At this point, I am using columns rather than making use of the Note property. Time will tell if that is a good strategy or not.

To make this feasible in practice, the list of “Note Types” should not be too large and the types should be sufficiently generic to apply across multiple projects. This is a new work in progress for me, my current list of note types is about 10 in size and I can see a few that I will probably drop. Some of my note types: Summary, Function, Biomarkers, Clinical, Distribution, Assays, Safety, Picture.

When I need to collect all notes that deal with Safety, it is simple to do a batch find or a sort by column. Likewise for Picture – I can very quickly home in on all the figures that I have copied from different sources.

I create a top level row that contains data for a single source: Title, Authors, Year, Note Type, Bookends. The Note Type cell is blank, the “Bookends” cell contains a hyperlink which will navigate back to the unique reference in the reference manager Bookends. It is easy to populate this row because I have created a custom citation format in Bookends that puts those pieces together with tab as the separator. In Bookends, Cmd-K issues the Copy Selected Formatted command. Back in OO3, I paste the clipboard contents and OO automatically parses the text into the cells of a new row. All notes I take from that source are children of that parent row. As I take notes, I set the Note Type field appropriately from the popup menu.

Things that would make this more seamless:

1) Rather than the cumbersome back and forth between apps, a scripted way to get the reference data from Bookends (it’s scripting support is quite poor).

2) A script that appends clipboard contents to the active cell in OmniOutliner, i.e. the selected text in my PDF reader (Preview or Skim). This should be doable, but I don’t yet know how to set the insertion point or insert text at the end of a cell in OO. The text also needs a little cleaning up as it comes out of Preview.

3) In step 2 above, can the inserted text in OO also be given a style within the script? (I like to give verbatim excerpts from sources a specific format).

4) Haven’t thought this far ahead yet, but eventually will need to get selected rows exported and keep the Bookends source information along. Would be nice if Bookends could insert citation codes into OO.

5) There is an apparent bug in OO3. I can set a keyboard shortcut for a command in the Action menu: Action > Substitutions > Replace Text. I can see the shortcut characters in the menu. But when I type them OO just beeps and doesn’t execute the menu item. This is one approach to performing the clean up of text snippets coming in from PDFs (Preview).

I am in the midst of a big research and writing project, so we’ll see how this work in progress develops — a technology diversion or actually helpful.