Well, I am in the same situation.
I don't have a worked-out solution, but here is how I would approach it.
(1) first of all, you need to batch things (obviously). It's a lot easier to batch in linux vs windows. It may be too big a pain to transfer into a linux environment. Anyways, you can probably get away with batching in windows, too.
(2) use pdftotext for each file (batch this) - name so that it relates to original pdf
(3) howto uniquely ID the paper?
(a) using text version of pdf (from step 2) - get journal name and volume/page/year info using a perl script.
(b) grab the title (perl again)
(c) I'll comment a little on this below
(4) get full citation information via pubmed (can again use perl to query the website)
(5) put this citation format into a zotero-compatible file format (again, probably perl is best but maybe an easier way)
(6) import into zotero

I know this requires some significant programming skills (perl, prob linux) and will invariably screw up with a subset of your pdfs. But, assuming that you are using the biomed literature (you mentioned Pubmed), I think this could be robust.

If I end up writing something like this myself, I will give details and post all code.

Mark

markb,

thanks for the thinking on this. you've outlined the steps. i've stumbled through the process to steps 5 and 6 using kludged together solutions to test feasibility. some new questions to refine my understanding of the next steps:

now i have a properly identified pdf, and its text file. i have read about 'layers' in PDFs, and I was kind of assuming that is what I would want to create to import to Zotero 'cause without the text the full text search wouldn't work on image-only PDFs. sorry if am being obtuse. but a number of journals are scanning their archives in 'image-only' PDF format. it seems that some of the workflows suggest applying Adobe or other OCR to these image-only PDFs, and if I understand it this OCR'd text does get stored as a text layer--cause PDF to text cannot extract 'text" from an 'image', right.

So do I need to create that type of PDF for Zotero? Any what tools. Not scared of Linux or command line, just want Zotero full of all my reprints :).

I have this idea, maybe stuid, that if I could make Zotero think my computer was the NLM it would find all my PDFs, rename them, index them, etc. Only half joking.

Again, I appreciate the dialog.

Rob

can u explain it in more details?
i don't understand the "perl" things
sorry...

lucky me, i just start writing my thesis when i found zotero
not yet many documents
its alright for me to redownload

but if there is other way, will give it a try

I also think this is an important topic. My last big project was done using Endnote and Word for the bib managment and writing, and UltraRecall for gathering, organising and searching material, mostly PDFs. UR has no bibliographic capability, so I still needed endnote but it seems zotero combines everything you need for managing and gathering information for academic writing. UR can search for text in a text-based pdf file to identify files containing the search terms, but as with zotero, you then have to enter the search again in acrobat to find the item location in the document. Is there a method of performing only a zotero search of PDF text and identifying the passages containing the search terms?

Thanks Dan,

If I understand you correctly the answer is "Yes, well.. no, but maybe sometime."

I suppose it is only reasonable that users should expect to continue to expend some of their own effort in their research. It would be even easier, wouldn't it, if zotero could guess what I ought to be thinking about then find it for me without any of that pesky typing at all.

Another option is c2bib (http://www.molspaces.com/d_cb2bib-overview.php), which works on windows too. If you import the list of pdf´s and do a network reference query for each of them you will get a nice bibtext file which you can import in zotero. It will take a few mouseclicks for each pdf but it certainly beats doing it all manually.

I imported a group of almost 400 PDFs into Zotero manually last summer. I came up with a method to automate some parts of the process, enough so that the importing was not unbearably tedious. :) Here's the method I used:

1) Make a list of the titles of the PDFs.
In my case, the PDFs all had versions of their respective titles in the filenames that contained enough information that I was able to find the articles using Google Scholar, along with some other data.
So, on linux, I used the shell (cat) to make a list of the filenames in the directory where the PDFs were located and then I used a command line text editor (sed) to edit that list so that only the names of the article titles remained, one to a line. And I saved all of that as a plain text file.
Of course there are plenty of other ways to make a list of the titles of the PDFs, that's just what was easiest for me.

2) Install the Firefox extension "Context Search"
https://addons.mozilla.org/en-US/firefox/addon/240
Context Search allows you to access all of the installed Firefox search engines from the right-click menu.
I then installed the Google Scholar search plugin, since I had already verified that my PDF articles were listed there.
http://mycroft.mozdev.org/search-engines.html?name=scholar.google.com
(1st on the list)
I also used "Manage Search Engines..." in the Firefox search toolbar to move the Google Scholar plugin to the top of the list.

3) Use Google Scholar to enter the articles into Zotero.
So I opened the text file containing the list of the articles in Firefox, selected an article title, right-clicked, and chose Google Scholar from the "Search for" list. This opened a new tab with the Google Scholar results, from which the article's metadata could be added to Zotero in normal way.

4) Add the PDF file to the Zotero item.
This was made easier by adding an entry to the Places menu in the GNOME file manager for the folder in which all the PDFs were stored.

It did take a while to go through all of the articles in this way, but not that long once I settled on the method. I put the articles into a separate Zotero collection sorted so that the most recently added item was on top, to make it easier to keep track of things, and I did it in batches.

The advantage of the manual import is that it allowed me to check the metadata in Zotero as I added the items, to make sure that they were accurate for my preferences (full author names, for example). I find that a quick manual check is always a good idea whenever adding new items into Zotero, because there's just too much inconsistency in the available metadata.

Even if it was time-consuming, I'd rather spend the time once as described above than to have to have to check, by hand, each individual reference and bibliography I make by hand in each of my projects, which is how I used to do things pre-Zotero.