Sense-making of Academic Literature Using Tinderbox

(Lew Friedland) #41

Grant, this is working beautifully. But I have one final question. I’m quoting an offline reply here so others can see it.
In your response you said:

However, in the case of Zotero there is a problem with journal articles having Journal Name mapped into the BookTitle KA. The problem here is that Zotero is using the RIS tag T2 to hold the Journal Name, while Tinderbox is expecting it be contained in RIS tag JA. RIS contains ambiguities. Again, you can add code that maps RIS tags into the appropriate TBx KAs.

I have tried to write a rule that would switch the tags following your original code, but am afraid I keep getting it wrong. Would you mind telling me what code snippet would let me reassign the T2 and JA RIS tags? OR you are welcome to point me to some part of TB Ref or elsewhere so I can learn how to do it myself.
Thanks again. With this one change, Zotero users can start to adapt Jeff Taekman’s system.

(Lew Friedland) #42

Sorry for reposting. Can anyone point me to a place in the TBRef or elsewhere where I could figure out the code for switching these two tags on the RIS import (see above). Thanks.

(Grant Lotter) #43


This one is actually easier than it looks. You don’t need to muck about with capturing the info from the RIS feed – this has already been done by Tinderbox. Here is the relevant code snippet to be added to the rule:


The first line assigns the Journal name from the BookTitle KA; the second line removes the BookTitle KA from view --since this is a Journal Article – to make things look a bit neater.

(Tammy Warner) #44

Wow. This is incredibly exciting. I am newly returning to an academic career after working in the “real world” for a number of years. I’m also a fairly new Mac user but avid fan of using apps as an external brain so that I can get everything accomplished that I need to.
I look forward to attempting every bit of the Zotero-to-supercharged-Tinderbox protocol from scratch, and might report back to this thread with my own “aha” moments if it seems appropriate.
Thanks All!

(Tammy Warner) #45

Hi all. Hoping to elicit some replies here rather than starting a new thread for these two specific questions.

I’ve imported some references from Zotero into TB, with Abstract field included (thank you contributors above!) and am now attempting to implement the agent search protocol. It works beautifully, but doesn’t return the information in the ideal form for my purposes. (I’m using this for a very preliminary literature search and sort to get myself familiar with a new topic - haven’t read the papers yet and only skimmed the abstracts in my U’s database.)

Two questions:

  1. When the references come into TB as notes in the Reference prototype format, the Book Title (Journal name) is displayed as the title of the note. I want the Article Title to show up as the name of the note. How can I make that happen?

  2. When I run those agents, I want the text of the abstract to appear in the text pane of the note - the white area on the right hand side under the metadata of the reference. I’m assuming that’s some sort of “agent action” but I don’t yet have the vocabulary to search how to accomplish this. Is there some language I can include in the agent definition to achieve this?

Thanks so much for your help.

(Tammy Warner) #46

Update: I followed the tutorial directions for including columns in the outline view; so I can display the ArticleTitle as a column which is awesome.

Still hoping for some code to copy the text of the abstract over to the text pane, if possible.

(eastgate) #47

How about a stamp:

$Text = $Abstract;

This will copy the abstract of the selected note(s) to the text of those notes.

(Tammy Warner) #48

Holy cow! It worked! Thanks!

(Rick) #49

Inspired by @jtaekman’s original post, I’ve started working on a somewhat similar kind of document. However, instead of adding all my abstracts, I’m making a topic-based document. And instead of including only abstracts, I’m including all the quotations from each paper. This is intended to be a more-or-less permanent reference document rather than one for a specific project.
The document has two major sections (though depending on people’s responses to this that may go up to three):

Agents: Pretty much the same as Jeff’s, though I’m planning to also leverage tags
Source Containers: Each container represents one paper. Inside it is multiple notes, each representing 1 quotation from that paper with the page number and sometimes with my comments.

I like using Maps and Treemaps as well as Outlines, so it’s preferable to be able to grasp the essence of each note without reading the content. Therefore, I take some time to choose a suitable title that captures the essence of each quotation without being mega-long (usually one sentence without subordinate clauses). And I use Andis-Regular as the NameFont for Maps with -1 NameLeading so that I can see a reasonably long portion of the title in most views. (That font choice seems to have carried over to other views, too, which wasn’t intended, but tant pis, as they don’t say in Germany.)

In Map view I have been using an oval note for the abstract, and rectangular notes arranged in concentric circles around the abstract for the quotation notes.

That brings me closer to my question related to organization. I have each paper in Sente, which is where I originally made the notes. Sente has good communication with Bookends (for which I also have a licence). Bookends has good communication with Tinderbox, so I’m copying references from Sente to Bookends and then option-command-dragging them into Tinderbox. (This has the desirable side-effect of speeding my transition away from the abandoned Sente.)

Two ways of organizing the References dragged in from Bookends occur to me:
(1) I could drag each one into the relevant source container. This is the one that occurred to me first and, at least at first, felt most natural. I could add a Reference-gathering agent to gather all the notes of Reference type for when I just need a list of all references.
(2) I could make a References container and put all the items dragged in from Bookends there. I could create a link from each source container to the relevant reference.

Any thoughts on the implications of choosing one or the other? I’m sure there are ways of rearranging things if I regret my choice but now that I’m just starting I’d prefer to go the way that is most likely to be the most sustainable/useful.

(Paul Walters) #50

I think you answered your own question. The agent in option #1 would get you to the same point as option #2, no?

Unless there’s some longterm reason to trace back from Tinderbox through Bookends to Sente, for archival documentation (and you could do that with attributes, anyway), then I don’t see the benefit of option #2.

(Rick) #51

Mmm, when you put it like that I guess the answer is pretty clear. I’ve gone for Option #1.

(Lew Friedland) #52

This is a new topic (I think) within the larger “Academic Literature” thread. I am at a pause in a large project and about to examine all of my writing to consolidate projects, examine new directions, etc. I have, probably six major TBX files I have worked from on various projects over the past five years. If others have done this, how do you:

  1. go about examining old files to consolidate into a new master file? File by file, note by note? Drag and drop, getting rid of old notes as you go? Or consolidating into one large master file and then using other techniques to parse and make sense of them? If so, what techniques?

  2. if the latter, how do you get different files’ prototypes to concord? For example, in the past, I have dragged older notes into a newer master file but because the prototypes do not necessarily match there is often “broken data,” mismatched or missing fields, etc (e.g. in an older version I set up a bibliography by hand, now there is the default reference prototype, which I have further modified to take advantage of Zotero RIS export).

Finally, I know multiple users of this thread use DevonThinkPro as do I. I use Zotero to store citations and PDFs, DTP for some PDFs and downloaded web pages/PDFs, and TBX for notes, of course. This is unwieldy since information is scattered across multiple sources in multiple formats. Any thoughts on linking these more systematically (or pointing me to other discussions) would be appreciated. I know both Jjvornov and Pat have discussed this.

(James Vornov) #53


Thanks for asking. Moving notes from one Tinderbox file to another has always been a challenge. I’ve always found myself branching new versions of a file when starting something new, pruning out what I don’t need from the old file. Copying and pasting simple notes from one file to another works fine, but not more complex objects. So for me, one file acts as a template for the next one.

(Martin Boycott-Brown) #54

I am trying to make more use of Tinderbox in my work, and it struck me that a useful thing for me to do was to create a Tbx specifically for the purpose of examining and thinking about what I am doing – or trying to do. I put notes in it about what sorts of prototypes and tags I might need, and how to organise my data. In a sense, the Tbx becomes the template for the work I will do. I have shamelessly poached from Mark Anderson’s starter Tbx, and altered some of the prototypes to suit my needs, as well as copying some I had before. The same applies to agents and stamps I will find useful.

But I have also found myself thinking about the flow of my work (I avoid writing “workflow” because I find that word slips past me too easily and I don’t think about what it means). In my case, the centre of everything has to be my bibliographic database (in Bookends in my case). Absolutely anything that might be considered a “source” goes into Bookends. Web pages, for example, I always print to pdf, as that freezes the content to what it was when I found it. I would do the same with emails, or anything else I could think of. I keep all these pdfs as attachments to references in Bookends, which stores them in a folder, renamed to Author -Year- Title. That folder is indexed by DEVONthink Pro Office. That gives me a solid base for my source documents, and two apps in which I can find them (and they are the same documents in each program – no scattering). At the moment I am using the practice of dragging references from Bookends into a Container simply called “References”. Each reference itself becomes a container inside which I put any notes or quotes relating to that work. So pdfs go in Bookends, but are available in DEVONthink, while my jottings and observations are in Tinderbox.

In my own “journey” with Tinderbox, I’ve found it useful to think about the prototypes first, and make ones that have “Attribute Overkill” – i.e. probably more attributes than I need, but I’ll get rid of the ones I don’t use at a later date. I think if I had a mixture of discordant prototypes I would just make ones in the new file that had all of the fields of the old ones and then use stamps to move the data to whichever field I decided was the one I wanted to use. But I’m not clever enough to use more than agricultural solutions to these problems.

For me, the key to making sense of things (insofar as I can) is to make liberal use of metadata in Tinderbox. At the top of every note I make I put a line which is “tags = §freud §psychoanalysis §hypnosis” or similar. I have a stamp kindly provided by Pat which copies those tags to the $Tags attribute. Using the Attributes Browser or Agents, I can find pretty much any combination I want. For something I am trying to write, I will just add “§chapter_1” or whatever to the tags at the top of the note. My Agent finds all the stuff related to Chapter 1, and then I have to think about what to do with it.

I’m not sure how much that helps, but I’m coming to look upon Agents as one of the most useful tools in the program. They do the heavy lifting, and one can tweak things afterwards. The great thing about using metadata to categorise notes is that it doesn’t matter where they are physically – you can still find them and gather them together.

I trust you will get much better contributions than this from other people!

(Lew Friedland) #55

This is a query of a reply that Grant Lotter made above Aug. 17.

Doing a final tweak of this system before launching a large project. All works well, excepting the title of the note itself is the “journal” field. So, for example, if I drag an article au: Abascal, ti: Love thy neighbor? jour: American Journal of Sociology, the display name of the note is “American Journal of Sociology.” Would like it to be the article title (to distinguish of course from all other AJS notes, articles by same author). I tried using the code snippet to write “$Name=$ArticleTitle” but then the name of the prototype goes blank as does any Zotero reference dragged over. What would be the right syntax/rule to assign the name of the note as the article title?

On a different subject, for some reason the prototype name has become permanently italicized. Have tried changing it back but cannot. Has anyone ever had this bug?

Thank you again for your help which has really opened up TBX for me.

(eastgate) #56

Aliases are distinguished by italicized names; you might be looking at an alias of the prototype and not the prototype.

(eastgate) #57

Please email me the RIS for this journal entry; we’d like to compare it to the Bookends output.

(Tammy Warner) #58

Did Lew’s query about the Note Title coming in from Zotero (via RIS) as the journal name rather than the Article Title ever get resolved?

(eastgate) #59

It’s resolved in the next backstage release and the next update.