Hacker News Board Hacker News, browsed like a classic message board
Live data from Hacker News

Zotero: An open-source tool to help collect, organize, cite, and share research

zotero.org

Post reply on HN
Print view View original

101–110 of 168 posts

Re: Zotero: An open-source tool to help collect, organize, cite, and share research

#101

Post by jknz »

I use a little script [1] and a passive approach to quickly find a PDF I am looking for among a few thousands of academic PDF. The workflow (illustrated in the GIF [2]):

- as I read new PDFs in the browser, the PDFs are passively downloaded typically in a Downloads/ folder.

- This results in thousands in papers lying in Downloads/ or elsewhere.

- The command p from the script [1] let me instantaneously fuzzy-search over the first page of each pdf (The first page of each pdf is extracted using pdftotext, but cached so it's fast). The first page of academic PDFs usually contains title, abstract, author names, institutions, keywords of the paper; so typing any combination of those will quickly find the pdf.

What is particularly convenient is that no time is spent trying to organize the papers into folders, or importing them into software such as zotero. The papers are passively downloaded, and if I remember ever downloading a paper, it's one fuzzy-search away. Of course it does not solve the problem of generating clean bibtex files.

[1]: the script: https://github.com/bellecp/fast-p

[2]: an illustration in GIF: https://user-images.githubusercontent.com/1019692/34446795-1...

edit: The script has been moved from the gist to the public repository https://github.com/bellecp/fast-p

Re: Zotero: An open-source tool to help collect, organize, cite, and share research

#102

Post by jhbadger »

nanna wrote: post #97
selimthegrim wrote: post #95

Earlier quoted context omitted.

Yes, I use that function in Zotero all the time.

Why not just use pdfgrep?

Because the info often isn't in the pdf file itself (at least in a parseable way). Typically metadata readers figure out what the paper is and then goes to a bibliographic database to pull out the full title, author list, page info, etc.

Re: Zotero: An open-source tool to help collect, organize, cite, and share research

#104

Post by jhbadger »

singingfish wrote: post #50

Zotero is awesome. 80% of the academic type people I've introduced it to have switched. The other 20% have Endnote stockholm syndrome.

Particularly bench biologists tend to have "The only way to write a paper is Microsoft Word and Endnote". Zotero is considered a bit eccentric and using LaTeX is practically unheard of. As a computational biologist I like Zotero and LaTeX but am often forced not to use them in collaborations.

Re: Zotero: An open-source tool to help collect, organize, cite, and share research

#105

Post by tonyg »

PaulRobinson wrote: post #88
tonyg wrote: post #62

Earlier quoted context omitted.

I have found syncing the PDFs via Dropbox works fine. Zotero puts them in a Dropbox folder with a reasonable filename, and then the regular embedded Dropbox PDF reader does an OK job on my phone/tablet. It'd be nice to have the database synced, though. Funny how "synchronization of replicas of information", for all its centrality to modern internet-based life, isn't something that our operating systems provide as a s…

> Funny how "synchronization of replicas of information", for all its centrality to modern internet-based life, isn't something that our operating systems provide as a system service. Just FYI on that front, macOS has iCloud, which does this. I put something on my Desktop, it appears on all my machines. I can access it from my phone, etc. etc. - it's basically a built-in Dropbox.

That's great for synchronising files. It's not really the kind of thing that would help with synchronisation of, say, contact databases, email folders, shared text documents, calendars, bibliographies, photo archives, etc etc. It'd be interesting to consider an OS-wide API for flexible data synchronisation and conflict resolution.

Re: Zotero: An open-source tool to help collect, organize, cite, and share research

#106

Post by nanna »

jhbadger wrote: post #100
nanna wrote: post #94

I used Zotero through my MA and into my PhD, when I discovered and began writing in LaTeX in emacs/AucTeX instead of LibreOffice. I used the Better BibTeX plugin [0] to maintain a BibLaTeX file, but as I developed my emacs skills I moved to RefTeX. At that point I realised that my BibLaTeX file was really a mess. Better BibTeX created tons of needless double curly brackets {{like this}} in the BibLaTeX file, making s…

I guess I don't see how you can easily add citations without something like Zotero (or its closed source equivalent Endnote). At least in my use case, I go to Pubmed and click the Zotero Chrome plugin to add the reference to Zotero. What do you do, manually enter the info?

Nah, not manual at all.

I just call up RefTeX by hitting ctrl-x + (or "C-x +" in emacs parlance). This calls up a list of all possible references and a fuzzy search box which lets me narrow it down. When I've found my reference I have ten options, including:

f1: Open associated pdf, url or doi

f3: Insert the citation into my thesis and then be asked for what kind of note I want to add (footnote? Title? author name? Year? Just a bibliography entry?), then any text to add before the reference (eg, "This argument has been made by,"), then after (p. 67). -- This answeres your question

f7: Attach pdf to email

f9: Show notes, if there's an .org file of the same name.

f10: Add pdf to library

If RefTeX can't find my query, not only does it ask if I want to add a new one, it asks whether to search various databases for it including arXiv, DBLP (computer science bibliography), Google Scholar, Bodleian Library, HAL, Library of Congress, British Library and others.

Adding entries to the database is as simple as editing a plain text file, and BibTeX provides quick shortcuts for all the different kinds of entries, checks them for you and provides a sane and customizable key.

Everything is completely integrated - my writing, my pdf library, my org notes, my bibliography database, my email as well as my thesaurus (wordnut), my pdf reader (pdf-tools) and my git repo (magit). It's just brilliant. All together it makes emacs the ultimate writers tool, as far as I'm concerned.

Re: Zotero: An open-source tool to help collect, organize, cite, and share research

#109

Post by innocenat »

danielecook wrote: post #90

I am a big fan of paperpile: https://paperpile.com I've used Endnote, Mendeley, and Zotero before and found them all to have their own issues. Paperpile is not perfect but it shines in a few places and I really like it. The chrome plugin adds an 'add to paperpile' button to places like google scholar making it easy to add citations. It also is designed for writing in Google Docs and makes it very easy and quick to ad…

Zotero also have chrome plugin that, while I don't remember it work on Google Scholar, I use it all the time on actual journal site (IEEE Xplore, arxiv, Nature, ACM, etc.)

Re: Zotero: An open-source tool to help collect, organize, cite, and share research

#110

Post by ipstone2014 »

msconnect wrote: post #98

It is ok not great. Lack many features. If they make app they can bring in many features from other citation managers very simple way. But all the citation managers out there half cooked softwares and so is this one. It is just a very basic tool with no features. Mendekey is better, papers is good, endnote is good but all those are expensive and not free except mendeley. So if they want it for just a regular bare min…

people should try readcube.com, it's not free, but the best I can find to organize papers/references from any platform (iOS, android, pc/mac/linux).
Post reply on HN