Off the wall: How do you organize your references (reading lists)

A place for users to ask each other questions, make suggestions, and discuss Bookends.
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Dellu
Posts: 268
Joined: Sun Mar 27, 2016 5:30 am

Off the wall: How do you organize your references (reading lists)

Post by Dellu »

Tinderbox forum has off-the-wall section where users use to discuss new (and probably wild), and only tangentially relevant issues. The developers are not supposed to respond on that section. Users discuss whatever they want--and, the developers might skim through the discussion in case there are ideas that are relevant for the future development (of the app).

In that tradition, I am here to ask other users how they are using BE for organizing, reading, and citing references. This is to share user experience; and share some insights and inspirations among us on how to make use of this wonderful software for our good.

So, the questions are:
1) Do you use BE just to insert citations in a Word processor, or use it beyond?
2) In relation to that, do you use BE to read pdf files?
3) If you are reading within BE, how do you organizing your reading list?
- are you using Labels or folders, groups or Tags or Keywords (if any) to organize the works you are reading, or you plan to read?
4) if you are using Be with other reading/organization apps, how do you do that?

I know there is no single best approach for everyone. But, sharing experiences could give us new inspirations and insights to better use of the apps--, especially for many people who are starting up with BE; or starting up to use BE for a specific purpose (for reading, or for organizing reading-list etc, the last one includes myself).
Last edited by Dellu on Fri Jul 07, 2023 1:20 am, edited 1 time in total.
Maximus
Posts: 27
Joined: Sun Oct 25, 2020 5:23 pm

Re: Off the wall: How do you organize your references (reading lists)

Post by Maximus »

It is a pity that this interesting question remained unanswered.
I'll put in my 5 cents.

1) Yes, I use BE as a reference database. It’s smartgroups as well as other features allow to manage bibliography lists for many projects.

2) Yes, I read pdf’s on IOS version of BE, using stylus. BE has all necessary functions to work with pdf. However, this mostly applies to articles. When I need to read longer texts (books), I use the eink reader.

3) I use labels to mark references that are in progress or being read.

4) I’ll try to put it in short. BE is great as a reference manager. Also thanks to IOS version and BE sync capability it is convenient to use it for reading pdf and taking notes. (In my opinion, BE's pdf reader is more convenient than reader in Devonthink).

I then export the notes to Devonthink (for saving and faster retrieval later). Some of my notes and thoughts are exported to Tinderbox, where one can work with them deeper, build mind maps, discover connections, and generate new ideas.

Would like to know how others use BE.
DrJJWMac
Posts: 345
Joined: Sat Jun 22, 2019 8:04 am
Location: Alabama USA

Re: Off the wall: How do you organize your references (reading lists)

Post by DrJJWMac »

I appreciate the reminder about this question.

1) I do not use BE to insert citations directly. My documents are in LaTeX. I export the citations from BE into a bib file.

2) I use BE on iPad to read and annotate. I find BE iPadOS to be well-suited for these tasks compared to other citation management apps.

3) I create smart groups that search for terms of relevance. I have a static group (e.g. called active). As I need/want, I move references in the BE macOS library or smart group into the active static group. I sync the library to my iPad, and I read + annotate the articles. When I am done, I sync back to macOS and move the reference out of the active static group. Along the way, I may add labels ...
BE Labels
BE Labels
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If I have annotated the file, I add a Finder tag "annotated" (in BE macOS) so that I can track the annotated PDF at the Finder level.

4) Although I have DevonThink, I do not use it with BE. This is likely more due to limits in the time I have to invest in getting through the initial learning curve on how best to coordinate the two apps for my research workflow.

I can add a bit more information on my use of BE.

* I have nearly a dozen different libraries across the disciplines/themes that I research. The ability to manage references across multiple libraries as well as in specific sub-folders, one for each library, is for me hands-down one of the best features of BE compared to any other citation management app.

* I use BE on macOS for the "heavy lifting" chores, such as removing duplicates and completing the missing citation information. I have a set of repair smart groups that search for issues such as missing DOI as well as funky or missing abstracts (where funky includes such things as a trailing set of ... marks). I have a set of status smart groups that track annotations and labels. I have a set of smart groups that look for specific annotation tags in attachment notes. I store them in a "Common Tools" library, where I can copy + paste them into any new library that I create.
BE Smart Groups
BE Smart Groups
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* More recently, I am figuring out how to share review reports from BE with my research team members who do use Windows. The ability for BE to create markdown reports that appear robustly in Obsidian is a break through in this regard.

I hope this addresses the questions in a useful way.
--
JJW
aroddick
Posts: 50
Joined: Tue Aug 29, 2017 1:27 pm

Re: Off the wall: How do you organize your references (reading lists)

Post by aroddick »

Ok, I’ll play too.

1) BE is my key PDF organizational tool on both my Mac and my iPad. It is a great way to avoid duplication, and to have a kind of main PDF HQ. All sorts of other tools, however, take advantage of that iCloud location.

2) Yes, I use BE to read PDFs, but always on the iPad and rarely on the Mac. (Although a quick return to PDFs certainly does happen on the Mac). I much prefer reading on a tablet with the pencil in hand. I used to export the PDF out to PDF Expert, but now find that BE is more than good enough. I am still somewhat frustrated by the friction of the annotation/notecard structure - As a very old school Sente user, I still think that approach on IPad was the best. As seen below, however, the extract feature and Obsidian has mostly resolved this.

3) I used to use reading lists pretty consistently, but got frustrated that they didn’t sync across. (Perhaps that has changed? I haven’t checked recently). I often find them fiddly. Although I really should try again, as I find the BE search on the iPad pretty bad. (That is where Devonthink shines). I do use tags and keywords frequently, especially as I’m working on a project - smart lists for the win.

4) I am a longtime DTPO user, and all my BE references are indexed over there where I can take advantage of the search and AI. Ever since Obsidian appeared on the scene, I much prefer to write/work with my notes there. I have taken advantage of some of the efforts by Ryan J. Murphy, including this excellent system. https://fulcra.design/Posts/Stream-anno ... EVONthink/ . That said, the new extract annotations process (which links back to specific pages in Bookends rather than the indexed DTPO folder) is almost preferable. My Obsidian notes are also indexed by DTPO. So, my workflow:

A) Find PDF, import to BE with all relevant metadata.

B) Read/mark up PDF in BE on Ipad.

C) Either wait for the Devonthink script to port over all notes to my indexed Obsidian folder, or simply use the extract annotations in Devonthink (on Mac…really hoping this becomes possible on IPad soon!).

D) then work on “literature notes” and “zettelkasten” notes in Obsidian. I tend to create “atomic notes”, each of which will have both a link to the Bookends reference but also now a deep link back to the page(s) where the information came from.
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E) Finally, I then use various plug-ins in Obsidian to search my notes. (I have been enjoying playing with “Connected Notes”, which uses ChapGPT to query your own notes - not sure it is “there” yet, but still interesting). Many times this might mean using the BE link (or now the “deep link) to quickly pop back to the original PDF.
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