I have a deep desire to streamline my research workflow (and move it entirely into the cloud) – but I don’t have the proper workflow yet. I don’t want to say that such a workflow is nonexistent, but I can’t find any single program that satisfies my desired workflow (I’ve looked at Endnote, Zotero, Biblioscape, Mendeley, and Refworks). The most promising competitor seems to be Evernote, though a comment in a Profhacker post captures my experience very accurately:

I find that Zotero is better for writing.Dropbox for sharing files.iDocument for document storage and recal.NeatWorks for reciepts.iPhoto for images.etc. A tool for a task.Evernote’s task is unique, which is why it’s good.Evernote is for keeping the bits of your infomration sorted (snap a pic with your iPhone, clip a bit here, etc) … [link]

Maybe you, reader, can identify a combination of programs (or, perhaps, a single unified program that I just have not stumbled upon), that achieves the following set of goals:

User interface that matches the core researches phases.

  • Early, I need the central interface to emphasize features for creating content in the form of notes, PDF annotations, ideas, and bibliographic citations.
  • As the project progresses, I will spend more time on organizing notes, forming categories, and outlining, so the UX needs to be able to gracefully switch between organizing files and organizing ideas.
  • Later in the project, the focus is on writing, so a distraction-free writing module should be integrated into the workflow.
  • Near the end of the project, I need to be able to quickly switch between these modes as I edit content, add another PDF with notes, reorganize citations, and basically re-do every step thus far.

Being able to highlight is great, but I want my handwritten notes translated to text while still remaining visually overlaid on the PDF.

Being able to highlight is great, but I want my handwritten notes translated to text – while still remaining visually overlaid on the PDF. (Image is of iAnnotate)

Beautiful PDF annotation functionality.

  • First and foremost, I want to be able to have older PDFs go through the OCR process to convert the image to text so I can search and copy and paste.
  • I would like an iPad version of the PDF annotation software so I can sit away from my computer but not lose the OCR and annotation functionality I need.
  • Writing directly onto the PDF is required. When I print out articles, I underline, star, add margin notes, etc., and I want to have a similar note-as-I-read experience with the digital PDF as I have with the paper version.
  • Related writing directly on to the PDF, especially with the iPad version, I want to have my handwritten notes recognized and converted into text. This way I can write onto the PDF or create a more lengthy set of handwritten notes and have them instantly converted to text and thus be searchable.
  • There should be a view to see just the original PDF, see my markup overlaid on the PDF, and a comment-only view that shows me all my notes in a scrollable doc.

Intuitive searching.

  • Searching should be visually powerful, allowing me to see the search result and a wide range of information attached to the result so I can quickly determine which result is the correct one, and then immediately jump to the PDF abstract, my notes, specific quotes, or the section of the paper I’ve associated with the search result object.
  • I would like snippets, just like you see in Google results, with the first X number of characters shown around the returned phrase.
  • I should be able to search everything: text, author, keywords, tags, notes, etc. – and not just my notes.

Syncing galore.

  • For backup purposes, as well as access from both home and campus, all the data should be stored in the cloud as well as being available in an offline version that syncs once I’m back on the internet.
  • I’d like to be able to upload documents directly and give URLs of documents for the system to index, and it should save a version into the system as well as into a desktop repository like DropBox.
  • All of the citations should sync with my bibliography software (such as Endnote, Zotero, Biblioscape, Mendeley, Refworks) – or, heck, maybe all of this functionality is built into the bibliography software.

If you have any ideas of how to achieve this workflow through a combination of programs (ideally linked together with some automation benefits) or through a single program to rule them all, please let me know in the comments.

– Brian Cody, Team Scholastica