Tinderbox for Academic Literature (Exported Bibliographies)


(John Wolf) #1

Hello World,

Newbie here looking to use Tinderbox for what I assume is one of its largest purposes - organizing academic literature. I have read through another post (Sense-making of Academic Literature) and am more confused than when I started. I assumed that there would be some way to read in RIS or other commonly exported biblio information from Papers, Endnote, BibTex, etc. so that each paper would be represented by a note containing these fields.

I was disappointed to see the author of the blog post was cutting and pasting things from Papers in order to get them into Tinderbox in appropriate fields. Can someone point me in a more efficient direction, or have an example of how to do this from an RIS export (not Bookends). Thanks for any guidance!

John


(Mark Anderson) #2

Tinderbox is a toolbox for notes so it’s generally a flawed assumption that lots of other people are doing any given task. Even when they are, unpicking the details shows style varies. IOW, looking for the ‘correct’ way to do things as you might with a single-purpose app, is less useful here. This also means it’s not a core role to deal with the idiosyncrasies of differing reference app’s choice of interchange.

Tinderbox has close integration with Bookends, with with it uses RIS data for transfer. By the same token Bibdesk files also use RIS data which can be imported. Pages appears to have limited export features but it does appear to export ‘bib’ and RIS files, which ought to be importable to Tinderbox via drag drop.

What reference data, i.e. RIS fields, are you trying to import?


(eastgate) #3

Tinderbox does import RIS in various forms – most often option-drags from Bookends and related citation managers.

What has proven tricky, though, is that a number of RIS fields have ambiguous definitions, and Tinderbox does not aways assign each field the way a particular scholar would prefer. In this case, it’s often useful to have a rule or a stamp that moves fields according to your preferences, or extracts bibliographic fields of which Tinderbox does not, at present, make any special use.


(James Vornov) #4

I think I’ve posted recently on my academic literature workflow, but like many others, it uses multiple programs, each for what it does best.

All of my PDFs live in Dropbox folder and I use Mendeley to provide an accurate citation, keywords, abstract and a standard title for the PDF file. I then index that folder with Devonthink Pro which provides me with a robust searchable PDF database. I love how I can copy PDFs from the sync database into other project specific databases. These databases function like the manilla folders full of xeroxed papers I used to have before libraries and literature became digital.

In Tinderbox I pull links to the files in Devonthink into notes for use when I want to refer back to the original documents. The idea is to keep my notes and summaries of the literature in a central place independent from all of the PDFs. Sometimes I will clip a critical table or figure out of a PDF and paste it into a Tinderbox note for repeated reference.

If I have any advice from my experience over the years, see how you might integrate a new powerful tool like Tinderbox into your existing workflow and build from there.


(John Wolf) #5

Yes, I saw some discussion about importing RIS data, but when I tried it I only got a text block with the various values, not attributes that could be searched, ordered, etc. Perhaps I am looking in the wrong place? Dragging/dropping is not the normal way I would import data - I was exporting it to a watched folder - but happy to try that if the fields get assigned properly.

I was hoping for the simple things - First Author, Senior Author, Title, Journal, Date, Abstract.

Perhaps I am doing this in the wrong way, or looking at the results in the wrong place, but the data appears to be in the text box only. Thanks for your help.


(John Wolf) #6

Is there a place in some documentation somewhere about these fields and how/where they are imported from a bog-standard RIS export, or what Tinderbox is expecting it to look like? Does the option drag trigger some sort of filter that assigns fields to the correct attributes?

I am totally fine with altering something that exists (i.e. a rule or stamp) but am stuck at the first step, which is getting the data into Tinderbox appropriately. Perhaps a watched folder of exported data isn’t the right way to do that.


(John Wolf) #7

Thanks James. This is a very interesting workflow to me, since I use Devonthink as well. Great idea to just link back to the data in the DT database, but I was hoping to have little “cards” for each paper in Tinderbox that had at least the title, etc. so that I know which paper I am writing a note on. So much of the literature in my field (neuroscience) has similar titles, authors, and journals that it starts to run together during a long discussion section. I so still find it easier to think about the literature as stacks of papers on my desk, probably since my desk still looks like that!


(Mark Anderson) #8

OK, it sounds like the Pages RIS export is just a dump for something that uses RIS - which for reasons explained above, Tinderbox isn’t one such app. There is tight integration with the Bookends reference app but that reflects that there are a reasonable number of users of both apps together and the developers of both apps are collaborating; you’ll note over time that some import features need specified versions of either/both apps as the devs have had to implement changes at both ends in order to make enhanced interchange just happen.

Also, as has been noted, whilst RIS is the de facto standard for reference data interchange not all apps use the same RIS fields the same way so it’s not safe to assume any inter-app reference data pathway works without testing with actual data.

I think you should look at using a tabular-data import, see here and here. For this you’ll need to set up your data export at the Pages end to make a CSV or Tab-delim file Tinderbox can then import. Worst case, if the initial export won’t generate the desired (Tinderbox attribute name) column titles you can edit those in a text editor post-export and pre-import to Tinderbox. If unsure on the Pages export, I assume it has a support forum similar to this that can help you (I don’t have/know much about Pages).


(James Vornov) #9

John

I’m a neuroscientist as well and I know what you mean. Here’s how I deal with it:

Part of my flow is to have Mendeley rename the PDFs as Author-Year-Title so that it’s easy to see which paper it is. When I copy the link out of DTP and paste into TBX I get a clickable link that is the full name of the PDF, like this:
Goyal et al. - 2015 - Randomized Assessment of Rapid Endovascular Treatment of Ischemic Stroke.pdf

You could easily set the the title of the note to that as well. I find the titles of my notes are actually Author-Year- Topic because as you said, the titles of papers don’t always tell you instantly what the subject is. For example the paper I referenced above, Goyal, is actually the NEJM report of the ESCAPE trial, which you’d never know based on the title. So I have notes on some recent endovascular stroke trials on a map with a summary note referencing all of them. I was asked how they defined time to therapy in the trials. So it was easy to assemble the relevant papers, click back to the original to carefully read the trial designs and abstract the information back into a tinderbox note on defining time to therapy for interventional stroke trials.


(eastgate) #10

Email me a sample file with, say, the first 6 references you’re seeking to import. Or, post it here, and perhaps ping me when you do so I don’t miss it. (WinterFest is keeping me on my toes today, we have a blizzard tomorrow, and I have a plane at the crack of dawn on Friday. So, striking while the iron is hot is a Good Idea.)


(eastgate) #11

The problem here turned out to be that the exported RIS files used the extension .ris, where Tinderbox 7.3.1 expects them to have a text extension.

For the moment, change the extension to .txt and all should be well again. In the future, Tinderbox will understand the .ris file extension.


(Lew Friedland) #12

James, I am a social scientist using TBX, DTP, and Zotero. This may be off topic, but can you say a bit more about how you index your PDFs from Mendeley to DTP and then use (drag?) those links into TBX? Or point me to another discussion if it exists? Thank you.


(James Vornov) #13

Lew

I keep all my PDF references in a Dropbox folder. Mendeley looks up the reference and names the PDF file with Author-Year-Title.

I then have a database in DTP that has a group that indexes that folder. That’s useful enough because I can search in DTP using it’s great tools. I also will set up project specific databases that have topical folders. I can drag the references to PDFs from the Mendeley database to those other databases and have references to those specific files. As I’ve written about, I’m just reproducing the system I’ve used for my whole career of having folders of references on a topic useful for writing papers, etc.

Mostly what I do in TBX is paste in links to the DTP files. I right click on the paper I want to reference and select “Copy Item Link” from the contextual menu. That link gets pasted into a TBX note where I write my summary, thoughts, etc. on the paper.

Even though the link copied looks like this:
x-devonthink-item://E9F74370-F266-44DA-A42D-5B0AC05FDF70

Tinderbox is smart enough to make a clickable link that looks like this:
Magill et al. - 1957 - Pharmacological and initial therapeutic observations on 6-Diazo-5-Oxo-L-Norleucine (Don) in human neoplastic dise.pdf