I had a great time as a guest on David Sparks and Katie Floyd’s milestone MacPowerUser Show 100 yesterday. Their podcast has been a staple on my iPod and iPhone for years. To celebrate they invited 10 guests to discuss workflows in their professional lives. Over the past several years, I have learned an incredible amount from Katie and David. It was nice to be able to give something back.

I had the pleasure of discussing a portion of my writing workflow–how I get information into my academic research library-Papers2. I’ve talked about why I use Papers in a previous entry. If you’re not familiar with Papers you should read my previous post first. Go ahead. I’ll wait.

——————————- Okay, welcome back.

When tackling a new writing project I pass through several stages:

  1. collecting
  2. organizing
  3. reading
  4. synthesizing
  5. citing

The workflow I covered on the MacPowerUsers had to do with collecting information. I usually obtain scientific literature in one of three ways:

  • as a recipient of an Endnote library (when writing collaboratively)
  • through personal searches on the web
  • as an attachment to a colleague’s email.

I’ll cover each of these contingencies below.

Endnote still has quite a foothold in academics. I often find my collaborators have not yet made the switch to Papers. Many times, when writing collaboratively, we must share libraries between the two applications (Endnote and Papers). Fortunately Papers can import (and export) Endnote libraries seamlessly (as long as they’re in Endnote XML format). Easy and no need for a workflow!

However, the other two situations are more complex (searching myself or receiving attachments to emails) and require a workflow–making use of the wonderful program called Hazel. Hazel monitors folders on my computer and acts on individual files according to rules I create. Hazel can even peek at the content of files and “recognize” what’s inside. I have Hazel monitoring about a dozen folders on my Mac, but my Downloads Folder keeps Hazel the busiest. I have about two dozen rules running on my Downloads Folder alone.

For this particular writing workflow I ask Hazel to look at the contents of every PDF in my Downloads Folder and match files that have words unique to scholarly publications.

I’ve found having Hazel search for the word “References” within each PDF works the best. When a PDF whose contents contain the word “References” is matched, Hazel automatically launches Papers and imports the manuscript. While importing, Papers fetches metadata, renames the PDF to the convention I’ve specified, and files the manuscript in a specified hierarchy on DropBox–all automatically. Another preference in Papers erases the original file once it’s imported.

I’ve tried other search words for Hazel including “abstract,” “methods,” “results,” and “discussion”–none work as well as references. Most every scholarly manuscripts has references (unfortunately, even the word “references” will not be 100% reliable–in a minority of publications, references will be called a “bibliographies” or “citations”).

You are probably wondering why I don’t just use the built in unified search window in Papers. My answer: it is faster and less frustrating to find full-text directly through our Library’s web page. Papers unified search will work through a fire wall (using proxy URLs in the search interface) – but it’s hit-or-miss whether a link in Papers will lead to a full-text article or merely a frustrating publisher’s login screen–most usually the latter. My hit rate is much higher on the web. I use Papers built-in search engine primarily to retrieve metadata (after the full text pdf has already been imported).

When I’m collecting full-text articles I save EVERYTHING to my Downloads Folder and let Hazel do the rest. When she finds a match, she launches Papers and imports each manuscript without any additional effort on my part. Using this method, I can conduct my search for scholarly information with minimal interruptions – Hazel does the rest.

Searching on my own is the most common way I get information into papers, but occasionally a colleague will mail me something they think I should read. For these situations here’s what I do. I have Hazel monitor my Mail Downloads folder (~/Library/Containers/com.apple.mail/Data/Library/Mail Downloads ) and copy EVERY attachment to my Downloads Folder (I do this for a host of reasons–not just publications–I’ll talk about why in a future entry) Once the paper is in the Downloads folder Hazel can work her magic using the rule mentioned earlier. Apple now hides the Library Folder by default. Here is a quick tutorial on how to find it on your hard drive (works for Lion or Mountain Lion).

So there it is: how I use Hazel to speed up the collection of information when writing or researching. I hope it’s helpful to you. In a future entry I’ll talk about an emerging trend in research paper management: social networking.

Cheers, Jeff

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14 Responses to Writing Workflows: Collecting Information in Papers2 (MacPowerUsers Show 100)

  1. Gary Kantor says:

    This is really helpful and I’m definitely going to try the workflow.

  2. Hi Jeff,

    Thanks so much for a great plug of Papers! Happy to hear you like the app so much!
    Best wishes,

  3. Andre Rangasamy says:

    Thanks Jeff. This sounds great, not just for academics!

    One question: If you receive a PDF electronically (not scanned, which can then be made searchable), how do you convert this to be searchable by Hazel? And is this process automated as well?

    • jeffrey.taekman says:

      Hazel can read contents of PDFs WITHOUT further manipulation–a really powerful feature. If you end up scanning a document programs like PDFPen automatically OCR. DevonthinkPro is another program that will automatically OCR scanned documents.

      • Andre says:

        Thanks, will try that out!

        Your Hazel rule to move mail attachments to Downloads folder is great. But this only seems to work on mail I open. Is that right? If I receive mail without opening or use a mail rule to file that email, the attachment does not appear in the mail attachments folder so Hazel cannot move it. Have to open the email, then attachment appears, then Hazel can move it. Am I missing something?

  4. Dave Anthold says:

    Jeff: this is awesome. Caught your workflow on the MacPowerUsers show and I can see a great use for this in my line of work as begin to use mor industry industry information. Thanks.

  5. Jonathan.Rubin says:

    FYI–the latest version of Papers lets you specify a watch folder. PDFs you drop in are automatically imported. Don’t need Hazel.

    • I’ve found Hazel works better for me. I put EVERYTHING in my Downloads folder (web searches, email attachements, downloads, pdfs, etc). When I had a designated Papers folder, I had to navigate away from the Download Folder each time I found something I wanted to save. Using Hazel, I don’t have to give a second thought to where the paper is downloaded-Hazel does the work for me.

      • Jonathan.Rubin says:

        I have my Papers watch folder inside Downloads. WIth Chrome, when I save a PDF I specify that folder. All subsequent saves have that folder set already in the dialog. Alternatively, with the Papers watch folder inside Downloads, it’s easy to drag files in the Downloads folder right into the watch folder.

  6. […] I must admit that everything I know about Mac has either been directly learned or inspired by Macpowerusers (MPU), a podcast I started listening to about 3 years ago. Recently, MPU had their Episode 100 where they talked, among other things, about academic workflows including Papers. Jeff Taekman (who has a great academic workflow blog) explained how he collects reference materials in Papers.  […]

  7. […] Writing Workflows: Collecting Information in Papers2 (MacPowerUsers Show 100) – Jeff Taekman&#… […]

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