in the course of just 2 weeks devonthink became central in my workflow. now that I am looking for a bibliographic software on the mac, I wonder which one would work better with DT and why.
My plan would be like this: importing abstract and/or fulltext (as pdf or rtf) into DT and importing the citation into Sente or Bookends for doing bibliographic work.
I hate endnote ever since using it in it´s early days (maybe it is better now, no idea) and found out about Sente and Bookends and wonder which software I should go for and why (I also found Bibdesk, but I do not use LaTex). Are there any recommendations? I am aware of Zotero, so hints about Zotero and DT would be welcome too. Thanks!
I’d suggest that you try both Sente and Bookends and decide which you prefer. I’ve been using both, I started with Bookends but I decided to give priority to Sente a few months ago. Anyhow both are good apps and both have room for improvement (proper scripting support would be great), but both are improving. I like Sente’s UI better, the note-taking system is very useful, although I’d love to have a way to see the notes directly in DEVONthink. But both apps are improving at a good pace, and sometimes I wish I could mix things from both. Check them for yourself.
How to combine DT and one of them is still a matter of discussion. You can read a discussion here http://www.devon-technologies.com/scripts/userforum/viewtopic.php?f=7&t=8006. I’ve for the time being opted for putting all pdfs that should have a reference into Sente, creating the reference and having Sente manage the linked files (I’ve created a custom file–rename style so it renames the files the way I want). I have the Sente attachments folder indexed by DT (not imported) and I’ve attached the Synchronize script to the indexed folder, so it updates automatically each time I use it.
When I start working on something I create a new Group (folder for the rest of us ) and replicate the docs I want to have at hand from the indexed folder to the new one. I don’t rename the files, but with the name style I’m using there’s no need to do it. I also put together (usually by replicating) other non referenced files I have in DT (bookmarks, drafts, notes, media files, etc.). I copy the notes I’ve taken in Sente and paste them into a new text document… and go on working.
I think both of them will work well with DT. I personally use Bookends with DTP and I think it works great. I have been a long-time Bookends fan and it is in my opinion BY FAR the best bibliography software out there. It is a little quirky and not as pretty as Sente (or Papers, for that matter), but once you have gotten around all the corners it is second to none in terms of features and usability.
I would even go as far as saying that you should use Bookends for the suggested work, rather than DT - it is much better at handling large numbers of articles, abstracts, etc. I really like DTP, but I wouldn’t prefer it over Bookends for this kind of work.
Thanks for the input, I downloaded both Sente and Bookends.
I still do not know how they compare in features, kind of hard to find out about.
I noticed the attachement feature of Bookends and could not find anything analog to it in Sente, but not sure if this really is missing and if so, if that would matter much for integration with DT. Any hints/experiences concerning this?
This might rather belong to the Sente forum, but anyhow…
You can attach a document to a Sente reference by dragging and dropping on the reference in the Reference list. If you drag and drop on the Library name, it will create a new reference with the document attached. You may attach more than one document to a reference. If it’s a pdf you’ll be able to see it in the Links pane. If it’s some other kind of document it’ll give you the option of opening it in it’s own application.
A year ago, I was in a similar dilemma in terms of choosing between the two programs. I downloaded both, and initially thought Sente would earn my money. While the UI is far prettier than bookends, Sente seems unstable and the customer service was way slow. I lost several weeks worth of work at a crucial time. I contacted their customer service and over a month later they contacted me. They were sheepish about the delay but by then I had migrated to Bookends. To-date I have not a single problem with Bookends and have found it indispensable, fwiw.
Charles, I had forgotten about the weirdness of the manual entry. It was sort of an unexpected element of the program. While I am very new to DT and am still working out a flow, I am really committed to bookends as it is very reliable. I am watching the thread to see what others have to say in regards to bookends/DT workflow. Vivian
thanks for your comments. I actually like Sente best, it seems to have all the features I would need. I also had a few issues and contacted the support. They did not answer within a day, but they did within 2-3 days, maybe the support has improved. Concerning DT integration I still have not found strong reasons for or against any of the two.
There is absolutely no need to use LaTeX in any way, shape, or form to use BibDesk. And on the plus side, not only is BibDesk free, with a very active development & user community, but it has good AppleScript capabilities.
Myself, I own Papers (http://mekentosj.com/papers/, but have stopped using it - there are some very simple needs (e.g. the ability to enter book chapters as such) that the developers haven’t bothered to address - I have no idea why not. And I looked at Sente and Bookends and just could not see the advantages of spending $$ on apps that did not do anything more for my needs than BibDesk.
At the risk of drifting off topic, importing your reading notes as an OmniOutliner .003 file arguably works better than importing as OPML:
The URLs are preserved
The contents of the file are still indexed by DT2 and visible in the DT2 contents pane
Editing the file is only 1 click away if you customize your toolbar and drag an “Edit in external editor or viewer” button into it.
Your approach could be implemented now by writing an XSLT sheet which transformed the Notes component of Sente XML to OPML or .oo3. The workflow would be to export Sente XML for the selected reference, and then drag it onto an Applescript droplet which:
converted it through XSLT to OPML or .oo3 (also an XML format)
Imported the translated file into DT2
Beginning to sound a little Baroque perhaps, so I might personally prefer to create an OmniOutliner 3 template with columns for Comment, Quotation, Pages and Sente Citation reference, and take my reading notes in OO3, storing them in DT2.
Thanks a lot for the answer. Although I’m no expert, I thought the notes had to be in (or easily convertible into) some kind of XML and thus could be brought into DT conveniently. Unfortunately, XSLT is not one of the languages I speak.
I hope I’m not getting too far off topic. I just try to figure out how I can work smoothly between Sente (the ref manager I like the best for the time being) and DT.
You may be right, but I like a lot the way Sente allows you to take notes from a pdf by selecting and clicking a button, and the fact that notes are somewhat structured (title, page number, quotation, comment in separate fields). Note-taking is easy in Skim too, but notes are not structured. And I know some people prefer working in an outliner like OO3. But copy and paste is becoming a bit primitive, isn’t it?
I also find useful to have each note in a different text document grouped by source, so I can then re-group replicants by topic.
I use DT Pro with Bookends. I am a biomedical researcher and here is my workflow, if anyone is interested:
Search Pubmed in Bookends (a nice touch: articles you already have are indicated). Bookends saves the attached PDF in the format Author- Title to a specific folder where I keep all of my scientific articles.
I synchronize DT by dragging the PDFs from the articles folder into DT Pro (as any alias to save disk space- I do not want my PDFs within the DT database). I mark articles that I have already imported by labeling them with a color in FInder.
I organize the articles within DT by topic, to help DT with making connections, building a concordance.
For most uses, Bookends helps me organize and track articles (articles to read, articles for a project, etc). Obviously, I also use Bookends to make bibliographies. Where DT really excels is during more in depth study or writing grants or manuscripts. Namely, if I am looking into a topic, I find the article in my DT database and ask DT to find similar articles. I find that DT helps make connections that I had forgotten and helps me remember to consult related articles that I would otherwise have neglected.
I found Sente to be unusably unstable. Any time I have tried to import my database from Bookmarks (no matter the format), Sente has failed/frozen/crashed. It is prettier, though. Also, Bookends support has been outstanding; posts to the forum are usually answered within hours by the programmer.
The user is prompted for the surname of the author (and, optionally, the year of publication).
If one or more matching references are found in Sente, a folder with a full citation name is created for each reference in the DEVONthink 2 Global Inbox, and any notes for that reference are copied from Sente (with a URL linking back to the Sente reference) into the DEVONthink folder.
This is great stuff, houthakker. Excellent. I always had the idea that there must be a way to get data out of the database into DT, but couldn’t find sqlite classes in applescript.
Do you know how to get a grip on an attached file? The link to it is stored in Sente’s DB AttachmentLocation table allegedly as “Carbon File Alias” in the LocatorData column, their values are veeery long hex numbers.
Should I ever have a few hours off in the next couple of weeks, I’ll try to write a script that replicates PDFs from Sente into DT groups corresponding with those Collections a Sente reference is stored in. Thanks to your work it shouldn’t be that hard.