Zettelkasten Forum


What RMS for a mix of academic papers, other pdfs and articles from the web?

Hi!

In my work as a journalist I use a lot of different kinds of sources. I read a fair share of academic papers, but also a lot of other pdf documents (published by magazines, government, businesses etc) and articles and blogposts on the web. So far, I've been using Devonthink to store local copies of everything I think I will need in the future.

What advantages would I get if I switch to a RMS like Zotero?

One big hurdle in my current workflow is how to extract highlights and annotations from the pdfs I read (preferably as markdown). Is that something Zotero (or any of the other more academic-tuned RMSs could help with)?

Are Zotero et al tailormade for academic papers that they wont fit my need for a RMS that also handles other pdfs and web archives?

/Anders

Comments

  • I wouldn't store any material besides texts that are so deep that you read them over and over again. The bible for a theologican, Nietzsche's Work for a philosopher or something similar would fall under that umbrella.

    I go thoroughly through any text and extract all what I can to notes and then the text will be deleted.

  • Zotero helps mostly with organizing and inserting metadata for academic references. It can also help in managing reading and annotations of PDFs. With the extension Zotfile you can send and retrieve PDFs to a dropbox location for easy access with an iPad for example and then keep track of changes. Zotero can then automatically extract annotations although you get them inside zotero and have to copy-paste to another location. Zotfile is also good for automatically moving and renaming PDFs to keep them linked to the Zotero database.

    There is this mac application called Highlights that promises to extract annotations directly to a nicely formatted Markdown file. That looks great and makes a Linux user envious :)

    http://highlightsapp.net/

  • @magnus said:

    Zotero helps mostly with organizing and inserting metadata for academic references. It can also help in managing reading and annotations of PDFs. With the extension Zotfile you can send and retrieve PDFs to a dropbox location for easy access with an iPad for example and then keep track of changes. Zotero can then automatically extract annotations although you get them inside zotero and have to copy-paste to another location. Zotfile is also good for automatically moving and renaming PDFs to keep them linked to the Zotero database.

    There is this mac application called Highlights that promises to extract annotations directly to a nicely formatted Markdown file. That looks great and makes a Linux user envious :)

    http://highlightsapp.net/

    Thanks for all the suggestions!

  • @sfast said:
    I go thoroughly through any text and extract all what I can to notes and then the text will be deleted.

    I might end up there eventually, but in the meantime I think I still want to store the original for easy access as well. :)

  • In that case, I would still delete it and if you need the text later on: Google it.

    But I don't think that is what you'd like. I think I would just put it in DevonThink or any other application that allows for full text search and then search it as I needed it. (For me this app would be google since I mostly would need science papers that are available via the wonder wold of the internet)

  • @sfast said:
    But I don't think that is what you'd like. I think I would just put it in DevonThink or any other application that allows for full text search and then search it as I needed it. (For me this app would be google since I mostly would need science papers that are available via the wonder wold of the internet)

    No, since scientific papers are only a small part of my research, I don’t trust my google-skills to find something again. Also, there is always the risk that what I’m looking for has been removed from the web.

  • That might be true for some sources, but DOI-backed PDFs should be very reliable to find again in science paper hubs, wink wink, even if the original goes down.

    Author at Zettelkasten.de • http://christiantietze.de/

  • @thoresson said:
    No, since scientific papers are only a small part of my research, I don’t trust my google-skills to find something again. Also, there is always the risk that what I’m looking for has been removed from the web.

    What are typical texts for you?

  • @sfast said:
    What are typical texts for you?

    Articles from Wired, New York Times etc, reports from research companies like Gartner and IDC, PDFs from governmental organizations, blogposts. But also podcasts and YouTube videos.

  • Ah, so more journalistic stuff? Then I would use the web archive for permalinks.

    The audio and video thing is a hassle. :disappointed:

  • edited July 18

    Contrary to the opinion of others, I would definitely attempt to store your resources.

    I'd throw all of that in DEVONthink. Work out a basic file-naming system for yourself, make some folders in DEVONthink and let it do the rest. It makes (most) things searchable and takes care of storing it for you. Perhaps even add some tags and create some smart folders for easier retrieval.

    One thing I like about DEVONthink is that it makes single paged PDFs from most webpages, conveniently storing the layout.

    Now of course it goes without saying that for the notes itself, the Zettelkasten system is much, much better suited (and not really achievable through DEVONthink, so I'd stick to The Archive for that).

  • At the moment, I lean towards Zotero. But I do the lion share of my writing in Ulysses , and having Zotero and Ulysses to work together doesn’t seem to be totally straight forward.

    Any suggestions for a RMS that makes it easy to insert cite keys in Ulysses (and The Archive) and also processing the final text, adding references and creating the bibliography?

  • With MultiMarkdown bibliography references (e.g. [p 27][#author1234]), you should be good to go if you e.g. use BibDesk to manage a .bib file, since you can convert the MultiMarkdown file to LaTeX and then include the original .bib file just like that. Ulysses doesn't offer nice syntax highlighting, so you'll be looking at the raw Markdown in this case.

    Author at Zettelkasten.de • http://christiantietze.de/

  • edited July 22

    @ctietze said:
    Ulysses doesn't offer nice syntax highlighting, so you'll be looking at the raw Markdown in this case.

    What do you mean with “raw Markdown”?

    But as long as I go with a software that can generate a .bib (I’m leaning towards Zotero) and MMD citations, I’m good (even tough I at the moment I’m struggling to the tutorials of how to make the actual inclusion of the footnotes and bibliography - does anyone know of one that works with Ulysses?)

    /Anders

  • edited July 23

    @thoresson said:

    What do you mean with “raw Markdown”?

    I don't have Ulysses around, but I think it'll display differently than regular links, which hide the square brackets and the link destination from you. Or images. It's more like an interactive, embedded widget to configure when you click to edit; with the unsupported bibliography references, you'll see the [123][#abcdefg1234] in your document plainly.

    Author at Zettelkasten.de • http://christiantietze.de/

  • +1 for storing locally what you know you’ll need. Even academic sites get reorganized and old links break and sometimes papers get lost, or deliberately removed.

    In addition to the above-mentioned apps, have you looked at Papers 3?

    I’ve used Highlights, but it was buggy. The developer has updated the app so I keep meaning to give it another try. It’s a great idea; it just needs to be less flakey.

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