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

zotero.org

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

#141
post #101

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 o…

this is amazing.

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

#142

I see references here about zotero being able to look up metadata for a pdf. I'm slightly confused what that means, is that just meta data in the pdf file, that isn't visually visible? For a while I've wanted to make something that can extract the title, authors, and bibliography visually from a pdf. Is that what zotero can do also?

It doesn't use embedded metadata in the file, which is usually pretty low quality. It looks for various identifiers (DOI, ISBN) in the first few pages that can be used to retrieve high-quality metadata from external services. It also does some analysis to try to identify the title, authors, abstract, etc., and compares those against known metadata for further lookups and/or to supplement the retrieved metadata. (This is a web service [1] because of the database requirements, but we don't log any data about the contents or results of searches, and it's an optional feature.)

For extracting metadata from a formatted bibliography you can use AnyStyle [2], which is a separate service written by a Zotero developer.

[1] https://github.com/zotero/recognizer-server [2] https://anystyle.io

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

#143

I see references here about zotero being able to look up metadata for a pdf. I'm slightly confused what that means, is that just meta data in the pdf file, that isn't visually visible? For a while I've wanted to make something that can extract the title, authors, and bibliography visually from a pdf. Is that what zotero can do also?

It doesn't use embedded metadata in the file, which is usually pretty low quality. It looks for various identifiers (DOI, ISBN) in the first few pages that can be used to retrieve high-quality metadata from external services. It also does some analysis to try to identify the title, authors, abstract, etc., and compares those against known metadata for further lookups and/or to supplement the retrieved metadata. (This…

Gotcha, thanks a lot for your reply!

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

#144
I want to love Zotero, I really do. But the last time I tried it seriously, I found that:

- metadata extraction/automated adding really doesn't work right with my research workflow (a lot of google scholar searches, a lot of humanities and social science sources)---lots of inaccurate or incomplete info, lots of downloading RIS files and then manually importing and separately manually importing the PDF.

- documentation for things that would be useful like hooking up to academic library proxies is nonexistent. Take a look at the chain of empty links when you try to get proxy info: https://www.zotero.org/support/proxies

- no better bibtex for zotero 5... Although maybe this has changed recently? Which would be amazing.

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

#145
post #101

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 o…

This is awesome! Interesting enhancement idea, slap a NLP topic model on top of it and explore by clusters. I'd pay for a product that did that (and if I ever find the time might try and do it myself).

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

#146
post #101

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 o…

I love the passive nature of your workflow. I’ve always thought that, as soon as I had consumed (read, viewed, heard) some content (text, audio, video) it would be nice to have a “shadow copy” of it stored in a personal, private knowledgebase, with a simple keyword or more complex semantic search on top. Basically, a personal search engine with a passively gathered corpus of my experienced content - maybe even filter…

Take a look at Recoll, and its web extension:

http://www.lesbonscomptes.com/recoll/faqsandhowtos/IndexWebH...

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

#147

I want to love Zotero, I really do. But the last time I tried it seriously, I found that: - metadata extraction/automated adding really doesn't work right with my research workflow (a lot of google scholar searches, a lot of humanities and social science sources)---lots of inaccurate or incomplete info, lots of downloading RIS files and then manually importing and separately manually importing the PDF. - documentatio…

> metadata extraction/automated adding really doesn't work right with my research workflow

I'm not sure exactly what you mean, but the primary way of adding items to Zotero is with the Zotero Connector browser extension, which lets you save high-quality metadata and PDFs with a single click from a huge variety of sources (certainly including humanities sources, since Zotero was created by historians). No other tool comes close to Zotero's abilities here. Metadata quality does vary by site, though — Google Scholar specifically only provides limited metadata, so you'll often get better results by clicking through to the linked article and saving from there. We have plans for functionality to flesh out incomplete metadata retrieved from subpar sources.

Zotero can also automatically retrieve metadata from PDFs you drag in, which should work for the vast majority of recent PDFs and many older ones with DOIs assigned, though that's not meant to be the primary workflow.

> documentation for things that would be useful like hooking up to academic library proxies is nonexistent

Current proxy documentation is here [1], and that's what's linked from the main documentation page. I've fixed the outdated page you pointed to — thanks.

Note, though, that the proxy functionality is meant to work automatically for the popular academic proxies, so most people don't need to configure anything to use it. (And as far as I know other competing tools don't offer anything like this.)

> no better bibtex for zotero 5

BBT has worked with Zotero 5 since last year.

Disclosure: Zotero developer

[1] https://www.zotero.org/support/connector_preferences#proxies...

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

#148
post #101

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 o…

I did something similar for search until I found Recoll. It has similar functions to what you describe(caching, fuzzy search) with a slick work flow that shows google scholar like context previews with an optional remote access to your library through a webui. It also searches compressed archives and generally simplifies searching many unorganized files.

http://www.lesbonscomptes.com/recoll/

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

#149
I'm a big fan of Zotero. One of the greatest features is that you can use your own WebDav-Server to store and sync PDF files. There is also this tutorial on how to install your own Zotero server [1], but I don't know how to config Zotero to use it. Anyone knows?

[1]: http://git.27o.de/dataserver/about/Installation-Instructions...

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

#150
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…

AucTeX can save snapshots of entire Web pages with images, PDFs, etc. in a personal library?
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