How it feels to come back to zotero


After using zotero for 4 years during my phd, I switched to papers 2 during my postdoc (there was a site license; and I couldn't resist the shiny look ;)
After recently joining yet another life science lab where no common bibliography management exist (although Mendeley is popular among phd students), I did a rather extensive comparison of bibliography software and a (more extensive than usual) analysis of my regular needs. I finally decided to come back to zotero.

Here I'd like to share what it feels like to come back to zotero after using papers for 3 years (from a life science scientist perspective). I'd be happy to get feedback on tricks to achieve the respective features and/or to open the corresponding feature requests if they do not exist yet.

- zotero works well! together with zotfile is totally usable on a daily basis.
Compared to papers, it's much more stable. And it's free and open!

- I lack very much a summary pane (similar to what they introduced in papers3). IMHO this could be the first tab in the right pane, displaying a formatted version of the article details, (why not a citation preview), tags as links (as in the tag viewer, but only the relevant subset), attachements titles as icons/links, (stripped down?) notes. It looks like this has already been discussed very much on the forum, with even a feature request on github. Would be happy to know more on the status of this…

- metadata import from pubmed is not straightforward at the moment: it cannot be used to fetch pdf metadata as far as I understand. So far, I load the pubmed page, click the import icon, download the pdf from the publisher and use the "Attach a new file contextual menu" from zotfile (ok but certainly more work than required).
So either import pdf metadata directly from pubmed (using GScholar only as a fallback for articles not indexed by pubmed), or following the doi found on pubmed so as to save the pdf from the publisher site automatically would be a really nice feature.

- on the mac, the ability to show the pdf in quick look when hitting space would be extremely nice

- a preference / contextual menu to choose in which viewer to open pdfs would be handy as well (though I realize it probably very much os dependent)

- I was glad to see that one of the limitation I used to complain about (exporting all pdf of a collection) could easily be circumvented with a saved search.
However, I know uses tags instead of collections and tag only the parent item, not the pdf , so this hack is not working. At the moment, I have to create a first saved search to filter by tag (checking "include parent/children items"), and a second one to get pdf from the first one. Do you have any more advance logical operators for saved searches (e.g. one condition would be a AND/OR/NOT and then have children conditions). I guess this would over a great deal of flexibility in saved search; logical operations would need to have the "include parent/children items" checkbox.

- un/fold selected items would deserve a (contextual) menu. Finding the +/- shortcut took me quite some time (thanks to the zoteroist :)

- finally, implementing the ID import feature (pubmed, isbn, etc) on zotero web would be extremely useful for those who want to use the web version only (to access group libraries for instance while they use a different software).

That's it for now. I hope that some of this can already be done with feature I'm not aware of / is already under development.
Thanks for your help.
  • quicklook:

    re pubmed: we'll likely be able to follow the links on pubmed and add the PDF automatically at some point--though that's not trivial, so won't be quick. But given the way PDF metadata extraction works, we can't use pubmed for that at all: it relies on full text indexing of the article text, which pubmed doesn't do.
  • zoteroquicklook is really cool!

    what about the progress toward having a summary pane?
  • any real progress on the summary tab would show up on the github issue you link to.
  • " But given the way PDF metadata extraction works, we can't use pubmed for that at all: it relies on full text indexing of the article text, which pubmed doesn't do.

    I understand this limitation (and already read this point before). Your answer makes me wonder about the following: would it be possible to implement a 2-steps pdf metadata retrieval
    1. use full text indexing of GS to find the most likely title / doi of the item
    2. pass this identifier (title / doi / whatever best suited) to pubmed, use pubmed entry if it exists, keep GS as a fallback…

    Given the much better quality of pubmed metadata in certain fields, there would be a clear added value.
  • Also, what about the ID import feature (pubmed, isbn, etc) on zotero web? Is it forecasted / totally unlikely?
Sign In or Register to comment.