Tell me about your paper-writing bookends workflow

A place for users to ask each other questions, make suggestions, and discuss Bookends.
fb3
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Joined: Tue Jan 09, 2018 8:23 am

Tell me about your paper-writing bookends workflow

Post by fb3 » Wed Jan 10, 2018 5:51 am

Hi.

Hope this topic is of interest? I wonder how other people use bookends to efficiently write a scientific paper. I'm migrating from Papers3 and want to take the chance of starting fresh to optimize my workflow (who isn't ;-))...

My main interest is: how do you organize your library?

1) One large library
2) One library for each broad topic (maybe research projects?)
3) Dedicated libraries for papers

I'd prefer 1), but have about 2200 PDFs in my old library and work on 3 manuscripts at this moment that originate from 3 quite different topics (but there is some overlap). Most of them have the PDFs, but there is a bit of chaos in there to be honest

I thought about marking papers that I use (or will use) in a manuscript (cite) either with a keyword/ tag (but I wanted to keep those for actually sciency keywords) or color. I like the idea that I a) could tell them apart visually (aka. stuff that was/ is useful as i cite it) and b) this would allow me to get good references that might need later for other work/ papers...
Colors would have the disadvantage that I might cite a paper in more then 1 manuscript... I like the idea of the tag cloud, not sure if this is more efficient than search for people?

I'm a bit of a collector and need to get more focus into my system. So I also want to build a metatag hierarchy for my stuff. Do people find that useful? Do you use that extensively? Are there any good examples, apart from the apples example?

Finally: Do you only store items you actually worked through in your library (annotated, excerpts, tagged), or do you dump everything in there?

Happy about any examples and recommendations...

fb

Jon
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Re: Tell me about your paper-writing bookends workflow

Post by Jon » Wed Jan 10, 2018 10:03 am

My 2 cents:

One large library (note: 2200 references is not large). Keep papers organized with groups (Paper 1, Paper2, etc.).

You can assign a number to a static group. When you press Command-# the selected references will be added to that group. But you don't have to be obsessive about adding the references to the Paper 1 group as you write. Remember that when you scan, the cited references are put in the Hits List. So it's easy to drag and drop them into a group (and if they're already in that group don't worry, they won't be added twice).

Jon
Sonny Software

aroddick
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Re: Tell me about your paper-writing bookends workflow

Post by aroddick » Wed Jan 10, 2018 11:56 am

I'm with Jon here -- my only difference is that I really rely on smart groups. I use the keyword field extensively, then have smart groups pull from there (for papers being written, classes being taught, etc). I also rely heavily on the color labels (specifically for "Reading" "Read- Notes Filed", "High Priority to Read" and "Clean up Reference"), which have their own smart groups as well. I find the combination results in a well organized workflow.

fb3
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Re: Tell me about your paper-writing bookends workflow

Post by fb3 » Wed Jan 10, 2018 3:00 pm

Thanks guys.

That sounds quite reasonable. How are you using colors? Espcially on the iOS version they - for me - are the most striking classification tool visually - but what would I associate with it? Broad topics maybe (statistics, climatology, soil science, modelling, ...)?

I really like this tag cloud, but I'm not sure what is most efficient? First I thought I simply use all keywords as often given in the articles, but they really vary in granularity and I would need to standardize them I guess... I also thought about my own tag system, but I guess I would have to tag the entre library for this to be useful.

Jon
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Re: Tell me about your paper-writing bookends workflow

Post by Jon » Wed Jan 10, 2018 6:09 pm

Some people like colors, I personally find them intrusive. So I would only use them for things that are relatively rare and subject to change (must read, don't forget to cite, things like that). But many people obviously disagree with me.

The tag cloud is great for drilling down through your references, but of course anything can be a tag in it (e.g. words in the title). If you mean tag as in keyword, then you usually create your own. Metatags can be helpful, but you still design and implement your own.

Then there are Finder file tags, which are a whole different thing, but many people find them quite useful.

Jon
Sonny Software

tristanlane
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Re: Tell me about your paper-writing bookends workflow

Post by tristanlane » Fri Jan 12, 2018 9:39 am

definitely agree with one library, and many groups.

as a convert I now preach the bookends way at work!

don't forget you can do smart groups as well

NilsMS
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Re: Tell me about your paper-writing bookends workflow

Post by NilsMS » Fri Jan 12, 2018 8:27 pm

Just my two cents:

I think a reference manager is not really useful without a proper text editor (I use Scrivener) and a repository for your pdfs (I use Devonthink Pro Office). I am of the conviction that in proper academic writing it would ask too much from Bookends to cover all the functions software like the one named above provide.

Furthermore, you should specify your area of interest. I tend to believe that libraries in the natural sciences with a very high turn-over rate will be organised differently than in the humanities.

fb3
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Re: Tell me about your paper-writing bookends workflow

Post by fb3 » Sat Jan 13, 2018 8:13 am

Hi.

I'm in Earth/ Geo Sciences (modelling, climate, ecosystem modelling...).

@NilsMS: So how does your setup work? So you have the PDFs inside DTP? Or do you index your bookends PDF folder (because of iOS iCloud Sync )?
I'm also switching to Scrivener3 at the moment and thus try to get into a new/ better workflow (Scrivern3, Pandoc, Bookends, maybe DTP (currently only used as a database for private documents/ paperless archive of important stuff etc))...

Cheers

tristanlane
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Re: Tell me about your paper-writing bookends workflow

Post by tristanlane » Mon Jan 15, 2018 9:25 am

I'm interested in how DTP helps with your PDF repository - Bookends does a swell job of that...

Arena of interest is clinical surgery.

iandol
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Re: Tell me about your paper-writing bookends workflow

Post by iandol » Mon Jan 15, 2018 10:32 pm

I've also never really needed something like DTP (or mind maps or whatever else I tried that never stuck). Working in Neuroscience I use Scrivener 3 for paper/project specific organisation and Bookends (one database) with annotated PDFs. To interoperate between my browser (for research), Scrivener and Bookends, I use a set of Applescripts wrapped in an Alfred workflow (see my sig), and for compiling out to a finished paper with a full bibliography automatically without ever needing to scan, I use Pandoc (also in signature).

The one sticking point is having to collaborate with endnote users! I wish there was a more automatic system to deal with conversion of unique IDs. Instead I use a Pandoc filter than takes an endnote temporary citation and converts it into a pandoc BiBKey citation which works for most refs unless there are multiple authorYEAR papers where it fails. There isn't a really simple solution to this...

fb3
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Re: Tell me about your paper-writing bookends workflow

Post by fb3 » Tue Jan 16, 2018 12:57 am

Regarding integration with Endnote users: has anyone discussed the use of universal citekeys as proposed and used by the Papers guys....?

Would that be a useful (external?) addition to the Bookends workflow? As an alternative to the buildin generate bibtex citekey? I kind of like the idea and implementation, but it doesn‘t seem like it gained traktion in general...

https://github.com/cparnot/universal-citekey-js

iandol
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Re: Tell me about your paper-writing bookends workflow

Post by iandol » Wed Jan 17, 2018 4:44 am

Oh, that is truly wonderful! Sadly Bookends doesn't support it, neither does anyone else I think. It would technically be possible to create a tool to convert Bookends Key format into this universal citekey (via Bookends Applescript support, you can read the DOI/title to generate the unique code), but you'd have to run it every so often to keep the database up-to-date. If Bookends could support this as an option that would be even better, robust keys would be excellent, but I wonder if the same could be done for Endnote?

fb3
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Re: Tell me about your paper-writing bookends workflow

Post by fb3 » Wed Jan 17, 2018 5:02 am

Yes, that was my idea.

If it's not a BE feature, I might just run an apple script from time to time (or even have it triggered automatically [only modifying/ filling keys not adhering to the universal cite key format / aka bibtex keys] - like an auto-export of the library as a bib file).

I read somewhere that there are still collisions possible, so I wonder if going from a 2-digit has to a 3-digit hash would get rid of that (loosing Papers3 compatibility - probably not worth it)?

However, my apple script skill are not really there (nor are any JavaScript skills), so I'll have to postpone that (or hope for more capable kind souls)...

MattN
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Re: Tell me about your paper-writing bookends workflow

Post by MattN » Wed Jan 17, 2018 7:28 am

The universal cite-key sounds interesting. What I don't understand is that the linked document mentions that some Author-Date combinations have many thousands of hits. Yet the proposed implementation only provides for up to a couple of hundred unique citekeys for a given author-year combination.
As mentioned by fb3 above, why not increase this to a 3 (or 4) digit hash? The citekey would still be relatively compact.

rickl
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Location: Japan

Re: Tell me about your paper-writing bookends workflow

Post by rickl » Sat May 11, 2019 12:19 am

Very late to the party here, but I thought adding to the existing discussion would be more useful than starting a new thread.

In a compromise with the one-big-database and different-databases-for-different-topics positions, I use two databases: One for my main research area (Foreign and Second Language Writing) and one for everything else. (A few items that intersect multiple research areas are held in both databases.) I know that it would be possible with skillful use of keywords and groups to replicate the Writing database view within one comprehensive database, but it seems easier to me to know that everything to do with writing (and nothing else) will be in my Writing database, and it means that I don't have to add the keyword writing to thousands of items (or put those thousands of items into a static group). It also means that, with my current iPad running out of space, I can sync only the Writing database if necessary. In addition, if one database became corrupt and I had neglected to create a recent backup (it did happen to me once), I don't lose everything. (I know this isn't great reasoning; if database corruption was a primary consideration, I guess the different-databases-for-different-topics strategy, coupled with a very rigourous backup plan, would make more sense.)

In the past I have tended to favour smart groups, based mainly on manually-assigned keywords. In order to avoid confusion between "sciency" or actual content-related keywords becoming confused with organizational ones such as those referring to the papers in which a reference item is cited, I have prepended the latter type with a special character. I used to use @ as the special character in all cases, but I now tend to use that with the names of students or friends to whom I want to recommend a paper and prefer $ for prepending to the names of papers in which a reference item is cited.

I should note that I haven't conducted or referred to any studies into whether it's quicker to drag a paper to a group or to type a keyword, but I've had a general feeling that it might be advantageous to have important information like that actually contained within a field belonging to that reference item rather than being part of the whole-database information that certain items belong to certain static groups. (If this is an illusory distinction, please disabuse me thereof!) I think I've also unconsciously carried over habits from other applications that don't allow for much hierarchy and that thereby put lefthand pane real estate at a premium. Because Bookends has folders in addition to static and smart groups, this consideration isn't really relevant.

Recently, though, considering convenience, I've been thinking that static groups might be easier. First of all, it's easier to drag items between groups (or change the name of a group) than it is to change tags in multiple references (such as changing @ to $). Additionally, smart groups don't sync over to the iPad, whereas static groups do. Keywords also don't really do anything on the iPad; as far as I can tell you can't tap on a keyword and thereby see all the items with that keyword. Although I'm happy to add items and do all my organizing on the Mac, I do like to be able to leverage that organization fully for reading and browsing when I only have the iPad with me.

As for integration,

(a) For writing, like many others, I use Scrivener 3. When I've finished my first draft of a paper, I sometimes use the basic function of selecting the cited references in Bookends and generating a formatted bibliography, which I copy and paste into the paper. I keep track of which papers to include "manually", using the methods mentioned above, and don't use any cite-while-you-write features. In my draft in Scrivener, I tend to insert the citations manually (Crawford, 2003); or put the full formatted citation into the Notes pane or in the main text right under the place where I mentioned it; or, most often, I create a new text in the same folder and show it in the righthand pane of a split window, and add formatted references to that as I cite them. You will understand from this that I am quite happy after finishing the content of the paper to fiddle around tidying up the text, arranging references in alphabetical order, etc. Maybe this is misguided, but it seems like such a small task, even if there are 100 or more references, compared to actually writing anything any good.

(b) For leveraging my Bookends database to keep track of information, generate ideas, etc., I like to put notes from Bookends into DevonThink. If I'm working with a paper that has a good literature review section I tend to take copious notes in Bookends using Command-Control-P to capture the exact wording used by the author along with the page number. If it's an important paper, I also take the time to add a title to each notecard as well as %tags to some of them. (As far as I can tell, those tags are not as useful as they could be: it isn't possible to generate tag clouds or browse using them, but it is possible to search for them, which in itself is very useful.)
What follows again applies only to important papers, but, once I've taken copious notes in Bookends, I export all the notes into a folder in DevonThink Pro named with a shortened version of the paper's title. I add a full formatted reference to the Comments field both of the folder and of every note therein. In DevonThink, in addition to folders dedicated to one paper, I also have a top-level folder containing a whole load of Subject folders. Selected notes from specific papers are replicated to the relevant Subject folder(s). For example, in a paper on vocabulary gains to be expected from certain amounts of reading, I read that:
Milton and Meara (1995) tallied learners’ vocabulary growth in periods abroad not at 1,000 but at 550 words a year.
That's useful information for my Study Abroad folder so I replicate to that folder. The entire note looks like this:
{Cobb, 2016, #16734@301}
@301 Milton and Meara (1995) tallied learners’ vocabulary growth in periods abroad not at 1,000 but at 550 words a year.

Milton, J., & Meara, P. (1995). How periods abroad affect vocabulary growth in a foreign language. ITL Review of Applied Linguistics, 107/108, 17–34.
Cobb, T. (2016). Numbers or Numerology? A Response to Nation (2014) and McQuillan (2016). Reading in a Foreign Language, 28(2), 299-304. Retrieved from https://files.eric.ed.gov/fulltext/EJ1117024.pdf

bookends://sonnysoftware.com/16734
This is where things are a bit messy and haphazard in terms of workflow. I think I have everything I need there: the actual quote, where it comes from (the Cobb 2016 paper), the orginal source of the information (Milton & Meara 1995), and a quick way to get from here to that information in Bookends. But I often forget keyboard shortcuts and still am uncertain what the fastest way to accomplish this is and tend to include redundant information.

Apologies for the ultra-long message. About 16 months have elapsed since the older messages in the thread. I'd be very interested in hearing about any evolution in people's thinking and workflows.

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