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Tinderbox Users >> Tinderbox applications >> Linking to Reference managers

Message started by Mark Anderson on Jun 30th, 2012, 1:59pm

Title: Linking to Reference managers
Post by Mark Anderson on Jun 30th, 2012, 1:59pm

This is branch from the thread "Tinderbox for Academic and Nonfiction Writers"

What is the simplest way to link notes in TBX to a document elsewhere?
Sorry to answer a question with a question, but what do you expect the link to do - or more to the point what are you going to do  after following the link? Open in an editor/viewer (e.g. Preview, etc.)), open it in a document manager/everything bucket (DevonThink, Yojimbo, etc.), open it in a Reference Manager. It's also pertinent to ask how many different references you will link to from a note (one / more than one). The best TB-based solution will vary depending on the answers to these. In general terms the issues are can I link to as many references as I need to, can I tell from the UI which link is to which reference and does the link open the reference in the right tool?

I did try and Google for an answer on inbound links to Zotero but without success. Is the a URL/likn format to link to a Zotero-stored reference? In other words, such as can be done with DevonThink or Bookends, etc., to open the desired reference item in a specific target app - in this case Zotero?

Title: Re: Linking to Reference managers
Post by Sallyanne Payton on Jul 1st, 2012, 1:05pm

Mark -- I would like to be able to link to a document stored in DevonThink or Yojimbo as easily as I can link to that document stored on disk.  

Title: Re: Linking to Reference managers
Post by David Bertenshaw on Jul 1st, 2012, 4:08pm

In DTP, select the document you want, type ctl-opt-cmd-c (for  Edit > Copy Item Link). This puts a link to your DTP document into the clipboard.

In Tinderbox you have two options:

a) In the relevant note text, type cmd-v and you'll get the link displayed as something like x-devonthink-item://A758ECDA-EACE-4021-9A95-E2F35E612D9F. Highlight the link, type shift-cmd-L (or Note > Create Web Link). The link should be added automatically in the dialogue box -- click enter to make the link clickable. Hold down cmd-opt and click on the link in the text and you'll be taken to the DTP document.

b) Create a new attribute of type URL and make it a key attribute for the relevant TBX template. Then all you need to do is click in the attribute and cmd-v the DTP link in. Click on the little globe icon and you'll be taken to the DTP document. Or you can just use the built-in URL attribute, but that means you can't also use it for internet links, so I prefer to create my own.

Hope this makes sense -- I'm away from my DTP / TBX machine...


Title: Re: Linking to Reference managers
Post by Mark Anderson on Jul 2nd, 2012, 3:04am

With Bookends, a Cmd+Opt+Drag (Modifier key use is necessary) from Bookends to a TB view (Map, Outline, etc.) will result in TB creating a note with a 'Reference'-type prototype. The prototype is added by TB if needed. Needs TB v5.11.0+ and Bookends v11.2.9+. One result is such a drag is the note's $URL becomes a link to that reference in Bookends, e.g. bookends://sonnysoftware.com/82637 where 82637 is the ID number of the reference in your Bookends library. Clicking the URL button in the note sidebar will open Bookends & its library if they are not already open.

A drag/drop from Yojimbo into a TB view works the same as as if dropping a URL dragged from a web browser, resulting is a note whose name is the title of the link (like anchor text) and whose $URL is the reference's stored URL; opening the note opens the link as $ViewInBrowser is set to true. It is to be assumed this action occurs because the info Yojimbo places in dragged data is a URL.

However, Yojimbo can create an inbound link reference (to the Yojimbo item). In Yojimbo, select the item of interest and use Edit -> Copy Item Link (Cmd+Opt+Shift+C). Now drag the item to TB. Select the item in TB and edit the $URL and paste the Yojimbo URL from the clipboard. You can turn off $ViewInBrowser as required. The new URL will be of a form like x-yojimbo-item://E7AF56F6-59B5-439D-B24B-68415C3123DE.

Tinderbox can't create the latter link-to-Yojimbo unless the data's there is the drag info; I suspect it isn't. However, Yojimbo is AppleScriptable and this opens the option to make a script for Yojimbo that could (not tested) collect the Yojimbo item link data and 'drop' it into Tinderbox, so as to create the desired type of link.

P.S. If there are any other popular reference/file managers with inbound links of the type discussed here, it would be good to know of them. such features may now be obvious to all (the Yojimbo feature above isn't in the app's manual - I found it by sheer chance).

Title: Re: Linking to Reference managers
Post by pierfranco on Jul 2nd, 2012, 4:05am

I post my reply to Lew in this new thread.

His last post of yesterday (01/07/2012) was:

Re: Tinderbox for Academic and Nonfiction Writers
Reply #10 - Today at 12:26pm  
Thank you very helpful.  So now I have a note that reads (as a text string):
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?

Now what I can say is that dragging from Zotero to Tinderbox in the way I have explained is not useful at all because as you have experienced yourself, you end with a new note whose content consists of a bibliographic record in the RIS format which can't be handled from Tinderbox in this way for whatever use since the note has no Key attribute.
Instead a useful way of importing records from Zotero to Tinderbox has been already explained somewhere in this Forum and consists of these steps:
1) export some records from Zotero in the BiBTeX format
2) install the application BibDesk and in BidDesk install the Template for exporting records in Tab Delimited Values which you can download from http://sourceforge.net/apps/mediawiki/bibdesk/index.php?title=Templates
3) open the BiBTeX file created with Zotero using BiBDesk and export your records using the template for Tab separated Values
4) open the new Tab Separated Values file in a text editor and click Cmd+C for copying data or import the file in and Excel and select the rows which contains your bibliographic data and click Cmd+C for copying them
5) open your TinderBox database and click Cmd+V
Then for each publication you have a new note empty, whose content is still awaiting your notes, buth each of these new notes has Key attributes already set and rightly populated with author names, article title, journal title, URLs, keywords, etc. So non need to use prototypes.

In conclusion: this workflow works, but the problem is that it is obviously cumbersome since it requires too many steps and the use of 2 other applications: BibDesk and a text editor for opening the Tab Separated Values file or Excel.


Title: Re: Linking to Reference managers
Post by Sallyanne Payton on Jul 2nd, 2012, 11:58am

Thanks, David.  I had been trying to drop the item link onto the TB note, but that was giving me an unclickable piece of text.  And dropping into the regular URL receptacle yielded no results at all.  

Considering that using item links is now a standard way of coordinating across programs, is it possible to put something about linking to and from Tinderbox notes into the explanatory documents?  Or did I just miss the explanation?  

Title: Re: Linking to Reference managers
Post by Mark Anderson on Jul 2nd, 2012, 1:14pm

OK, after wasting a lot of item finding what Yojimbo can't do, the only way to get a Yojimbo in-link is manually via the Edit menu (or selection context menu) -> Copy item link. This places the URL on the clipboard.

Your next problem is that TB expects you to be dragging references and we've nothing to drag from. So, do one of:
  • Inspector (Cmd+1). Select 'Net' from the left pop-up and 'URL' from the right. Paste (Cmd+v) the Yojimbo link into the input box and click 'Apply'. $URL is now set.
  • Info view (Cmd+Opt+i). Select 'Net' from the top pop-up, and double-click the right column box for URL. Paste into the edit box and click 'OK'. $URL is now set
  • Display $URL as a key attribute for the note and paste directly into that.
I've meanwhile fired off feature suggestions (to Yojimbo) that a Cmd+Opt+drag results in a Yojimbo in-link and (to Tinderbox) that the sidebar $URL button(even if empty) has a right click menu with a paste option.  Either of this would help a lot!

Title: Re: Linking to Reference managers
Post by David Bertenshaw on Jul 2nd, 2012, 3:51pm


It's sort of hinted at in the Help file / Links page and in the aTbref webpage in a little more detail, but you may be right that it could be more explicit.

Perhaps you should post a request in the Documentation forum? (I don't know if you were posting your comment for me, or generally, but I'm not involved with Eastgate, so have no say in the documentation!)

Title: Re: Linking to Reference managers
Post by Mark Anderson on Jul 2nd, 2012, 6:03pm

@Sallyanne, if you haven't already seen it, linking out from Tinderbox is covered in this section of aTbRef.

You can't link into a Tinderbox note, as you can a DT, Yojimbo or Bookends item, though I know this is a feature suggestion so may yet appear (I have no hand in the latter as I too don't work for Eastgate).

Linking out from TB, there are host of options depending on what exactly you want to do. For instance, are you linking to a reference in a utility or directly to the asset that reference represents?  Are you linking via a URL or a file path, etc? The user has to make some of these choices - the app (and the Help) can't just impose a single solution as it doesn't fit well for all users. If the docs don't give you enough to figure the answer, ask here. We often assume our question is simple when in fact the reality is more nuanced - which is why not everything can fit in the manual; it can't hope to pre-empt every question.

Title: Re: Linking to Reference managers
Post by Lew Friedland on Jul 5th, 2012, 12:05pm

Pierfranco, thank you for that fix. It is useful, but, as you say, quite a workaround.  Are other Zotero users interested in a more direct solution? What would that entail?  Is it possible to create a prototype that would simply trans-code RIS info into a bibliographic entry? I assume not since it might have already been done.  Does it require modification at the global TBX level?  or just a script?

Title: Re: Linking to Reference managers
Post by pierfranco on Jul 5th, 2012, 12:31pm

Interesting questions. Me too I would like to know whether there is an easier way to use both Zotero and Tinderbox. There a lot of Zotero users. I expect they are much more than Bookends users for several reasons not tied to personal preferences but to efficiency and the use of resources which are located online and whose metadata can be captured by Zotero authomatically. But Zotero is not as useful when it comes to take notes and order them. I understand the advantages of using Tinderbox + Bookends. But these advantages are not enough to stop using Zotero and using the two (Z and B) of them is again only a way to make things more difficult.


Title: Re: Linking to Reference managers
Post by Mark Anderson on Jul 5th, 2012, 1:09pm

Zotero documentation doesn't describe the format of how it loads a drag drop - something any receiving app will want to know. Meanwhile, I just did a search on the Zotero forums and there seems no discussion of this topic. If no one posts there then likely the open-source coders of Zotero likely won't know about the issue of doing simple export.

Googling on this, it is seems formats like CSV & tab-delim aren't routinely supported over issues of flattening data from a relational database; Zotero uses SQLite to store data. Basically those with the technical smarts need those with the export problem to explain a suitable compromise (i.e. whether flattening the data matters).

Easier than integrating drag drop would likely be doing output to flat file; tab-delim would be good for drag-import to TB. So the debate to have in Zotero is how multi-value (MV) data is handled during output. Why not  suggest MV things like multiple contributors concatenate values with a semi-colon as TB can parse that as a list -assuming the data is passed to a list/set type of attribute.  It would also help if whoever writes the Zotero export template allows the user to set the header row (i.e. the values used to map to Tinderbox attributes on import). Otherwise, it's likely that after Zotero export you'd need to edit line #1 of the text file and re-title the headings before importing so the data goes to the desired attribute.

Another approach might be to see if Bookends accepts Zotero output, then you could go from ZT -> BE -> TB.

My suggestions are those of a fellow TB user (I don't have Zotero). If you want changes within Tinderbox such that drag/drop ZT-?TB 'just works', I urge you to write in directly to Eastgate and explain your needs. Meanwhile, don't forget to ask in the Zotero forums - they won't know about your needs if you don't let anyone there know.

Title: Re: Linking to Reference managers
Post by Derek Van Ittersum on Jul 5th, 2012, 2:12pm

Pierfranco's bibdesk description is not completely accurate. I am able to drag a reference out of bib desk directly into tinderbox in the same way that users of bookends are--no need to go into excel/numbers first. There is an option in bib desk for associating the "command drag" with a template, here, just use the tab separated values template.

Granted, this took a bit of work for me to manage and suss out--not the turn key solution that bookends is. However, once sorted out, the process is simple:

1. install zot2bib extension in firefox--this keeps bibdesk and zotero linked up so that any new entry in zotero gets fed to bib desk file as well.
2. manage template as needed in bib desk to get the attributes you want exported to tinderbox (author, title, year, etc.). (this only needs to be done once)
3. Drag citations from bib desk to create notes in tinderbox. Tinderbox will automatically create attributes based on the names exported from Bibdesk.

Title: Re: Linking to Reference managers
Post by pierfranco on Jul 5th, 2012, 4:23pm

Thanks Derek for the added explanation about dragging from BibDesK in Tinderbox. Now I would like to know if you also know how to solve these 2 problems:
1) since in the BibTeX format the publication type is not introduced by a specific label, but it is put at the beginning of each bibliographic record, preceded ony by the character @, e.g. @book, or @article, his there a way to import this value in a specific Tinderderbox attribute. Only dragging does not work, the publication type is not imported in Zotero because it has no label
2) as to the attached file/files which Zotero captures from the Web and stores in his directory: apparently there is no way to obtain from the BiBTeX export from Zotero a useful path to these files. So, when you need to open the full text file containing an article or any other document, you have no useful data in Tinderbox for finding it in your file systems and you need to open Zotero and make a search. Obviously this workflow is rather unefficient.
Moreover, there is no way to have a direct link from Tindebox to BiBDesK, or better, to Zotero. From this point of view clearly Bookends wins (as the DevonThink for the same ability). In conclusion, without the ability to have a direct link, the use of BibDesK as an intermediate platform between Zotero and Tinderbox, appears more as a disadvantage than a real advantage. This is why, all in all, exporting solutions and the use of dragging do not represent a real advantage and it remains to find an efficient way to use the 2 applications together, Zotero and Tinderbox.

Title: Re: Linking to Reference managers
Post by Derek Van Ittersum on Jul 6th, 2012, 1:11pm

Hi pierfranco:

unfortunately, I can't help you too much with either of these, sorry!

1) I only drag author, title, and year over from bib desk, so I don't know about publication type. It is possible to fully customize the templates, though, so you may be able to get that working by mucking with the tab separated values template. I got some help with this from the bib desk email list, so I imagine you might ask about this over there if you're having trouble. I've found that list to be as useful as this forum.

2) I don't use attachments in zotero, so I'm not sure whether this could be circumvented.

As you say, it's true that my method doesn't give you clickable links back to anything. But, that's not too important to me since I can easily find what i need just with author/title/year in DT, zotero, dropbox, or TBX. Automating it with links seems like overkill for my uses.

Title: Re: Linking to Reference managers
Post by Jacek Gwizdka on Jul 14th, 2012, 12:50am

I have somewhat similar needs. I want to get data from Zotero (citation info (w abstract) + tags + notes + related article links + link to a local copy of a PDF). Then I would like to import it to Tinderbox so that each citation becomes an item (an object), with notes, tags etc attached to it as separate note items. I would like to preserve related links between articles, so that those could be used to generate a map view of literature. It would be great to be able to open PDFs by using Zotero storage links. I am thinking if one might achieve these goals writing a new exporter for Zotero (see in zotero.org under support dev translators).

One other thing I would like to be able to do is to visualize using maps links between articles based on their citations (i.e. using a list of references to common citations between articles). And, of course, I do not want to construct it manually, but generate automatically from data available for indexing databases (eg., WOS, Scopus).  

Note I am very very new to TB.  So, I am speculating on what's possible.

Title: Re: Linking to Reference managers
Post by pierfranco on Jul 14th, 2012, 4:27am


what you describe would be really amazing. I could say: it's a dream. It would complement Zotero, which lacks features for analyzing connections between publications and the ability of displayng maps. It would be especially useful for anyone involved in social and humanities studies, where so much depends on the analysis of the literature and the ability to develop original literature reviews.
The feasibility, as you say, would depend on a new Zotero export format. It would make the bundle Zotero+Tinderbox a very original tool that no company can offer now. I Unfortunately so far nothing of the kind exists.
I think the posts of this series can be also useful to Tinderbox developers to show the potentialities of Zotero as a tool for doing qualitative research, in this case in any field of scientific literature.

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