Option to save my highlights and comments in the PDF documents themselves.
The comment and highlighting functions in Mendeley are great. However, I would like to have the option to save these changes straight into the pdf. The markups are very important for me in my work and I'm afraid that they will all be gone if I should for some reason loose my Mendeley installation. Additionally that way I can send that pdf and my collegues will see my markups. At this point I'm still doing my markups in another program because I know they are safe there (saved inside the pdf document). I don't have that feeling with Mendeley yet.
Why do you save highlighted text and notes in PDFs in your own proprietary format? why not Adobe's standard format? that would make it much easier to use this information in other applications and read/edit the PDFs e.g. with Adobe Acrobat
The ability to do this automatically is not yet available. However, it has been raised with our Development Team
Miro Soares commented
I also join the chorus. I love mendeley, but this specific point I really dont like! I feel also much more confortable saving the highlights and comments using Adobe PDF software. I my point of view it seems that mendely wants to force a kind of proprietary format for notes, which is hard to accept. I would be very glad if Mendeley could only apply the changes in the pdf, or even simply link to open the PDF in the user preferable PDF viewer.
Griffin Howlett commented
This makes Mendeley practically unusable at this point...
Oscar has a point in asking the original PDFs to be left untouched, but it must be possible to export ALL annotated PDFs in one step; the current version of 'Export PDF with annotations' can only be a work-around as long as you have to do it for each PDF separately from the PDF viewer.
Could it be implemented that one can 'Export PDF with annotations' from the table view for all selected PDFs in one go??
As others said before, these annotations are very valuable to some users and unless one can store them with the PDFs it is to risky. A year ago a Mendeley bug wiped out half of my PDF library - the bug was fixed in the following update, but since then I am cautious. I would like to use the great annotation functionality, but will wait until a backup via export is possible.
Kyle Davis commented
This feature would be very useful for researchers that use multiple computers. Please implement a way to activate automatic saving of highlights and comments, would make some task much easier. Thanks.
I fully agree, too. Please, either add an option to use Adobe’s standard PDF format or a bulk export option.
The option exists! 'Export PDF with annotations'.
I would not accept that the program 'automatically' saves the highlight... For example: I'd like that my student read the papers and forge their ideas, not just copy mine.
It would be great to have the highlighted text and notes stored in the Adobe standard format.
I would make the work with Mendeley much more transportable, e.g. send an annotated file
to a colleague not (yet) running Mendeley. Actually I do not understand why to use a proprietary format.... Please, at least implement this as option!
Ihor Rokach commented
I also think that it would be better for Mendeley users to have all annotations in standard Adobe Acrobat format (at least as an option). All non-standard formats are the main obstacles in sharing of the scientific information. If Mendeley use _standard_ PDF files why it should use proprietary (means _non-standard_) format for notes?
Please use Adobe’s standard PDF format for annotations. I frequently have to open pdfs in other viewers and cannot see annotations and highlights. At least a bulk export for the PDFs including annotations would reduce my frustration as I have more than 800 refs in Mendeley
I fully agree, especially when combining Mendeley with other programmes (e.g. mind mapping software) it would be very helpful to be able to access all annotations & highlightings in these other programmes, too.
But having to go through the "Export PDF with Annotations" is a pain if you want to do that with a large number of files. I often open PDFs outside of Mendeley, and not having access to my annotations is a big problem.
Is there a way to export ALL of my PDFs with annotations?
John Anderson commented
Agreed - this needs to happen. Automatic reading/converting of comments from (at the very least adobe reader/acrobat) and other programs would help to salvage much of the utility of this program. I also like the suggestion that comments in Mendeley should be automatically read by these programs as comments as well. I was trying to convince my lab to switch to Mendeley, and this was one of the only sore points.
Echoing Steve's request: Commenting in Mendeley should use the adobe pdf standard, and write to the pdf on exit (or sync). THis could be a preference. Mark-up from other applications (eg on iPad) could then be viewed in Mendeley.
OR, make the Mendeley iPad app able to comment please.
AdminRobert Knight (Admin, Mendeley) commented
Mendeley doesn't store highlights and notes in the PDF at all. They are stored in Mendeley's local database. This simplifies syncing the data with Mendeley Web and dealing with migrations/backups/sync metadata in the same way that we handle other data.
You can get a copy of the PDF with annotations in the standard format using File -> Export PDF with Annotations.
I think the developers should go further than this. Annotation and highlighting is supported in the PDF format itself and so the software should follow this standard, to maximise compatibility with other software. I use another application (GoodReader for the iPad) to annotate my readings and synchronise this with Dropbox, and I have the relevant Dropbox folder as a watched folder in Mendeley, so it would be useful for me if Mendeley could recognise the annotations I have already made in other software. This would therefore also be useful for those who have already annotated a file in Adobe Reader, or other similar software.
I actually meant that it should be done automatically. I've seen that there is an option to export the pdf file and I guess that's about halfway to what I want. It's quite a hassle to find the right folder to export the pdf and replace the unedited one. What I really want is just a save button that does automatically exports the pdf file and replaces the unedited one. The markups are then seen by any pdf reader but it should still be possible to edit with mendeley. This is how pdf Xchange works which I'm currently using.
Robert Knight commented
I should clarify that I am interpreting this as the ability to export an article with embedded annotations, rather than the ability for Mendeley to automatically embed annotations in PDFs - which is something that may come later, though we would need to improve the file sync process and several parts of our back-end services first.
Robert Knight commented
Hello - You can export a PDF containing highlights and notes as PDF annotations via File -> Export PDF with Annotations in the internal PDF viewer. We are also making some improvements to this functionality in the next release.