Actually I’d also like to see an enhancement to provide a preference to change the default behaviour of DTPro so that double-clicking on a PDF always open the document externally.
BTW for anyone put off Skim by reports of instability the current version 0.6.1 seems very stable.
Any official Devon word on perhaps including the ability to parse skim notes by DevonThink?
I know that there has been discussion in the past of including basic annotation functions in DT (and hopefully leopard will make this simutaneously easier and more powerful.) However, one wonders if it might not just be easier to co-opt this freely available and open source solution.
I’m asking now because as I use skim to markup and highlight more and more pdf articles, I’m committing to a system which I’m not sure will eventually be compatible with DT.
Skim became vastly improved when a recent update enabled pdf files and any annotations/notes you make to all be saved in a single file. Trouble is, whereas Skim pdfs can be saved in DT the Skim pdf bundle does seem seem to be accepted.
Like the previous post I have found Skim so useful I’m now heavily commited to using it but this apparent lack of compatibility with DT (I’m still using OS X 10.4) means I am starting to pull my pdf files out of the DT database. I suppose what Skim has done for me is to make me realise that for scientific work I find being able to mark up/make notes on pdfs (and later return to amend/add to those notes) is far more important than the database where I make my own hierarchies and subject folders anyway. I’ve had 50 Skim pdf bundles cluttering my desktop(!) because I can’t get them into DT and have at last started my own filing system instead…
Have any Skim users tried the new Preview annotations in Leopard? I’m assuming it will be these Leopard Preview annotations that will be part of DT2 when it comes out.
The nice thing is that the annotations made in Preview in Leopard seem to be compatible with Adobe Acrobat. So yes, we will of course use this.
Now all someone needs to do is write some sort of script that will convert skim annotations to leopard preview annotations, so Skim users could get back to using DT when v.2 comes out 
It’s not that I don’t believe that v2 will never arrive, but given the absence of information or schedule, waiting is pointless. I know you didn’t say you were waiting, but I couldn’t resist the barb.
Was Beckett a pessimist? He as much as said that he didn’t know or care about Godot and his characters could have better occupied their time. 
Fortunately, that long-discussed version 2 won’t be meaningless like Godot.
But it, like Beckett’s characters, has been waiting for Leopard. In this case, though, the waiting will be worthwhile. And I’ve been getting lots of work done in versions 1.x.
I, too, have been accomplishing much with 1.x and I have full confidence that v.2 will be a worthwhile improvement. I look forward to sending in more money for the useful features – whatever they happen to be. And, of course, whenever it happens to be.
I’m glad you’ve got thick skin, Bill, and a robust sense of humor. Thanks for that.
PDFPen seems to be a good alternative to the PDF annotations in Leopard. everything is visible in DT, and the program is much cheaper than acrobat or this shiny feline upgrade, by the way.
I appreciate the suggestions so far for workarounds - but which don’t cut the mustard for me. The summary so far (Dec 2007) regarding the Skim pdf file handler would seem to be:
a) don’t go there if you are a dedicated DT user,
b) at least some of Skim’s features may be on the horizon with DT v.2,
c) if like you me you’ve been an enthusiastic supporter of DT but have found Skim’s handling/marking up of pdf’s just too valuable (e.g. greatly facilitating the writing of academic papers) to abandon then you have to find a replacement for DT.
I think DEVONtechnologies are in a difficult situation here. Thanks to whoever pointed out that Skim adopts a proprietary way of handling pdfs (but also allowing pdf-with-notes to be saved as normal pdfs) and we understand why DT doesn’t want to go that way. But there is clearly some head of steam here because Skim is so useful, DT has earned a good reputation as a pdf database yet Skim and DT are effectively incompatible if you need to keep re-visiting and marking up pdfs. If you Google ‘Devonthink’ and other database software, notably ‘Eaglefinder’ you will find software reviews and blogs where others have already walked the path I am about to take - because the demands of work push me to adopt the most efficient pdf management right now. As far as DEVONtechnologies are concerned, I expect we are a minority group, of scientists especially, and I understand that.
I am spelling out the Skim situation here, intended as an archive comment, because technically I suppose the comment on the DT website is correct - but from a practical point of view I find the summary misleading:
DEVONthink: At a Glance
Store any kind of document, from text to PDFs, MP3s to movies, bookmarks and more.
Michael
Have you also posted this comment to the Skim support forum? My guess is that they have chosen to use a proprietary format precisely because it makes using other programs difficult. It’s in their interest to make the barrier to switching as high as users are willing to tolerate. And, since it’s their format, there’s only so much that DT (and others) can do. It’s really up to users to decide how dependent on one company they are willing to be.
Katherine
This isn’t misleading at all. DT can store any document or file type. It does not claim to make all of them viewable in DT. Go ahead and store your skim files in DT, and open them with Skim by right clicking them in DT and opening them with Skim.
Katherine’s caution about proprietary formats is of course well made - trouble is I am not alone in finding Skim the best kid on the block for those of us for whom work necessitates spending hours reading pdf files: tis a case of expediency in a pressurised environment.
Thank you, Danzac, you’ve sort of solved the problem:
“DT can store any document or file type. It does not claim to make all of them viewable in DT”. What I had missed - apologies - is that under DTP: Preferences\Import, by default the option to import unknown file types is not checked. Without checking that box Skim pdf bundles, all nicely highlighted and written on, could neither be dragged and dropped nor imported via the file menu.
The future for us Skim enthusiasts? Taking heart(?) from Bill’s comments (8th Nov above) on comparison with Waiting for Godot, maybe those pdf files can reside in DTP until Leopard greatly enhances pdf handling and DEVONthink v… arrives.
Michael
Apple has been improving annotation in Preview, from the early version which (frustratingly) turned text notes to images of text notes, to much improved notes in Leopard, which are also compatible with Acrobat.
In the current Leopard-compatible versions of the DT applications one can view the text notes attached to a PDF document. Although there’s not at this time provision to add notes from within the DEVONthink application, the document can easily be opened in Leopard’s Preview and annotated. When saved, the notes can be clicked on and read or closed within DEVONthink.
Those text notes are not currently indexed by DT, so one cannot use Search on the note content of an annotated PDF. That’s also true currently of the Search feature of Preview and, I think, of Spotlight.
There are visual cues to text notes attached to a PDF, so they have become useful for attaching text notes to any position on a PDF page – marginalia, if you wish.
Although PDF notes are not currently editable from within a DT application, they remain editable under Leopard’s Preview (and also Acrobat). So from your database select a PDF, choose Launch Path or Open With, add, delete or edit notes, then choose Save. Back in your database, choose that PDF, choose File > Synchronize and the changes are visible.
I would expect to see further enhancements of PDF notes under Leopard. Compatibility with Acrobat adds value for those who wish to share annotated PDFs.
With due respect, this is not a satisfactory answer. An application heralding itself as the premier content and document data manager MUST be able to access text entered in PDF files, both through Preview and Skim. This is a basic reqirement in this age. (And I believe EagleFiler can handle this task.) This is one more example of limited handling of metadata and such. It is time for DT to mature.
Why isn’t it satisfactory?
We’re talking about PDF files. Notes are an add-on, not part of the “text layer” of the format. For years Adobe has provided an indexing feature that provides for searching among a group of indexed PDFs. Notes are not indexed by Acrobat.
Notes are not yet searchable in Preview or in Apple’s PDFKit.
That’s the current status. Nevertheless, notes in Leopard’s Preview are a significant improvement over the past and are more usable now, with the advantage that they are compatible in Acrobat as well, for sharing with others. That’s an advantage over Skim.
PDFs are among the most universal of file types, so that one can share PDFs across all commonly used computer platforms. But making annotations that can easily be shared has been largely the province of owners of Acrobat, which is not cheap (although Adobe’s Reader is free.) Preview is “free” to Mac users, as part of the operating system.
My previous post emphasized that the ability to search PDF notes would be a good thing, perhaps similar to the way DEVONthink’s Search can search the text of a document’s Comment field. And it would be great to do annotations of PDFs directly within the database environment. Both features will depend on the tools available in Apple’s PDFKit. I’m optimistic that such features are in DEVONthink’s future.
Thanks for your response.
It is not satisfactory PRECISELY because “PDFs are among the most universal of file types”, which means that many DT users (epecially in academe) annotate them. The lure of DT is the elusive “paperless office”, which is why we prefer to annotate the PDFs, and not a hard copy. The annotations are often more informative to us than the rest of the PDF, but these two elements must remain together.
That would be great. But this feature has been requested as early as October 2003.
I can only say that I agree that it’s the notes that are important (but also the text), but I’m not sure that Skim is the way to go. I personally would prefer something that is a part of the PDF format.
(but I don’t want to use Adobe software since I dislike their programs (bad UI, slow, etc))
AsafKeller, I was doing scholarly literature research, including development of multi-volume bibliographies with thousands of citations, before the majority of DEVONthink users were born, and before computers were available as tools to provide assistance for such endeavors.
People have been doing scholarly research, making notes about literature and so on for thousands of years. The traditions and skills of modern literature research and citation were largely developed over the past 300 years or so.
And those traditions and skills have involved an incredible amount of drudgery. I detest drudgery.
I’ve always been awed by the work of an early 20th century historian of chemistry, who had an incredible grasp of the literature. He had to have been a monomaniac to have published so much. Accounts are that his study (and other rooms) were piled high with stacks of books, journals and paper. He had an eidetic memory and could unerringly find anything he needed at the moment; but often he didn’t need to find the original, for he could recall what he had read, including page numbers. Very few of us can do that, and so we appreciate computer assistance.
I’ve always liked the PDF file format, because it can be so widely shared. But the format wasn’t designed for post-editing (it’s really intransigent for editing) or annotation, and even features such as notes and other annotations are still very primitive, isolated from the indexing and search tools that have been developed for the PDF’s text layer. And text notes are plain text, so one can’t add hyperlinks to them. So it remains difficult for a document management and information analysis tool such as DEVONthink to seamlessly get at all of the information content of an annotated PDF.
But that’s what we want and need to make annotation more effective and efficient.
Personally, when I’m really into taking notes I use separate rich text documents and/or Papyrus 12 hybrid PDF documents that I can link to the referenced PDF as well as to other documents, even files outside the database or on the Web. For a couple of projects I’ve appended to the source PDF file additional pages of notes and comments, with hyperlinks to the referred source pages. The contents of those associated notes are not only searchable, but are indexed in the DEVONthink Concordance and are available to AI operations such as See Also. I’ve developed workflows that make that approach effective. But I wish I could accomplish that more directly “in” the PDF file itself; currently, no one can do that. But I’m think that will be possible in the future.