somehow specify the metadata and add annotations. Then all this would automagically be turned into a bib file for external processing. Ah, I can dream.
Matt
I use Bookends and am very happy with it. But I don’t see any obvious way for it to talk to DT, or vice-versa.
I suppose my ideal solution for this would be some sort of central data base which DT could use for exploring and organizing facts & ideas, while Bookends used the exact same data to present properly formatted bibliographic text as needed. The requirements of bibliographic styles are so arcane and specialized (and irrelevant to problems of thinking and writing) that I don’t see how DT can do bibliographic work easily. Maybe I’m missing something . . .
I too have had to do this, none too happily. It’d be nice to see this addressed.
David
This point made me realize there is another possible path to this problem on the horizon: A number of writing programs (CopyWrite, which I sometimes use), Ulysses (tried it, sorry, but I like italics, don’t want a lecture on why I don’t need to see them) and Jer’s Novel Writer will let you maintain a notes window right next to any text you’re creating. Jer’s Novel Writer lets you link these notes to specific words in the text. CopyWrite will have this feature in its next big revamp, I’m told.
If such a feature is robust and exportable, then notes could be done in the most natural way – you see the text, you see the note right next to it. You drop in the formatted bibliographic data from whatever app holds it. Irrelevancies – endnote or footnote, size of font, where on the page? – are left for whatever program you use to handle that stuff.
IF – big if – the note feature is able to handle hundreds of notes in any of these apps.
David
As would I.
Yeah, that’s more or less what I’ve been doing. I had been putting the BibTeX info in the comments field, but decided that that wasn’t too useful, as there was no good way to generate a list of entries from a group of files. Unfortunately, as the size of my master BibTeX file has grown, it’s become more and more unwieldy to work with. And so I’m currently evaluating Sente and BibDesk to decide which one works better for me.
But I’d like to second (third, fourth?) the suggested to do list add on of managing references for the documents. Combine that with a smart folders type of interface or an iTunes-like interface, complete with playlists where dragging and dropping creates replicants, and a good annotation solution, and DEVONthink might become my new OS.
Good to know, but the problem is, there is no way to see URL’s for items that have been stored as pdfs or texts or whatever. Anything I grab with stickbrain automatically as its URL displayed. But when I show info for a downloaded pdf in DT, the URL window is blank.
Like other posters, I have found this to be a big hang-up. Perhaps if I learn to archive more stuff found in Devonagent, it will be less of a problem. But it would be nice if this were handled automatically. Stickybrain shows it can be done.
David
The new Bookends 8 version allows for some integration with DEVONthink as it can act as web server. You would need to create a HTML page that contains a search form, the posted query will be processed by Bookends and you get the formatted results back in your web page. If you make a link to this search form in DEVONthink then you can do the search within DT and get the formatted results back in DT. The reference format can be specified in the search form too, you can even have links to the full paper on your Mac or to PubMed if you create such a reference format within Bookends. It is not too difficult. The server does not allow you to edit the reference library in Bookends, you can only search it. Of course, the main advantage of the server is that a user can connect to it from a different computer and search the database without having Bookends installed on her/his own computer. If you have both, DT and Bookends, on the same Mac then you may prefer to use them side by side anyway.
I’ll use this as an opportunity to mention that there’s currently no way to cancel or undo any accidental edits of fields in the Info window. That became unforgettably apparent to me after irreversibly updating the automatically selected Name field a few times. 
I recently submitted a support e-mail about that and “negotiating” a short-term workaround, e.g. removing the field auto-selection.