I have been thinking along related lines. It seems to me that what's needed for this kind of information management is a flexible relational database tool such as Filemaker, which would allow searching & reorganization of material along any number of lines; also export would be easy. It doesn't allow arbitrary reordering of notes such as you describe, though (as far as I know). I currently use OmniOutliner for that kind of work, and wish I could combine the functionality of the two apps. Also, I have no way to link either Filemaker or OmniOutliner to my BibDesk file--I just copy the BibDesk CiteKey into the notes for reference.
The end result is that I have all my notes in a separate app, and never get around to moving them back into BibDesk as annotations. --Ingrid Giffin On 1/30/08 12:51 PM, "James Harrison" <[EMAIL PROTECTED]> wrote: > I hope this isn't regarded as too off topic, but I've been having some > thoughts about software and writing workflow in science that I think > are appropriate for discussion in relation to BibDesk, and especially > BibDesk + Skim + <your editor here>. > > As I've been working with BibDesk, Skim and Pages recently, my > standard writing workflow has been changing (this a workflow that's > been stable for more than 15 years). This has happened particularly > after I started using a template for BibDesk's preview that shows Skim > notes from article PDFs in addition to the title, authors, abstract > and annotations. I also have written Applescripts that will display > article lists in the same format (including Skim notes) in TextEdit or > Pages for review or printing. I'm reading electronically a lot more, > making Skim highlights and notes as I go, and reviewing those notes in > aggregated article lists targeted to particular writing projects, > either on-screen or printed. > > In retrospect, software for writing has been pretty stagnant for about > 15 years with a few notable exceptions (I know Ulysses has been around > for a while). This is changing now with the development of tools > specifically to support authoring rather than just typing. Scrivener > is an interesting example, with a note card metaphor that allows you > to create snippets of information that can be mixed, matched and > ordered into manuscript precursor lists, which are then expanded into > manuscripts with additional text. My impression is that these programs > are most often targeted to single writers and, while they have > interesting facilities for organizing spans of text representing > concepts, they don't usually provide effective bibliographic or > collaborative authoring tools. > > After Pages v. 3 appeared, change tracking and commenting became > available in a word processor I found comfortable to use and documents > could be round-trip-shared to Word-using colleagues with preservation > of commenting and change tracking. What was missing was bibliographic > management and that was the genesis of the CiteInPages Applescripts, > whose strategy has the additional advantage of cross-program placement > and editing of working citations: only the final formatting needs to > be done in Pages. > > Now I've found that I can read articles electronically and mark or add > important concepts in Skim, and manage and summarize those articles > and annotations in BibDesk. The last missing link in the chain is a > way to organize and select the annotations representing key concepts, > and bring them into my writing environment. My ideas on this are hazy > as yet, but I think I understand the gap that exists. > > This isn't a feature request for BibDesk and Skim...it's more of an > early attempt at a use case or workflow description, and what might be > needed to support it. I think I'd like to be able to manipulate Skim > notes individually, as they may represent different concepts that > could appear at different points in a manuscript. I'd like to be able > to search for specific notes across an aggregate of references, with > the result display, perhaps on a palette or in a pane, having a > primary focus on the contents of the found notes with a secondary > focus on the reference from which the note derived. Individual note > objects should arbitrarily orderable on the palette by dragging. Notes > on the palette would have a compact display of their content with > links back to their PDFs and BibDesk entries. It's possible that it > would be useful to allow the entry of new text notes on the fly in > between dragged note objects, and to be able to order the notes > hierarchically (essentially, an outline). It's also possible that it > would be useful to enter additional text to notes on the palette after > dragging. This wouldn't necessarily need to edit or add to the Skim > notes, it could be a local annotation specific to the palette. > Palettes should be savable with names so that they can be reopened, > and notes should be draggable between palettes. > > Palettes represent manuscripts or manuscript sections. Once the notes > were organized in the correct sequence and adequately annotated, I'd > like to be able to export their content, in order, to my editor of > choice as a starting point for writing. You could also envision > dumping these concept-rich snippets to a database. For my own > purposes, I wouldn't mind if export were via Applescript, with script/ > template access to the individual elements of the note data model so I > could control the choice, order and layout of the data transferred to > the writing environment. However it's accomplished, I'd like that > level of control. > > The note data model might contain the following: > Highlighted text in the PDF (if any) > User entered text in the PDF (if any) > Some type of optional keyword or tag list > Date created > Associated PDF file > Kind of note > Page location in PDF > BibDesk cite key > BibDesk file identifier (name, path or ID; last mod date?) > Annotation text (added by user, not in PDF, might be specific to a > particular palette) > > The combination of the cite key with the BibDesk file identifier would > provide the link to the reference in BibDesk and give access to all > its information there. > > With the addition of something like this, tools would be available for > finding and storing references, reading and annotating concepts in > references, organizing those annotations and adding information to > them, moving the annotations into a writing environment, and citing > them there while developing the manuscript content collaboratively. > Since it deals with groups of references, the functionality probably > shouldn't go into Skim. Theoretically it might fit into BibDesk, or it > might be a separate application that worked with BibDesk and Skim. > > I don't mean to make specific suggestions about user interface or > other details and I recognize that some of this scenario may be naive > or impractical. I do think, however, that it identifies a gap in our > current tools, and I'd be interested in whether others also see the > gap and would fill it in a similar or different way. > > Best wishes, > > Jim Harrison > UVa > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. 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