Hello all. Am launching a topic here for those of us who (mostly) write in an academic mode, use Tinderbox, Scrivener, some other bibliography manager (Endnote, Bookends, Zotero, Sente, etc.) and often/sometimes a database like Devonthink.  There have been a number of great threads here on academic note taking, organizing/writing a Ph.D., with great contributors like Derek, Jean, Russ, and of course Marks A and B.  

I anticipate three kinds of discussions here that have floated through academic writers' questions on the forum.

First, the basic issues about tools and organizations: which ones, how do they work together.  The new Scrivener integration is a huge advance for many of us, but, for example, those of us who use Zotero because of its openness to the web and groups might want to figure out how to get the same or similar drag and drop capabilities that are now built into Bookends (at least I would).

A similar question, one that's been scattered through bits of the forum: how do people manage PDFs, other files, and how to link them in a TBX document?  For example,  I add new PDFs to Devonthink, use this for storage and exploration, but when I actually start to write notes and use them, these go in TBX. What is the simplest way to link notes in TBX to a document elsewhere?

The second kinds of questions have to do with the kinds of code use issues that crop up among many of us.  What are the most important bits of code to learn to unlock Tinderbox's full capabilities?  This is, of course, as much a question of how to organize academic files in TBX and take notes as it is one of the "right" codes. But that's the point: these issues get tangled up and sometimes it takes someone writing in a similar vein to help untangle them.  

Finally, there are other basic questions of note taking and writing craft. For example, how to other users take notes on books and longer documents?  Do you use a single container for a book and then go "vertical" with containers within containers for chapters?  How to avoid losing one's place if notes on books become buried (note to Marks, I do know that agents search deeply, etc. But I use a lot of maps so having first level display is part of how I use TBX which is an ongoing paradox).
Or, I have at least 75 Tinderbox files.  Does it make sense to consolidate those that are substantively related for a larger project? If so, what's the best way to do this?

So, fellow academics and non-fiction writer, let me know if this is a thread that seems useful or not and we'll see if it's worth continuing.

I'll throw out two starting questions: how do you link Zotero or other bibliographic DBs entries in TBX files?

How do you use TBX with PDFs?

Mark, thank you. Already very useful.  I have used Bookends and like it. But Zotero has a large open source community, is very flexible at downloading data from web, etc. Mostly good for collaboration.
Main point is that if there is a way to adapt an RIS solution more generally, I would be interested in helping out (although not sure what I could do).

But yes, one focus of this group should be relatively large projects over time.  So hopefully a discussion of emergent note taking strategies from multiple sources.

So as not to derail the thread, I've branched to a new thread some issues on the simple mechanics of inter-app linking.

Reading further into RIS, I can across this, which seems to be a map of the RIS tag list which is big, some 57 tags. Full RIS might mean adding 57 new attributes to you TBX. TB doesn't mind that many attributes, but do you actually want all that info in TB? If not, IMO it's it best to let the full reference reside in your reference manager and use a 'shallow' reference in TB. It's in our nature to just want one tool for everything but it would be a very complex one.

That drag and drop so often just works tends to make it appear simple.  The problem seems to be (I am not a software engineer!) as to how/if the receiving app can correctly deduce the structure/type of the data being passed.  In other words, it the originating app sends incorrect info, the receiving app can't identify it or has to build costly/fragile workarounds to accommodate the problem.

I'd assume (again I'm not a coder - Mark B's better placed to comment) that now TB can understand RIS data from Bookends, it can likely understand RIS from Zotero. But, does Zotero actually pass RIS-foratted data via drag-drop? If not, the place to fix this is at the Zotero end rather than the TB end.

Looking the other way along the inter-app linking, note the question in my side thread - can you link *into* Zotero? How else does TB open a Zotero reference (as opposed to simply opening the referenced s
document or resource.

Pierfranco, thanks for joining the thread. I'm afraid I have gotten us off to more of a "tools" based discussion than I had intended. But now we might as well run the issue to ground. Please tell us how you drag and drop from Zotero retaining RIS information. It is not as simple as just dragging a cite. That's what I do, and get a note that is just a text string. Is there some other intermediate step? Must be.

As to your second issue re Zotero, I think that is a big issue for many of us in this area. How to manage PDFs, etc. without absurd duplication (e.g. put PDFs in Zotero, Devon, links in TBX (which I actually don't know how to do if not on web).  So organizing PDF workflows is probably a major topic.  Any more thoughts on how you (or others) do this would be welcome.

Thank you very helpful.  So now I have a note that reads (as a text string):
TY  - BOOK
ID  - 252
T1  - The new urban America : growth and politics in Sunbelt cities
CY  - Chapel Hill
A1  - Abbott,Carl
PB  - University of North Carolina Press
PY  - 1987///
N1  - 86040490
Carl Abbott.
Bibliography: p. [291]-327.
Includes index.
KW  - Cities and towns Sunbelt States Growth.
KW  - Metropolitan areas Sunbelt States.
KW  - Regional planning Sunbelt States.
SN  - 0807841803 (pbk.)
ER  -
I am assuming that one must set up a specific TBX bibliographic prototype that matches the fields of RIS precisely?   If so, can you point to how?

Yes, happy to do that.  Although much discussion of academic writing on the forum migrates back to workflow.  The larger problem here is bibliographic management in/with Tinderbox, how much sync do we need between tools. When 50% plus of all notes refer to sources (and for most of us the threshold is closer to 80%) then this is a real problem that crops up repeatedly. As you point out, the specifics of tool management we should move elsewhere, the problems of flow, perhaps not?

Very much like Derek I do not depend on linking to pdfs and so on very much.
Pdfs go into DevonThink, Bookends is purely for creating bibliographies in the end while I write my papers in Scrivener.
I put all my excracts of what I have read the last 10 years into one single Tinderbox file just weeks before the possibility of drag & drop from Bookends. However, it was also ok to manage the task by exporting all relevant bibliographic information via a numbers document from Bookends and back into Tinderbox. The extracts came from rtfs which had lived in DT. Lately I have been arranging notes on what I have read in mindmaps in Tinderbox. This makes the information much more accessible for me even after memory has blurred on what I have read excactly.

So Tinderbox does mainly three things for my writing:
1. a repository for extracts from papers, books and archival stuff
2. a bucket for all sorts of ideas which come across my mind for future projects and papers (mostly a list sometimes evolving into some sort of map)
3. a mindmap for carving out the actual structure for what I want to write which then moves into Scrivener when done

These three things happen in different documents however and I have not yet found a compelling way to bring them together in one. Hence they are not linked very well. I even don't know wether it makes sense to streamline this process into one document… which might become extremly bulky anyway since it would hold probably about 10.000 single notes.