Mori for Research and Reference Notes

Recently I’ve started to use Mori to make and organize research notes. I haven’t yet left off using Jabref as a bibliography and citation manager, but I need somewhere to store and retrieve my comments and ideas as I read through papers and books. My workflow is still very rudimentary, but I was encouraged to share it here, and hope that with some feedback and discussion it will become more refined.

The basic unit now is that for a single reference:

• Johnson2000, the citation tag, reference title
  • paper, links to the pdf file
  • figures, representative figures from the work
  • notes, all the notes concerning the work, including figures and quotes
  • refs, other papers/books referred to by the work that might be worth looking into

Johnson2000

this entry serves as the header for the reference. I use a bibtex key (authorYear) as a unique identifier here, for the pdf file name (helps Jabref with auto matching citation to file), and in the citation manager.

I put my own keywords or tags in the note so that might notes will also come up under spotlight searches for the tags.

paper

in the paper note I put two things: 1) a link to the external file, 2) and an image reference to the file to accomplish #1

1. type “paper” in the note and select it (or some appropriate tag)
2. choose: Text -> Make Link…
3. type in the path to the file

to accomplish #2

1. drag the file from the Finder into the note field and push the control key before you release the drag
2. the control key will make it a link to the file rather than a copy of the file

figures

Most of the papers I read include engineering diagrams and those diagrams become one of the most memorable impressions of the paper. When I have trouble remembering which paper described a certain process or technique, I often browse through papers looking for the figures I remember. Eventually, I would like to use some unix tools to extract and assemble image collages from the pdf’s automatically, but for now, I find that Quicksilver lets me do it manually without too much trouble. As I read through the paper, I continuously use cmd+shift+cntl+4 (I’m going to set my middle mouse button to this key combo) to screenshot figures to the clipboard. Once I’ve finished, I go back to Mori and activate Quicksilver’s clipboard module and drag all the images out into the “figures” note and to the Notes section if they relate to one of the comments I sent over through Note-chan (see below.)

notes

I use the script/app that I uploaded to the Scripts & Plugins section (called Note-chan) to take notes while I read a paper. It presents a small window that I can keep open adjacent to or on top of Preview or Safari, and type in my thoughts or comments about certain passages. You can also attach automatically clipboard contents to the note when you send it to Mori. All notes get sent to an “Inbox” (similar to the Quicksilver script posted by Leo)

refs

This is where I cut and paste any references cited in the work that I might also want to check out. I will probably link to them from here once they are into the notebook as their own reference.

Usage

It might seem inefficient to put all of these things in separate enteries that have identical names (e.g. every ref has a “figures” entry) but now I can have two smart folders set up, that will gather all of these entries and make it easy for me to very quickly browse through all the figures, for example.

Also I wrote a script that will automatically insert a new reference entry along with subentries based on a template (see “Prototype” under the Scripts and Plugins.)

Future Directions

I’m not sure how my use will evolve, but I’ve considered a number of things:

*an applet to automatically generate an entry and link to the file *improve Note-chan to allow the automatic attachment of images to my comments *full citation (probably bibtex) import and export

I would very much like to hear how others are using Mori in this regard (alone or in conjuction with other software.) Or if you have ideas for techniques or methods that could be implemented with additional features, we could also discuss how they might be implemented.