Note 1: This thread is closely related to the thread "Organizing notes, quotes, and ideas".
Note 2: Sorry if this is already common knowledge but I haven't come across it yet.
Many of us have talked about the problem of workflow: how do we integrate keeping track of references with other research tasks like writing? Bookends is a narrowly focused application and, while it's perfectly possible to write notes on one specific source in the Notes field, those notes belong only to that one reference and can't link to another related source.
One way is of course to use Mellel or another suitable word processor to write while pulling in citations from Bookends. But many of us don't feel that's enough (though I'm not sure how to explain that inadequacy).
A big theme of OS X Tiger is lowering the barriers between applications. So Spotlight can search pretty much anything; VoodooPad and StickyBrain can link to vCards in Address Book; and so on. And now DevonThink has things called sheets (which are actually like mini-databases) and the ability to import BibTeX.
All you need to do is select all the references in a Bookends database and use the Bibliography Formatter to export them as a BibTeX file. Then in DevonThink go to Import Files and Folders and select the BibTeX file. What you get is something that looks like an Excel spreadsheet, with Author, Title, Year, etc. columns. Now, assuming you have WikiLinks...Automatic...Names and Aliases checked in DevonThink preferences, every time you mention a source by title (full title without any mistakes!) it becomes a link to that record in the sheet, and clicking on it opens the record (where you can add comments, keywords, abstract etc. if desired, though it's better to go back to Bookends for data entry). If you open up several records in different windows, you can see complete data for all those records at the same time (like arranging index cards on your desk), something which isn't possible in Bookends.
It isn't perfect. You can define aliases for records but then typing the alias in a document takes you to the sheet as a whole rather than the individual record. So you need to remember or check the correct title (and if you know that maybe you don't really need to link to it?!). And of course the sheet will become out-of-date as soon as you've added something new to Bookends. But reexporting every week isn't a particularly onerous task.
I'd be grateful for any corrections, updates, or comments on this. And I'm still not exactly sure just how useful this is and how exactly I'll take advantage of it. But I think there is some potential for enhancing our workflows. Maybe the Bookends-DevonThink-Circus Ponies Notebook (or variations)-Mellel axis, which seems to be becoming something of a standard, can now comfortably be cut down to Bookends-DevonThink-Mellel?
Bookends & DevonThink Pro integration
explain this more
Dear Rickl, I've been reading your and other posts. Can you explain to me, what exactly does DevonThink do for you? From your post, I don't really understand what Devonthink does for you that the abstract field doesn't do for you. Thanks Rickl
~I swore to myself that if I ever got to walk around the room as manager people would laugh as they saw me coming and applaud as I walked away~
DT and Bookends
Hi Danzac,
That's a difficult question to answer in a short post. DT is designed to store and index large amounts of information, and then show you the relationships between them. It does a better job than Spotlight at straight searches, but it really comes into its own when you use features like "See Also", which looks for related documents. This is of course useful when you're reading a PDF, for example, but also works well with references imported from Bookends when an abstract is present.
I guess there are 2 key points:
1. The algorithm used to decide what is similar to something else works very well, way better than simply checking the presence or absence of one or two keywords.
2. Bookends is a simple database with a very clear and limited purpose. It isn't relational so you can't refer, for example, from the notes field of one reference to another reference. Bringing the references into DT allows you to work with them in another way.
If you work with a reasonably small number of sources, or if you're very well-organized, I can see that DT may not be very useful. And you certainly couldn't replace Bookends with DT, because DT doesn't download references, nor can it output them. But it does give you a new way to use the information within a Bookends database, integrated with all the other information on your computer.
Probably the best description of DT in use is by Steven Berlin Johnson:
http://www.stevenberlinjohnson.com/mova ... 00230.html
Hope this helps.
That's a difficult question to answer in a short post. DT is designed to store and index large amounts of information, and then show you the relationships between them. It does a better job than Spotlight at straight searches, but it really comes into its own when you use features like "See Also", which looks for related documents. This is of course useful when you're reading a PDF, for example, but also works well with references imported from Bookends when an abstract is present.
I guess there are 2 key points:
1. The algorithm used to decide what is similar to something else works very well, way better than simply checking the presence or absence of one or two keywords.
2. Bookends is a simple database with a very clear and limited purpose. It isn't relational so you can't refer, for example, from the notes field of one reference to another reference. Bringing the references into DT allows you to work with them in another way.
If you work with a reasonably small number of sources, or if you're very well-organized, I can see that DT may not be very useful. And you certainly couldn't replace Bookends with DT, because DT doesn't download references, nor can it output them. But it does give you a new way to use the information within a Bookends database, integrated with all the other information on your computer.
Probably the best description of DT in use is by Steven Berlin Johnson:
http://www.stevenberlinjohnson.com/mova ... 00230.html
Hope this helps.
DevonThink/Bookends/Mellel
Well it has been a few weeks now since your post Rickl, but I read what you said, what you pointed me to, and looked at DevonThink for myself. Well you got me hooked!! I've already purchased and use it on a daily basis. It really is great, thanks.
Here is a couple of my humble observations on things you have said;
I am not entirely sure of the need to export references from Bookends to DevonThink is necessary because of the great Static/smart group feature in Bookends, and the Listview. While this does not enable you to see all of the entries info at the same time, you can see a significant portion (date, author, title, etc) and the Info Drawer lets you see the notes and abstract field. For myself, when I write an essay, all of the entries I am using for my paper are placed in a static group, letting me navigate and view and copy those quickly from the List view into Mellel.
Back to DevonThink, you are right about its ability to connect and store myriad of data, it is awesome. And I agree with you that the combination of Mellel/Bookends/DevonThink is a formidable trio. And I think it would be in DevonThink's interest to try and accomodate/make itself more compatible with Mellel and Bookends. Two ideas I immediately have is that DevonThink should be able to read and edit mellel documents (perhaps Redlers would have to provide a plugin) and in the instances where bibliographic entries need to be placed into DevonThink, there should be a quick way to simply copy and paste from Bookends to Mellel (perhaps a special 'Copy as XML' function in Bookends or something).
In any case, I think this trio needs to be played up more at the development level, but I understand this will take some time. As it stands now, Mellel still has got its work cut out for them trying to employ abilities which its users are asking for (highlighting, applescripts, flipping from footnotes to in-text notes, better compatibility with Bookends, etc) before compatibility issues with DevonThink can be settled. I can't think of much that needs to be enhanced in Bookends, I'm really pleased with how great it is working. But I think this connection needs to be played up, especially in view of the rave reviews I have heard about Note Bene from PC users (Note Bene fulfills the function of mellel/Bookends/DevonThink all together).
Anyhow, that's my 2 cents. Thanks again for turning me on to DevonThink, I love it. Danny
Here is a couple of my humble observations on things you have said;
I am not entirely sure of the need to export references from Bookends to DevonThink is necessary because of the great Static/smart group feature in Bookends, and the Listview. While this does not enable you to see all of the entries info at the same time, you can see a significant portion (date, author, title, etc) and the Info Drawer lets you see the notes and abstract field. For myself, when I write an essay, all of the entries I am using for my paper are placed in a static group, letting me navigate and view and copy those quickly from the List view into Mellel.
Back to DevonThink, you are right about its ability to connect and store myriad of data, it is awesome. And I agree with you that the combination of Mellel/Bookends/DevonThink is a formidable trio. And I think it would be in DevonThink's interest to try and accomodate/make itself more compatible with Mellel and Bookends. Two ideas I immediately have is that DevonThink should be able to read and edit mellel documents (perhaps Redlers would have to provide a plugin) and in the instances where bibliographic entries need to be placed into DevonThink, there should be a quick way to simply copy and paste from Bookends to Mellel (perhaps a special 'Copy as XML' function in Bookends or something).
In any case, I think this trio needs to be played up more at the development level, but I understand this will take some time. As it stands now, Mellel still has got its work cut out for them trying to employ abilities which its users are asking for (highlighting, applescripts, flipping from footnotes to in-text notes, better compatibility with Bookends, etc) before compatibility issues with DevonThink can be settled. I can't think of much that needs to be enhanced in Bookends, I'm really pleased with how great it is working. But I think this connection needs to be played up, especially in view of the rave reviews I have heard about Note Bene from PC users (Note Bene fulfills the function of mellel/Bookends/DevonThink all together).
Anyhow, that's my 2 cents. Thanks again for turning me on to DevonThink, I love it. Danny
~I swore to myself that if I ever got to walk around the room as manager people would laugh as they saw me coming and applaud as I walked away~
dear Rickl
Hi again. Hopefully you'll see this. You explained how to export your references to a sheet, but it did not work for me. choose all references, then export, choose Bibliography format, and then bibtex in the first and second menu. Is this correct? I tried to import into DevonThink but it did not work.
Thanks
Thanks
~I swore to myself that if I ever got to walk around the room as manager people would laugh as they saw me coming and applaud as I walked away~
bibtex
it must be a problem with DT, so I'll post there. I saw the process explained here, so that's why I posted it here. Importing as plain text does not seem to work either, which is strange. Thanks for the suggestion though.
~I swore to myself that if I ever got to walk around the room as manager people would laugh as they saw me coming and applaud as I walked away~
BibTeX to DevonThink
I think it's good that you're taking this discussion over to DT as well, but don't give up on this forum!
I notice that Jon advised exporting as Plain Text, but in your reply you referred to importing as plain text not working.
I've been struggling with the same problem as you, so let me run through in possibly unnecessary detail how I have got it to work.
0. In Bookends, Sort the database (Refs menu) by authors, editors, & title. (This isn't crucial, but will help with troubleshooting--see number 6 below.)
1. In Bookends, select all the references (using the Refs menu), or a subset of references.
2. In the Biblio menu, choose Bibliography Formatter. In the 3 sets of options, choose BibTeX as Plain Text (ASCII) to Disk, and then Make Bib.
3. In the Finder, change the extension of the file Bookends created for you from .txt to .bib.
4. In DT Pro, go to File - Import - Files & Folders and select the .bib file. Don't fiddle with any of the options at the bottom of the window.
5. If everything goes to plan, that should be enough. But note that DT Pro appears to be quite fussy. If any of your references is defective in any way (e.g. no BibTeX Key), that reference and all subsequent references will fail to import. If you notice that the number of references in DT Pro is smaller than it should be, scroll down to see the last imported reference.
6. Assuming you sorted the database, it's easy to see which reference caused a problem. Search in Bookends for the last successfully imported reference and then use the up arrow to go to the next reference. Unmark it.
7. Repeat steps 2-4. There will probably be more references successfully imported than the previous time, but there may be another choke point somewhere. If so, repeat steps 5 & 6.
In this way, unless your Bookends database is riddled with problems, you should be able to get all your references barring 2 or 3 problematic ones into DT. I had always assumed that in Step 2 I should choose BibTeX as BibTeX to Disk, making Step 3 unnecessary, and it wasn't until I hit on the extension change trick that I started getting somewhere.
Good luck!
I notice that Jon advised exporting as Plain Text, but in your reply you referred to importing as plain text not working.
I've been struggling with the same problem as you, so let me run through in possibly unnecessary detail how I have got it to work.
0. In Bookends, Sort the database (Refs menu) by authors, editors, & title. (This isn't crucial, but will help with troubleshooting--see number 6 below.)
1. In Bookends, select all the references (using the Refs menu), or a subset of references.
2. In the Biblio menu, choose Bibliography Formatter. In the 3 sets of options, choose BibTeX as Plain Text (ASCII) to Disk, and then Make Bib.
3. In the Finder, change the extension of the file Bookends created for you from .txt to .bib.
4. In DT Pro, go to File - Import - Files & Folders and select the .bib file. Don't fiddle with any of the options at the bottom of the window.
5. If everything goes to plan, that should be enough. But note that DT Pro appears to be quite fussy. If any of your references is defective in any way (e.g. no BibTeX Key), that reference and all subsequent references will fail to import. If you notice that the number of references in DT Pro is smaller than it should be, scroll down to see the last imported reference.
6. Assuming you sorted the database, it's easy to see which reference caused a problem. Search in Bookends for the last successfully imported reference and then use the up arrow to go to the next reference. Unmark it.
7. Repeat steps 2-4. There will probably be more references successfully imported than the previous time, but there may be another choke point somewhere. If so, repeat steps 5 & 6.
In this way, unless your Bookends database is riddled with problems, you should be able to get all your references barring 2 or 3 problematic ones into DT. I had always assumed that in Step 2 I should choose BibTeX as BibTeX to Disk, making Step 3 unnecessary, and it wasn't until I hit on the extension change trick that I started getting somewhere.
Good luck!
BibTex into DT import
I followed all your instructions, and didn't work. Then I realized it was because of DT's need for BibTex key. I "forgot" that I had disabled BibTex and no longer use the BibTex key (now I think maybe I should have kept it) but no biggie. I hope at some point DT will be able to make a sheet for Bookends References (maybe XML exporting, then it can support unfortunate Endnote users) but i won't lose sleep over it....yet. Thanks for your help.
~I swore to myself that if I ever got to walk around the room as manager people would laugh as they saw me coming and applaud as I walked away~
Re: BibTeX to DevonThink
Hi rickl,rickl wrote:3. In the Finder, change the extension of the file Bookends created for you from .txt to .bib.
I had always assumed that in Step 2 I should choose BibTeX as BibTeX to Disk, making Step 3 unnecessary, and it wasn't until I hit on the extension change trick that I started getting somewhere.
What version of Bookends are you using? A BibTeX format sent to disk in BibTeX markup should have the .bib extension assigned to it by Bookends (this change was made somewhere around 8.0.3 or so)...
Jon
Sonny Software
Re: BibTex into DT import
Indeed no biggie. I often forget to create a BibTeX key for references. When I find one of these, I just press Command Shift K. If you have a large number without keys, I think the standard method is to export all your references and then, after making sure BibTeX is enabled, reimport them, or something along those lines.danzac wrote:I followed all your instructions, and didn't work. Then I realized it was because of DT's need for BibTex key. I "forgot" that I had disabled BibTex and no longer use the BibTex key (now I think maybe I should have kept it) but no biggie.
Re: BibTeX to DevonThink
That would be easiest if it worked for me. But I get errors when exporting to .bib. So the small extra step is well worth it for me.Jon wrote:What version of Bookends are you using? A BibTeX format sent to disk in BibTeX markup should have the .bib extension assigned to it by Bookends (this change was made somewhere around 8.0.3 or so)...