5 ms·

Ask HN: What system do you use for tracking and annotating academic papers?

• aheilbut 11y ago
  Mendeley is not bad at all. I save papers to a Dropbox folder, organized directories by general topic / relevance to project. Mendeley (on one computer) watches that folder, and imports the papers and fills out the bibliographic info, mostly automatically. Mendeley lets you tag and organize things in virtual folders, as well as store notes and annotations. The bibliographic info for subsets of papers (eg. with a particular tag) can be exported to bibtex files when writing. Mendeley is available on all platforms, and syncs across multiple computers. The only catch is that the links to PDFs are only maintained on the 'master' that watches the folder. (If you try to watch folders on multiple instances of the same synced database, all hell breaks loose.) Pubchase (www.pubchase.com) can also sync with your Mendeley library, and does a surprisingly good job of recommending papers of interest.
  • jessriedel 11y ago
    What is the advantage of Mendeley over Zotero? My understanding is that Zotero implements essentially all of Mendeley's features, and is free and open-source. (Here's the comparison according to Mendeley: https://www.mendeley.com/compare-mendeley/ https://www.mendeley.com/compare-mendeley/ ). I think most people just haven't heard of it. It's supported and developed by a foundation, and if you ever stop liking it you can take all your data and move it to Mendeley very quickly. On the other hand, I don't think it's easy to leave Mendeley: https://feedback.mendeley.com/forums/4941-general/suggestions/1186641-bulk-export-pdf https://feedback.mendeley.com/forums/4941-general/suggestion... EDIT: Here's how Docear compares them: http://www.docear.org/2014/01/15/comprehensive-comparison-of-reference-managers-mendeley-vs-zotero-vs-docear/ http://www.docear.org/2014/01/15/comprehensive-comparison-of... Zotero lacks Android/iOS apps (except for Zandy on Android, which is poor).
    • aheilbut 11y ago
      I should probably give Zotero another try. At the time I started using Mendeley, it was really the best at automatically importing metadata for pdfs. And I don't think Zotero does the watch folder thing. One thing I do like about Mendeley is that it's content to leave my pdfs alone in the filesystem (and I can rely on Dropbox for syncing those), whereas Zotero seems to want to import everything and manage the files itself.
      • jessriedel 11y ago
        You're right about Zotero wanting to manage the PDFs. With regard to a watch folder, there's ZotFile which works very nicely (but of course something that's fully integrated is always preferable). http://zotfile.com/ http://zotfile.com/
  • saboot 11y ago
    I like that mendeley can rename files according to a format, however it only works when it's setup to use its own local folder (which mirrors the mendeley cloud space).
  • praseodym 11y ago
    I'm currently using Mendeley, but its BibTeX export is really lacking: - http://feedback.mendeley.com/forums/4941-general/suggestions/444383-fix-capitalization-of-journal-titles http://feedback.mendeley.com/forums/4941-general/suggestions... - https://feedback.mendeley.com/forums/4941-general/suggestions/1543195-possibility-for-choosing-which-fields-are-included https://feedback.mendeley.com/forums/4941-general/suggestion... - https://feedback.mendeley.com/forums/4941-general/suggestions/859693-improve-support-for-diacritics-in-bibtex https://feedback.mendeley.com/forums/4941-general/suggestion...
• GFK_of_xmaspast 11y ago
  I use Zotero (https://www.zotero.org https://www.zotero.org), and am liking it a lot. (It's also independent, as opposed to Mendeley which is owned by Elsevier)
• jessriedel 11y ago
  I use Zotero, with annotations typed as PDF comments. The biggest thing I am lacking is a hardware device and compatible software for hand-written notations that actually works smoothly in practice.
  • pedrodelfino 11y ago
    Same here. Handwriting is much better in order to retain the information, science has already proved this. However, currently, there is not a very good product (software and hardware) in the market to allow this. Unfortunately, I still read important things in the printed versions.
• pen2l 11y ago
  Reuters' Endnote. (have any of you guys tried it? Curious to hear your thoughts)
• huac 11y ago
  when I have to take notes from pdf's, webpages, and other sources, I've found Word to still be the most effective. i paste relevant sections in (with a macro to keep only text), and highlight the most important stuff. i have macros set up for condensing text, cutting whitespace, click-and-drag underlining the biggest advantage of this is how flexible and easily searchable it is if i'm working with different content types.
• 88e282102ae2e5b 11y ago
  I disliked Mendeley, Zotero and Referencer. I've been thinking about going back to just taking notes in a git repo in markdown (and keeping it on Gitlab or somewhere else that renders markdown properly. Also uploading the PDF to the repo alongside the notes, and having the main README have titles, DOIs and links to the relevant notes. Obviously you can't make citations easy like in any of the actual applications designed for this but I'm more focused on just understanding the material for now.
• therobot24 11y ago
  I use Qippa (http://www.qiqqa.com/ http://www.qiqqa.com/) simply because it's fast. It's probably similar to Mendeley - i can tag, organize, mind-map, highlight, share, etc.
• RogerL 11y ago
  PDFs in structured folders. I.e papers papers\filtering papers\math papers\languages papers\filtering\IMM papers\filtering\MHT You get the idea. When I read I highlight using the yellow highlighter, and type notes in Evernote. Evernote is searchable. I make this 'cloud'y by using bittorrent sync to share across computers. That's all free. The folder method of holding papers/book/topics is nonideal - a paper can cover 2+ topics, for example. But it works, sort of, and I can still search. I use Everything (from void tools) to search on title or author, and then you can search inside pdfs with various tools. Mendeley and such were nonstarters for me. Any service that makes me pay for cloud storage has lost the war, IMO. I already have 1TB each from Dropbox and google, more from Microsoft, why am I paying you for cloud storage? I was having trouble with syncing with Mendeley, but reading the other comments aheilbut worked out the issues, so maybe i'll give it another go. I want to control the cloud, syncing, and file structure choices, not have a program decide those for me. I don't worry about reading lists - I need to read what I need to read. When I get around to that topic there may be more relevant stuff than I selected back at the time, anyway. YMMV. If I see a paper of remote interest that I can legally grab I grab it, dump it into my file structure, and then rely on search to bring it to my attention again at the appropriate time.
• gone35 11y ago
  Academic here. If you don't mind closed-source, use OmniOutliner.
• bosie 11y ago
  I use Papers (http://www.papersapp.com/ http://www.papersapp.com/) and DevonThink (http://www.devontechnologies.com/products/devonthink/overview.html http://www.devontechnologies.com/products/devonthink/overvie...). The latter holds my notes, highlights and every piece of information I find somewhere; it can do basically any format, not just PDFs. Additionally it links them up with other things in your database (https://static1.squarespace.com/static/544bf5dae4b0dd27d7018fa8/t/55acedcfe4b0b14a3f0ff0ba/1437396435522/ https://static1.squarespace.com/static/544bf5dae4b0dd27d7018...). This plus the superior search makes retrieval a lot easier than in any other application I have found so far.
  • quantisan 11y ago
    I use Papers too. I've set it up so that all my loaded papers are automatically re-saved in a structured library as plain PDFs /Category/Year-Author-Title.pdf. That library folder is on my Dropbox. So I can access it anywhere else without Papers installed.
• jmathai 11y ago
  Surprised to see no one has mentioned Hypothes.is. Open source and already being used to annotate academic/scholarly works. https://hypothes.is/blog/ https://hypothes.is/blog/
  • dwhly 11y ago
    Thanks @jmathai. I'm the founder of Hypothes.is, and here to say that we're delighted for researchers us to use us in this way. So far, our primary emphasis has been on collaborative annotation with others on documents vs individual annotation. That said, we hope to layer on additional features where appropriate, and to collaborate with other products and services when we can--particularly ones that support open standards and open source software. On Dec 1, we announced an initiative to bring an open annotation client to all scholarly works over the next several years. https://hypothes.is/annotating-all-knowledge/ https://hypothes.is/annotating-all-knowledge/
• wgjordan 11y ago
  For organizing your papers, Paperpile (http://paperpile.com http://paperpile.com) is an excellent up-and-coming reference management tool. It integrates with Google Drive and has a full-featured PDF annotator and note-taker. It's helped me out tremendously in organizing my academic research.
  • saboot 11y ago
    Paperpile looks especially interesting, especially since I already use google drive to organize all of my documents. But $36 recurring yearly? .. Eh.. It would be nice if the single user mode was free, and the paid model included the collaborative features.
• fsmunoz 11y ago
  Docear (http://www.docear.org/ http://www.docear.org/) + Zotero (https://www.zotero.org/ https://www.zotero.org/), with Emacs+AucTeX for the writing. They all fit together. >- recording notes and ideas from papers Docear's core is a mind-mapping application that is used for taking and linking to different notes - you can take notes using whatever app you want and then add it to the mind map- > - recording where I got a paper from, ie was it referenced from another paper or found on a particular site? With Zotero this can be as simple as a click, it adds the current page and document along with metadata and can export it to bibtex or the like, thus tying it to docear. > - even how to read a paper. This is not a technology problem, investigate approaches such as SQ3R (https://en.wikipedia.org/wiki/SQ3R https://en.wikipedia.org/wiki/SQ3R) which is the one I use (actually the variation SQW3R) or PQRST (https://en.wikipedia.org/wiki/Study_skills#Reading_and_listening https://en.wikipedia.org/wiki/Study_skills#Reading_and_liste...). I keep a low-tech approach on purpose for this, but there is nothing preventing using Docear for this as well of course. >Right now I use google docs with sub folders for unread, read and implemented papers. I tend to use Acrobat to highlight sections of a paper that I find important and Evernote for saving more important notes. Docear is supposed to be used with PDF annotators, it then scans the PDFs and automatically creates the references mind map. > If anyone has a good system for how to read papers more efficiently, how to store notes/annotations for a given paper, or how to track a todo reading list I'd be very appreciative! For reading them take a look at those I mentioned before, SQ3R has been useful for me in terms of articles and books. To store things Zotero is very good for anything which is done via browser. Docear is useful for managing different "projects" (could be disciplines, specific papers, etc). For TODOs you can either also keep them in Docear (since it has a mind mapper you can create a new node and add the references you exported from Zotero there, actually Docear scans the library and automatically adds any PDF to a specific node) or use something like Evernote.
• rdc12 11y ago
  Currently I am just using an org-mode file, but this is more like a reading log along with a bit of meta-data (author, keywords etc). So far it has suited my needs quite well, but I don't really annotate them, but I do add a one or two sentence overview, which is enough for me.
• veddox 11y ago
  I use Mendeley, and have found to be quite good for my needs. Previously I used ReadCube, which was also quite good - unfortunately it doesn't run on Linux, so I had to ditch it. I would love to try out Citavi, it sounds even better than Mendeley, but again it doesn't do Linux. (Note: Citavi carries a fairly hefty price tag, but if you're affiliated with some university, chances are you can get it for free. The other two are freeware with the option to upgrade to premium plans.) All of these are closed-source, so if you're an FSF-fan, steer well clear. Otherwise: well worth the use of!
• zhte415 11y ago
  Email yourself if you're afraid of remembering. Works for pretty much every kind of idea. Then, just remember.