How organized are your pdf files

[The Mercurian]

Have you tested Papers and/or BibDesk?

As I said before, I will be using .bib (latex bibliography database) quite a bit, which would make BibDesk natural choice. However, since BibDesk uses .bib file to store EVERYTHING it breaks latex functionality sometimes; this is from my limited experience as well as according to some on-line reading.

R>

I downloaded trial version of papers but didn't like it. a) I just didn't like the interface, b) it isn't free like Mendeley/Zotero,Readcube, CiteULike, and c)I wanted a cross platform option

As to Bibdesk I don't know it but I despise anything latex related so I probably didn't bother to look

Readcube could be worth a look if they have developed some extra features. Its very pretty looking

 

[EmpyreanUK]

I've been pulling my hair out over this, on and off, for about a year now. My focus is history, so while I need some method to organise and catalogue journal articles, what is more important to me is primary source material, which could come in PDF format, but also in a variety of image formats.

My needs are fairly simple: I'm looking for an application into which I can import documents, record meta-data pertaining to such documents (author(s), publication date, digitisation date, etc.) and then tag them, so documents can easily be organised into different projects and themes whilst retaining a 'flat' file-structure. It would preferably be able to use Quick Look so that I can easily preview a file.

Yet I've been unable to find something that fulfils even these simple requirements. I've tried Yojimbo, Together, DevonTHINK, Evernote, Sente, Paperless, Yep!, Bookends, Punakea, EagleFiler and Chikoo, and I've tried to invent some method of doing this through a combination of the Finder and Spotlight —*perhaps using OpenMeta —*to no avail. The closest I've come is to something satisfactory is creating a custom database using Bento 4, but this doesn't feel like a sustainable solution to me (I'd like this personal library/collection to remain viable for years and years), as Bento is a severely limited app, and I've heard bad things about the developers and their attitude to upgrades.

I'm at the point where I'm considering creating a solution myself using PHP and MySQL. I'm reasonably proficient in both, but I really don't want to have to run a web server on my home computer to achieve this, and it would also have practically non-existent OS integration, in that links to files would have to be in a static file:// format (meaning if I move a file I'll have to manually update my application), and Quick Look support would be out of the question.

Considering that I'm not even looking for citation management capabilities, as many of the posters in this thread are, it seems to me that this a dearth in quality in the applications that exist on OS X for personal library and collection management. It's pretty exasperating, especially when we cannot endlessly wait until somebody does actually provide a solution to this set of problems!

 

[ozaz]

while I need some method to organise and catalogue journal articles, what is more important to me is primary source material, which could come in PDF format, but also in a variety of image formats.

My needs are fairly simple: I'm looking for an application into which I can import documents, record meta-data pertaining to such documents (author(s), publication date, digitisation date, etc.) and then tag them, so documents can easily be organised into different projects and themes whilst retaining a 'flat' file-structure. It would preferably be able to use Quick Look so that I can easily preview a file.

Whilst mendeley is optimised as a journal article pdf manager and viewer, it's not restricted to organising only PDFs. You can use it to catalogue any file type. Catalogue entries for a variety of types of source material are available, as is a "generic" entry type. Tagging is supported.

However, it only has a built in viewer for pdfs. To view any other files catalogued in the library, mendeley will launch the default 3rd party application (unfortunately, it does not seem like OS X quick look is currently supported from within the Mendeley application).

Multiple files can also be attached to a single entry in your Mendeley library. e.g. supplemental figures and movies for a journal article.
http://blog.mendeley.com/tipstricks...upplementary-data-to-references-part-6-of-12/

 

[radek42]

Thanks for your comments. As somebody mentioned already, it is surprising that seemingly every single tool out there lacks some core functionality. I am slowly giving up on different aspects of my "idealized" workflow since I cannot find a tool to actually achieve it.

To your particular issue: I think the previous post is pretty close to what you want to achieve with some (minor?) issues. I'd almost say that converting your images into pdf, either individual or merged, and adding them as supplementary information might be way to go.

I am still struggling myself with all those programs although I haven't tried as many as you did. I actually widen my scope to include JabRef. So for me now it's "Papers", "Mendely", BibDesk, and "JabRef" (yes, I actually do want latex stuff

As I noted last night, Papers under OSX work much better than win couterpart so some of my earlier issues are gone. However, it did horrible job filling out meta data from on-line searches. It seemed to export .bib file nicely, but I had to edit all (I tried ~10 entries) but one which is frankly unacceptable.

Mendeley does pretty good job. The "watch folder" function is neat plus it picks up meta data from pdf files quite nicely (at least stuff downloaded from WoS). Export to .bib seems ok as well. For some reason I do not like it .... I am not sure why.

I took JabRef for a spin again last night after couple of years. It still has fairly simplistic interface and tons of options including journal abbreviations, various formats, etc. Its .bib file seems nice and clean as well. Again, there is something about it that does not sit well with me; can't quite put my fingers on it.

My outstanding issues:
1. special characters: they can be included in .bib file. JabRef seems to be ok with it; Papers/Mendely did not like it.
2. formatted refereces (rft format) for occasional Word usage. Mendeley works. Not sure how to do it with JabRef.

I want to try if one could go between Mendeley-JabRef databases and maintain pdf links. Perhaps combination of these two programs could give me functionality I am looking for. However, I'd rather use a single program.

This is getting tiresome

R>

I've been pulling my hair out over this, on and off, for about a year now. My focus is history, so while I need some method to organise and catalogue journal articles, what is more important to me is primary source material, which could come in PDF format, but also in a variety of image formats.

My needs are fairly simple: I'm looking for an application into which I can import documents, record meta-data pertaining to such documents (author(s), publication date, digitisation date, etc.) and then tag them, so documents can easily be organised into different projects and themes whilst retaining a 'flat' file-structure. It would preferably be able to use Quick Look so that I can easily preview a file.

Yet I've been unable to find something that fulfils even these simple requirements. I've tried Yojimbo, Together, DevonTHINK, Evernote, Sente, Paperless, Yep!, Bookends, Punakea, EagleFiler and Chikoo, and I've tried to invent some method of doing this through a combination of the Finder and Spotlight —*perhaps using OpenMeta —*to no avail. The closest I've come is to something satisfactory is creating a custom database using Bento 4, but this doesn't feel like a sustainable solution to me (I'd like this personal library/collection to remain viable for years and years), as Bento is a severely limited app, and I've heard bad things about the developers and their attitude to upgrades.

I'm at the point where I'm considering creating a solution myself using PHP and MySQL. I'm reasonably proficient in both, but I really don't want to have to run a web server on my home computer to achieve this, and it would also have practically non-existent OS integration, in that links to files would have to be in a static file:// format (meaning if I move a file I'll have to manually update my application), and Quick Look support would be out of the question.

Considering that I'm not even looking for citation management capabilities, as many of the posters in this thread are, it seems to me that this a dearth in quality in the applications that exist on OS X for personal library and collection management. It's pretty exasperating, especially when we cannot endlessly wait until somebody does actually provide a solution to this set of problems!

 

[The Mercurian]

Hey OP

I have over the last few days started to use Mendeley to manage citations in a new paper written in MS Word for Mac 2011 (well my thesis actually).

It appears to work very well. It adjusts the number in real time as I add new references early in the manuscript for example.

I've by no means tested it exhaustively and have not generated the bibliography yet - but so far I am pleasantly surprised!

 

[radek42]

Thanks for your thoughts.

At the end I tested three apps:
1. Papers2;
2. Mendeley desktop; and
3. JabRef.

I really wanted something that plays well with latex/bibtex; I was less concern about Word. At the end, both Papers and Mendeley failed to work properly with journal abbreviations. Moreover, Papers2 did not allow to move/rename pdf file names once in the database.

Ultimately, JabRef might not be as friendly as other two, but it works well enough and most importantly plays well with latex.

I have to say that Mendeley came close second tho. I might revisit in some time.

Slightly off-topic: I am not sure what are your constrains in terms what to use/not use for your thesis nor its extend (bachelor, masters, phd), but I would stay away from Word for anything over 10 pages or 5 equations. I had nothing but trouble with Word for writing papers couple pages long, from no easy way to properly number equations to shuffled reference list after parts of the paper were moved/deleted.

Latex might take couple days to get used to, but believe me, you'll be glad in couple weeks you picked it for references alone. There are many WYSWYG editors which makes transition relatively easy (although I never used one myself). After couple weeks you'll remember most commands anyway and it's easier and faster just to type it in.

I used Texworks (cross-platform editor) as well as Texwors (Mac only) and they are both excellent. I prefer Texworks on mac tho.

Good luck.

Radek

Hey OP

I have over the last few days started to use Mendeley to manage citations in a new paper written in MS Word for Mac 2011 (well my thesis actually).

It appears to work very well. It adjusts the number in real time as I add new references early in the manuscript for example.

I've by no means tested it exhaustively and have not generated the bibliography yet - but so far I am pleasantly surprised!

 

[The Mercurian]

Slightly off-topic: I am not sure what are your constrains in terms what to use/not use for your thesis nor its extend (bachelor, masters, phd), but I would stay away from Word for anything over 10 pages or 5 equations. I had nothing but trouble with Word for writing papers couple pages long, from no easy way to properly number equations to shuffled reference list after parts of the paper were moved/deleted.

Latex might take couple days to get used to, but believe me, you'll be glad in couple weeks you picked it for references alone. There are many WYSWYG editors which makes transition relatively easy (although I never used one myself). After couple weeks you'll remember most commands anyway and it's easier and faster just to type it in.

I used Texworks (cross-platform editor) as well as Texwors (Mac only) and they are both excellent. I prefer Texworks on mac tho.

Good luck.

Radek

I've been using Word for years for numerous journal articles and college papers etc. Never have problems (ok no it used to have problems - but in last few years I have none)

I have used latex yonks ago but have no interest nor need for it now. Word does all I need it to do and it does it well

 

[campasoft]

Hi all

as I was frustrated about current PDF organizers, I built mine from scratch. It is called FingerPDF (http://www.campasoft.com) and currently it is in Public Beta.

I built it with these organization principles in mind:

1. File System is my primary organization unit. In particular I am used to put my digital library on a dropbox folder. So the organizer has to be filesystem friendly. I want to connect to my file system with other devices or systems and I want to move/copy/reorganize files, without corrupting anything.
FingerPDF automatically synchronizes with first level folders of a central directory.

2. Tagging. I need to tag easily files according several criterias. FingerPDF supports easily tagging

3. I do not want to care about database backup or corruption. FingerPDF embeds automatically every data (note, metadata, tag) inside the PDF. So If I change computer or I have to start from scratch I re-import pdf into the app and et-voila' all my previous saved data is there

4. Searching. When I have 100 or 200 books I have about 100.000 pages. If I search for a KEYWORD I do not want to know books that contain it but I want to quickly jump to that page ! And I want to easily skim through all the other retrieved pages

5. Repository of knowledge. I do not want an app only for scientific papers. I want an app to manage a Repository of Knowledge. So it has to manage books, magazines, papers and web articles !

6. Mac-styled User Interface and Zenware. I wanted a cool Mac-styled user interface. The goal of zenware is to disappear, supporting you when you need it but staying out of your way as much as possible. You should forget the software is there at all. So the app can remain on status bar and can be called with shortcuts

Sorry if I talked about my product but I think it can be useful for organization

Piero

 

[spravtek]

Hi all

as I was frustrated about current PDF organizers, I built mine from scratch. It is called FingerPDF (http://www.campasoft.com) and currently it is in Public Beta.

I built it with these organization principles in mind:

1. File System is my primary organization unit. In particular I am used to put my digital library on a dropbox folder. So the organizer has to be filesystem friendly. I want to connect to my file system with other devices or systems and I want to move/copy/reorganize files, without corrupting anything.
FingerPDF automatically synchronizes with first level folders of a central directory.

2. Tagging. I need to tag easily files according several criterias. FingerPDF supports easily tagging

3. I do not want to care about database backup or corruption. FingerPDF embeds automatically every data (note, metadata, tag) inside the PDF. So If I change computer or I have to start from scratch I re-import pdf into the app and et-voila' all my previous saved data is there

4. Searching. When I have 100 or 200 books I have about 100.000 pages. If I search for a KEYWORD I do not want to know books that contain it but I want to quickly jump to that page ! And I want to easily skim through all the other retrieved pages

5. Repository of knowledge. I do not want an app only for scientific papers. I want an app to manage a Repository of Knowledge. So it has to manage books, magazines, papers and web articles !

6. Mac-styled User Interface and Zenware. I wanted a cool Mac-styled user interface. The goal of zenware is to disappear, supporting you when you need it but staying out of your way as much as possible. You should forget the software is there at all. So the app can remain on status bar and can be called with shortcuts

Sorry if I talked about my product but I think it can be useful for organization

Piero

That is exactly what I'm looking for with the amounts of technical PDF's I'm holding, I'll give the beta a try, thanks for mentioning it!

 

[jdelgado]

campasoft - FingerPDF

That is exactly what I'm looking for with the amounts of technical PDF's I'm holding, I'll give the beta a try, thanks for mentioning it!

Me too!

I have also been looking for something similar to this:
1. Edit standard fields of the file (keywords, author, description, source, etc)
2. Let the fields be searchable within Mac standard tools (Spotlight, Finder Find, Houdahspot or similar app)
3. Ability to add notes/comments/annotations to the pdf that are searchable within the Mac standard tools.

There are other applications that do the above (eg, PDFPen, Acrobat), but they have more features than needed and clutter my workflow. I tend to prefer simpler, focused tools.

I downloaded the beta. I will send my comments by email.

 

[TheGenerous]

I use BibDesk to manage a bibliography that I use in a LaTeX document. To find the pdf I rely on the filestructure,

Project folder\

[tag,tag,tag]year_authorlastname-title.pdf

All pdfs in one single folder with lower caps look good when named this way. Example, for articles in astrophysics (tag=astro), diatoms (tag=dia), optical tweezers (tag=otw), adding prefiex like suppl for supplementary documents. This is how they look in Finder;

[astro,dwarf]2012_dean-laterally propagating detonations in thin helium layers on accreting white dwarfs.pdf
[dia,biofilm]2012_berk-molecular architecture and assembly principles of vibrio cholerae biofilms.pdf
[dia,biofilm]2012_berk-molecular architecture and assembly principles of vibrio cholerae biofilms_suppl.pdf
[otw,rnapii]2013_zhou-single-molecule studies of rnapii elongation.pdf
[fracta,wavelet,book]2001_yves nievergelt-wavelets made easy.pdf

 

[mollyparrot]

I suppose I am replying in part to some really old posts, but Circus Ponies Notebooks has a lot of the functionality that people are looking for. You can drag pretty much any sort of media into the notebooks that you create, annotate, index, etc.

I use it a lot now for my lesson planning brain storming, but it was invaluable when organizing research, notes, pdf, bibliographies, etc during my geology degrees. I did not use it nearly as much for my math based papers--I have to admit that for those, I found it easiest to just maintain pdf archive in a folder along with my Excel data and mostly work from low tech hard copies. But, for my more qualitative papers and research Ponies was really invaluable. One nice feature is that you can export an entire notebook as a webpage. The webpage it puts up isn't lovely, but its amazing to be able to access your data from anywhere and to easily share it with your research group.

There is also an ipad app that syncs reasonable well. It is super pricey for ipad (or was), and kind of buggy still, but overall I would recommend it. I think the Mac version was also around $30, but it was well worth it.

There are templates and user groups based around sharing layouts, but most of that seems geared towards legal users.

(no, I don't work for them! I've just been happily and productively using it for about 5 or 6 years after having tried a boatload of other programs.)

 

[saberahul]

For a long time, I've had a folder based system on my work pc which is duplicated on to dropbox, and from there I access it on my Air and my iPad. On my iPad, my entire research library is synced to iAnnotate. In many ways, this works quite well for me, and for the most part I find that I can locate the documents I need when I need them.

Having said that, I'm in the process of setting up a library in Papers, which is going a bit slowly because I'm partially questioning the need for it. Initially, I wanted to use Papers as a cite while you write tool, so my purchase was motivated by that. For pdf management, I think the main advantage of Papers versus my current file folders is the opportunity to tag documents. Even though I find that my current thematically organised file groups work quite well for my purposes, a lot of the articles could potentially belong to more than one category. So, by adding multiple tags in in Papers, I can place the same document in more than one category without duplicating the file, and I can also have a more fine grained categorical system because adding more tags doesn't mean adding more versions of the same document.

If I didn't work in a Windows environment, I would probably have no hesitations switching to Papers as my main pdf organisation app. However, since I will need to work cross platforms for the time being, I'm in two minds about whether to make the full switch to Papers on my mac/iPad. That hesitation is reinforced by the fact that the iPad version of Papers has very limited annotation capacities compared to iAnnotate or PDF Expert.

Couldn't agree more. With the introduction of tags in mavericks, you could replicate the same process though finder.

 

[jojoba]

I suppose I am replying in part to some really old posts, but Circus Ponies Notebooks has a lot of the functionality that people are looking for. You can drag pretty much any sort of media into the notebooks that you create, annotate, index, etc.

I use it a lot now for my lesson planning brain storming, but it was invaluable when organizing research, notes, pdf, bibliographies, etc during my geology degrees. I did not use it nearly as much for my math based papers--I have to admit that for those, I found it easiest to just maintain pdf archive in a folder along with my Excel data and mostly work from low tech hard copies. But, for my more qualitative papers and research Ponies was really invaluable. One nice feature is that you can export an entire notebook as a webpage. The webpage it puts up isn't lovely, but its amazing to be able to access your data from anywhere and to easily share it with your research group.

There is also an ipad app that syncs reasonable well. It is super pricey for ipad (or was), and kind of buggy still, but overall I would recommend it. I think the Mac version was also around $30, but it was well worth it.

There are templates and user groups based around sharing layouts, but most of that seems geared towards legal users.

(no, I don't work for them! I've just been happily and productively using it for about 5 or 6 years after having tried a boatload of other programs.)

I use CPN a lot now for note taking. I didn't realise I could export a whole notebook as a web page, I'm going to check that out. I agree with you on the iPad version. I think the mac version is brilliant and wish they'd match up on the iPad (especially with that price tag). I also use it to sync to my iPad, very useful. I've written some blog posts on the app here:

http://macademise.wordpress.com/tag/circus-ponies-notebooks/

Couldn't agree more. With the introduction of tags in mavericks, you could replicate the same process though finder.

Although, after having written all of that, I eventually took the step and organised all of my papers, first in Sente and later in Bookends! And I'm happy I did, it works very well for me now. I always have my iPad with me even if I'm at work at my Windows computer, and all attachments are synced to Dropbox and hence available from anywhere. Works well for me.