I need a better research workflow


More and more of my process for research goes into native Apple apps and utilities, with a few 3rd party apps used based on potency. Having said that, most of my researching and filing are done on an iMac, taking advantage of simple nested folder structures and a simple file-naming taxonomy, stored in iCloud, that can later be accessed via the Files app on iOS through various means.

I understand the desire to dump things into piles and just use tagging for everything, but I find that the extra steps I take to deliberately file items (with a minimal bit of tagging) helps me stay mentally organized as well, allowing me to feel on top of any project I have going.



There are numerous web services that will send you pdfs of web pages.

From Safari on iOS if you have Dropbox installed you can Share>Save To Dropbox and you’ll save a PDF of the page! And since iOS 11 you’ve been able in Safari to Create PDF, then Save File To and choose iCloud Drive (maybe other cloud services, I haven’t tried).

There are a number of Mac apps that convert sites to PDFs (I think the one I last used was Capto which has its own browser built into the app), and there are simple workflows from there to upload to a cloud service.



Sharing a web page to PDF Viewer will also create a PDF which will be waiting for you when you next open the app. Like Shortcuts, it doesn’t give you any fine control over the rendering though. It must be using different settings though, because they’re not the same. I sometimes use it if the Shortcut above doesn’t give good results.

I’ve thought of putting together something in Pythonista to try to replicate much of the functionality of the Mac print dialog (page size etc.) but haven’t got anywhere with it.

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Keep It is sort of a nicer version of DEVONThink and Evernote.

It’s a subscription service, a little less expensive than Evernote, but it has some nice ways of importing on iOS. Federico Viticci has some nice Shortcuts for it as well, too.

If all you want is a PDF of a website, you can do that with the tools already mentioned, and/or with Shortcuts… but I wouldn’t be surprised if that doesn’t actually end up being as nice of an experience as you’d like.

If so, definitely check out Keep It.

My $0.02.



Thanks, this one seems to give good results. I didn’t know that save to Dropbox creates a Pdf, that could also be handy (but it also creates an iPhone optimized Pdf, but at least with links).
The iOS-wide Pdf tool doesn’t preserve the links, as I said above.



I still love the Clipper of Devonthink on the Mac. You can easily choose the destination, apply tags, notes etc. But then again I hate DT: Today I clipped a bunch of webpages and for the first time really made use of the „notes“ field that you can attach to a DT-file. But then I realized I have no idea where I find these notes from within DT! I‘m sure I will find out (didn’t have the time to research this morning and I‘m not on my Mac right now). But the fact that I have to RESEARCH where to find the notes is typical for DT on the Mac.
On iOS I like DT much more. But here I miss the clipper.
Maybe I’ll stick with DT for file management and use that converting service to get my Pdfs when capturing something from iOS. I could probably save those files to a watched folder to import them to DT automatically.



DEVONthink’s Help file mentions this – the “notes” are put into the [Spotlight] comments field of the document – when is good because if you ever export the document then the comments are preserved and viewable in Finder’s get info panel.

(Note that there is also a separate “comments” field that is available for PDF files – which is a standard metadata element available to most apps that work with PDFs. DEVONthink didn’t create this additional “comments” field, it just supports viewing and editing it.)



Hey thanks! I saw this, but I didn’t understand it’s the same as the comments I made in the clipping tool (where it isn’t called spotlight).



Yes, they have a very bad habit of using multiple names for the same feature — “Notes” == “Comments” (sometimes) == “Spotlight Comments”.

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Option + 4 on Mac :wink:

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I think this can all be accomplished in Apple Notes. Check out this Shortcut:

https://www.icloud.com/shortcuts/df780cbebe504dc28de4cae15d3b1550 (Updated)

It’s based on the one I posted above with a bit more functionality added. Steps:

  • Select pages
  • Create a note pre-populated with page title, URL, date saved, and PDF file name (and you can add whatever else you want)
  • Add the PDF to the newly created note

You can’t search the metadata by field but it’s all natively indexed in Spotlight on iOS and Mac so you can search the full text of metadata and the PDF itself. And you can annotate the PDF itself within Notes (as well as write up further notes etc. about it).



That’s an interesting approach. I‘ll look into that.



I am really struggling with my workflow. I’d love to have everything in one place (software), but every product has significant strenghts and weaknesses.

Papers: I manage them in Papers 3. Reason: I can search databases (PubMed) and import stuff, creating proper references is a breeze.

Books: I have many eBooks and scanned a lot of books. I could stick them into Papers, but that would bloat it. Papers/articles are in Papers because I review them on the go (iPad) and putting all my reference books into it would be too much. That’s why they live in Calibre.

Referencing: I export .bib files from both Papers 3 and Calibre and add both sources into TeX/LaTeX documents. So, as sources I have articles.bib and books.bib. I also use BibTeX to manage a third .bib file which includes legal sources I often need to point to. Seems complicated, but it’s the easiest way to go. What I disklike: Papers3 has a great citation tool (just press CTRL+CTRL and a small search window allows appears). Referencing books and laws isn’t that easy any more. I am considering importing both of them into Papers (without the PDFs), but not yet convinced.

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Hmm…using a separate system for articles and books seems a big hassle. Plus there are all the miscellaneous grey lit. type docs which might not fit either…can Papers reallly not handle all the books? I haven’t looked at it for a while and don’t know how it handles sync.

How is your legal bib file set up? I am working on some stuff for which in 3-6 months I will need to start getting out which will mean getting all my citations of legislation, court cases, etc. in order & at this point these are all just in various notes. I’d like to get all the refs. into BibDesk but none of these are standard BibTeX publication types so presumably I’d need to start creating custom types or find a source for prototypes somewhere.



Quorm, it sounds like you have used MN quite a lot. I just downloaded it and am struggling some with the UI. I cannot find a user manual or basic instructions. Can you point me toward anything that would provide a good overview of using the app? Thank you!



There is a “Quick Guide” available from the Help Menu. I agree that a manual would be helpful.

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Just browsing the MarginNote site, I found this URL with a manual and some how to videos. It might be useful if you haven’t already found it.

Update: I see the manual link 404s. Found a version of it on Scribe.



Papers library right now: 1,87GB. Calibre library (the books): 55GB. I don’t want to move that huge pile of data into the Papers library, which is synced through Dropbox to the iPad. I quess I`ll just import the references.

Nothing fancy. I don’t do legal work, sometimes I just need to point out some regulation/law. Since everything I refer to is available online, I set the up as “webpage”. Last year I had to answer a lot of stuff with “the GDPR says so in §3”, so I have an entry for GDRP (in German, but you get the meaning):
author = {{Europ{"a}isches Parlament, Rat der Europ{"a}ischen Union}},
title = {Verordnung (EU) 2016/679 des Europ{"a}ischen Parlaments und des Rates vom 27. April 2016 zum Schutz nat{"u}rlicher Personen bei der Verarbeitung personenbezogener Daten, zum freien Datenverkehr und zur Aufhebung der Richtlinie 95/46/EG (Datenschutz-Grundverordnung)},
year = {2016},
bdsk-url-1 = {https://eur-lex.europa.eu/legal-content/DE/TXT/PDF/?uri=CELEX:32016R0679&from=DE},
date-added = {2019-02-01 14:44:45 +0100},
date-modified = {2019-02-01 14:56:33 +0100},
url = {https://eur-lex.europa.eu/legal-content/DE/TXT/PDF/?uri=CELEX:32016R0679&from=DE},

So, with \cite{DSGVO}, I can include a reference to the GDRP and in the reference list, the full title and the link to the online resource are added. My legal.bib isn’t that big, just the regulations/laws I often need to refer to when answering stuff. And the full title of some of them is a pain to spell out. You might ask why not just create Text Expander snippents: I prefer to include references and the link in the list and with cite/citep/citet/citetitle I can get different formats. I can even use citeurl to just include the link to the online resource.



The manual version on Scribd is v2.x – the app is currently on v3 and is very different than 2.x.



So can I make annotations in MarginNote and then export them? Or is that feature only in LiquidText?

I have a 95 page PDF that I have to copy edit and send back to the designer. Looking for the easiest way to get her the comments.

All recommendations gratefully accepted!