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1131
Sorry for posting and then not replying for a while. Great to see so many interesting suggestions. It's hard for me to post back on all the interesting stuff you post about but I'm eagerly reading every bit of it.

urlwolf (anrmado, cnewtonne, ... ),
ok, I'll be sure to try the latest Adobe Acrobat trial and see how the note features have evolved.

Urlwolf (and others): You say the notes can be searched. Does that include "cross-document" searching? Also, when using an external indexing search tool like google desktop search, are such notes in pdf files also indexed or only the original pdf text?

When googling I found this post on a feature for summarizing notes in freestanding pdf files. That sounds very useful. Have anyone tried it and have comments?  http://blogs.adobe.com/acrobatineducation/2006/02/using_acrobat_for_summarizing.html

Darwin,
Yes I'm also sceptical about using EndNote for pdf notes since it can't really do margin notes, underlining and so on on (or overlaying) the pdf pages, right? It can connect separate note files and pdf files in its bibliography database. But maybe the best solution will be a tagteam of Acrobat and some database/organizer tool and so maybe EndNote could be that tag partner.

Great descriptions and screenshots of PaperPort Professional! Sounds like another contender as a pdf note application. And they do have a 15-day trial now it seems ( http://www.nuance.com/paperport/trial/ ) so I'll try that out too. Thanks for the heads up about slow indexing also.

I think the possibility of making notes for edit protected pdf files was one of the things that got me thinking about a system with free-standing note files layered "on top" of the regular pdf files. For personal use it is easy to remove the proctection for most pdf files and I have no qualms about doing so for the sake of entering notes or something like that. But sharing notes by passing around the unlocked files might be another thing... The prospect of just sending a small note file that works for anyone with the original, still protected pdf file is more appealing. Especially if we want, like I want, large, online and free archives of these kinds of margin notes, underlinings and so on. (one obvious problem with that vision, apart from it being a dream and no actual product  :), is that the document properties needed to position the underlining, margin notes and so on might not be available if the document is in protected mode)

Armando, 
Interesting what you write about your manual tagging system. I've made some such attempts (not as systematic as what you describe though) but often feel discouraged by my own inconsistencies from too quickly typing the various tags. I think more gui guided/programmatic tagging is the way to go really so I'll check out some of those tools you mention.

Re:hyperlinks: if journal article pdf files consistently cointain doi ID numbers as some type of metadata (I don't know if they do, but it wouldn't surprise me), then maybe some rather simple script could be made to extract doi+page number, make a string and paste into any external note file. Later, selecting that string in the notes and running the script again searches for a doi-matching document, opens it and jumps to the matching page.

"with X1, Copernic, Farr, the right tagging and file naming system, the right organization structure, the pretty standard "commenting" ability found in many software, and a good note taking software (myBase, EverNote, etc.),  a good OCR program and a fast scanner, it doesn't seem like a terribly difficult task."

Ok, maybe such a multiple program approach is the way to go. Does apps like myBase, Evernote,... get all their notes indexed by such local search tools? Does the indexing tools also index tags for notes made with the note applications internal tagging tools (in contrast to manual tags as plain text phrases on the notes page)?


cnewtonne,
UltraRecall sounds very powerful at least for notes on/in non-pdf documents. If I understand it correctly RepliGo has highlighting only on separate copies of the original pdf and seems very geared toward mobile users. I'll put it on my "to try" list though that i getting long right now so... :-) Are the copies RG makes pure image files or is the text still searchable and so on?

"software psychologist" - yeah, bring'em on  ;D

1132
Hi,
I'd like to bring up a sub-topic concerning tools/strategies for note taking related to reading PDF files (or locally saved, static text files more generally).

Like many others I read a lot of articles, reports, books that come as PDF files. Fairly often, I find myself falling back to a very primitive two part note taking system:
system 1. print PDF to paper, then jot down brief margin notes, underline, mark and so on during the first, quick read.
system 2. During a second, more thorough reading, type summary, copy&paste key quote sections, add thoughts/comments and so on in notepad or similar. Save notes for "article123.pdf" in "article123.txt" next to the PDF.

This common (perhaps apart from the last detail on naming/saving) system has advantages (+) and drawbacks (-).

system 1: notes on PDF-printout
+ quick for short notes
+ no computer needed
+ notes located right next to relevant source (no separate quoting needed, context is clear)
- no programmatic searching, indexing, comparison, editing, tagging
- timeconsuming for long notes
- physical archive needed
- costs related to paper (economical, environmental. Lessened, not removed, by FinePrint)

system 2: notes in separate plain-text files
inverse many +/- above. Also:
- rich formats lost when qouting
- for long notes, less overview due to plain text. Using manual sectioning (1 , 1.2 , 1.3 ... ) takes time and is error prone.
+ independent/portable between computers, operating systems, software and so on

My impression is that many of the applications discussed in this enormous thread replace system 2 with complex software that allow rich text formats, search, indexing, editing, tagging and so on. Such replacement is not my focus here so I'll just say that I've tried many such programs, find many of them impressive but have not yet settled on any single one. Mainly since first making a complete commitment to an application and then later wanting to switch after all could come at a high cost (time, format conversion issues, re-learning and so on). So I keep trying out different software. In the meantime I also often fall back on system 2, complemented with separate rich text files when needed (usually via the Open Office apps)

Now, what I really want to discuss is software that replaces system 1. Specifically, software that emulates and improves on manual notes on/around a printed source text and also ideally connects/combines systems 1 & 2.

I know of three types of software that do some of that: complex pdf-viewers/editors (Acrobat), bibliography tools (EndNote), general information aggregators (OneNote). I don't have a lot of experience with any of these tools but my vague impression is that they are all still pretty crude in this regard. They may lack in customizability, easy portability and/or cross-document searching, indexing, tagging of notes. Maybe the OneNote type of applications are most promising for now, especially combined with input tech like tablet PCs with pens and OCR for hand written text. Such tech is of course needed if we at some time want to import all previous, hand written notes.

Anyway, here are three features I think an future, ideal such system should have:

A. co-location: notes should be inputable/viewable right next to the relevant source section. So underlining, adding margin notes and so should be possible in or in the context of the pdf-viewer, not (only) in a separate document in a separate window. And even additional notes in a separate document should somehow be (hyper)linked to the source text parts that they concern.

B. independence/portability: notes should be easily portable between different users, computers, operating systems, applications.

C. systematicity: cross-document searching, indexing, tagging and so on of notes should be supported.

Combining A-C seems like a very hard task. B seems to require some standardized format for such notes, a format that different applications can follow or at least import/export from/to.

One way to tackle this design problem would be to find an area with similarities to on-the-page note taking and that already has working solutions with features A-C. An interesting such comparison that I thought of is plain-text .srt-subtitle files for video: http://en.wikipedia.org/wiki/SubRip . These contain a list of paired timestamps and dialog text snippets. Put "movie123.srt" in the same folder as the movie file "movie123.avi" the subtitle was made for, start the video and chances are your media player will recognize and display the subtitle automatically.

Can a similar system be had for notes in PDF files? The .srt system relies on static video files and many pdf files are static enough too. For example pdf versions of professional journal articles. Where .srt files tie content (dialog text) to points in time (timestamps), the pdf notes can instead be tied to page number, X/Y coordinates and other properties of the original pdf text.

With such a system sharing of notes would be very easy if the same source pdf files are already available. Just copy/paste upload/download the note files. Specific sites could host large note archives. Notes could be tied to articles/books through filename and DOI ( http://www.doi.org/ ) or ISBN ( http://en.wikipedia.org/wiki/International_Standard_Book_Number ) numbers. For a very rough analogy on how such a site could work, see this german site  http://www.cutlist.de/  that seems to share timestamps for when to start/stop cropping when removing commercials from PVR recorded programs (my german is bad so I'm not completely sure though).
 
Also, multiple notes for one single pdf file could potentially be combined and switched on/off individually, like layers in Photoshop ( http://en.wikipedia.org/wiki/Layers_(digital_image_editing) ). Imagine a pdf viewer window with two panes. The left displays the pdf and also has a row of tabs/checkboxes on top. Someone studying ancient literature has a free pdf version of the Iliad. She then adds and compares on-the-page notes on the Iliad from scholar 1, scholar 2 and so on by clicking on the different note layer tabs. It would be as easy as browsing through the various audio tracks on a DVD disc! The right pane contains more extensive and general notes. Some hyperlinking systems connects these panes, so double clicking on a section in the right pane jumps the left pane the the related pdf section and vice versa.

Also, users could in the pdf viewer customize the display style for one and the same basic note file (like what a .css can do for a .html). For example, switch underline display color from red to green.

Another advantage with such a standardized system is that it would allow different software developers to continually compete and allows users to switch back and forth between various software. The notes aren't locked into one specific software.

Ok, I've written long enough for now. I'd love some feedback on the ideas sketched above. I know they're a bit utopian. ;D

Also, I have a more specific question to all readers of this thread:
Do you think that there already is some good software that does something close to A-C for pdf notes?

1133
An alternative if you have Win XP is to use Scheduled Task. Here's a tutorial: http://www.iopus.com/guides/winscheduler.htm

1134
-42!  :) After quite a few attempts I should add.
The same author also made the spiderman like Double Wires: http://ishi.blog2.fc2.com/blog-entry-199.html
It has the same great gravity feel to it.

1135
Impressive how complex the flash games are becoming nowadays.

Here's a more simplistic new game that is great fun:
Cat with Bow Golf   http://ishi.blog2.fc2.com/blog-entry-211.html?new

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