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Literature review/sensemaking of scientific papers (Read 27997 times)
Jodi Schneider
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Literature review/sensemaking of scientific papers
Nov 20th, 2012, 9:44am
 
I am looking for advice and examples of using Tinderbox for sensemaking of scientific papers. Any prototype documents you could share? Or suggestions for how to learn Tinderbox in this context?

My goal is to synthesize the literature on a topic. I plan to
* produce an annotated bibliography of a small list of key papers, to share with collaborators and on my blog
* write about the topic in the related work/state of the art section of my Ph.D. dissertation.

I also want an enduring representation for later use** -- and to learn Tinderbox (which seems awesome but requires that I grasp a new mental model).

So far I have gathered 50 papers that are related to various aspects of a topic (claim representation/argument extraction/...).

I learn best from examples, so I'd be really grateful if you could share an Tinderbox document organizing papers, or suggest ideas for other tools that might help me get started. I've done lit reviews before, hoping to improve on the process and have an enduring record.

-Jodi
jodischneider.com/jodi.html

**For instance, I might later produce other papers related to this topic (e.g. a lit review with an analysis of gaps and opportunities for future work)
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Mark Bernstein
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Re: Literature review/sensemaking of scientific papers
Reply #1 - Nov 20th, 2012, 3:53pm
 
One starting point might be to look at the built-in Reference prototype.  It's just a starting point -- it may have too many fields for your field, or the fields might be the wrong ones for you.  Feel free to adapt it!

You might also want to use Bookends to help import those references to Tinderbox, though it's not really that much work just to paste the information from wherever you have it.

I'd suggest spending a couple of hours just noodling around with your references and notes. Import, arrange, organize. See how that goes!  Then come back and let's explore how things might work.

Though not your field, the References episode in the Tinderbox World Building seminar might be useful, too.  http://www.eastgate.com/Tinderbox/WorldBuilding/References.html
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Ted Goranson
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Re: Literature review/sensemaking of scientific papers
Reply #2 - Nov 25th, 2012, 9:50pm
 
Jodi —

I am also starting something like this, in addition to my other TBx uses.

It may be enough different to not matter, but here goes.

The task is that I get a lot of scientific information. When I find something interesting, I clip it in some way — frustratingly many ways. Now I have an unusable mountain of stuff. The task is to go through it and perform a triage:

— Some information is merely interesting. Read it and discard.

— Some information is interesting but the source is not essential to keep. In this case, I excerpt the bits in my own terms and enter it into TBx. Over time, the expectation is that this will result in a coherent survey of how things that interest me work. The source is then tossed.

— Some information is like the above, but I want to keep the source for perhaps a scientific paper. In this case, the ideas are excerpted as above, but an in-line reference is made. The process in my case is simple:

1) Open the PDF in PDFPenPro and clean it up, or make it a PDF if it is not.

2) Enter the paper in Bookends, adding the PDF as an attachment. You'll need to use a reference database eventually. I've spent countless hours evaluating these and can save you some time; just go with BE.

3) Make an inline linked reference to the BE entry, using the technique mentioned in a recent thread. (I'll ask Mark A to point us to that). This gives you something that looks like the entry in a final document but that links to BE and the original document.

There are several other options, and I am sure you will hear them. But this to my mind uses TBx where it excels (evolving structure from small notes), and BE where it excels.
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Mark Anderson
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Re: Literature review/sensemaking of scientific papers
Reply #3 - Nov 26th, 2012, 2:56am
 
I believe the thread to which Ted refers is this one.
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Jodi Schneider
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Re: Literature review/sensemaking of scientific papers
Reply #4 - Nov 27th, 2012, 9:10am
 
Thanks, Ted. For inline annotation of papers, Sente [1] is great. (I'd love to hear what made you choose Bookends; I'm continually evaluating citation management software.)

I think the triage process you go through is a common one!

I didn't realize that stuff could be drag&dropped from Bookends; I'll give that a try since rekeying citation info drives me nuts.

[1] http://www.thirdstreetsoftware.com/site/SenteForMac.html
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Mark Bernstein
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Re: Literature review/sensemaking of scientific papers
Reply #5 - Nov 27th, 2012, 10:56am
 
One nice thing about citation software right now is that it's reasonably inter-operable; you can move easily between lots of programs.

Don't rekey citations!  There's bound to be a better way Smiley

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Jodi Schneider
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Re: Literature review/sensemaking of scientific papers
Reply #6 - Nov 27th, 2012, 11:08am
 
The best approach is to capture metadata when getting PDFs in the first place (e.g. with Zotero or within "targeted search" features of most bibliographic managers).

However, in my experience, the "detect metadata from PDF" angle is sorely lacking -- in part because publishers don't include the metadata, so it's pulled out with content-based heuristics (and for old PDFs, also OCR). Mendeley, for instance, seems to be the best software at this but it thinks that everything is a journal article. So continually requires correction (which is what I mean by 'rekeying' here). Bookends, as it turns out, wants me to input metadata for the PDFs since it doesn't auto-detect; nor can you just dump a folder into it, it wants files one-by-one.
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Mark Anderson
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Re: Literature review/sensemaking of scientific papers
Reply #7 - Nov 28th, 2012, 6:32am
 
Readers of this thread have asked (off forum) if the admin can plit off some branches to keep the topic on track. So, your forum admin has made 2 new threads holding sub-thread originally part of this one:
Before anyone ask, absolutely no censure is implied at what anyone has written. Indeed it's all of use, but those posts do branch from the original question in which there are clearly more people interested than active posters.
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« Last Edit: Nov 28th, 2012, 6:43am by Mark Anderson »  

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Mark Anderson
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Mark Bernstein
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Re: Literature review/sensemaking of scientific papers
Reply #8 - Nov 28th, 2012, 5:06pm
 
The lead developer at Bookends asked me to pass the following along:

Quote:
In my experience, the "detect metadata from PDF" angle is
sorely lacking -- in part because publishers don't include the
metadata, so it's pulled out with content-based heuristics (and for
old PDFs, also OCR). Mendeley, for instance, seems to be the best
software at this but it thinks that everything is a journal article.
So continually requires correction (which is what I mean by
'rekeying' here). Bookends, as it turns out, wants me to input
metadata for the PDFs since it doesn't auto-detect; nor can you just
dump a folder into it, it wants files one-by-one.

1. Bookends will detect dois in pdfs. If it finds and resolves one,
it will enter the metadata for you automatically.

2. If it cannot find a doi, it will still get the metadata for you
(if it can) if you use the Autocomplete Paper feature. With this,
you choose a source (e.g. Google Scholar, PubMed, etc), enter a few
bits of info about the paper (author and perhaps a few words from
the title) and Bookends will fetch the metadata for you.

3. Finally, try drag and drop of a folder *with the Command key held
down*. Bookends will offer to attach each pdf in the folder to its
own record, and autofill the metadata if it can (and if not, you can
Autocomplete Paper on the ones that didn't have a doi).

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