Calibre for scientific publications or other documents?

[excaliber]

Hi all,

I currently use Calibre only to organize my ebooks which is perfect for this purpose. Now I am wondering if Calibre is also suitable for organizing documents like scientific publications, manuals, etc. and how does it compare to reference management software like Zotero. For example when I put a document into Zotero it will get from the Web the metadata for it. I've tried to do the same with Calibre via a plugin ("Google Scholar") but I got an error. This plugin is no longer maintained. I haven't found any other working plugins.

What do you think about it? Does anyone use Calibre for other kind of documents apart from books and magazines? Does anyone had success with downloading metadata automatically for them and how?

Thanks in advance!

[Joanna]

I use Calibre occasionally for research articles and manuals (and regularly for lots of other stuff, such as audiobooks and language learning materials) but wouldn't go with it as my main tool for research. Right now, I'm pretty happy with my simple and slightly chaotic way of organizing scientific publications in regular folders on my hard drive but if I wanted to get a more systematic solution, I would certainly use something like Zotero, Mendeley or Citavi (not only because of metadata download features but also the simplicity of generating references).

[theducks]

Originally Posted by excaliber

Hi all,

I currently use Calibre only to organize my ebooks which is perfect for this purpose. Now I am wondering if Calibre is also suitable for organizing documents like scientific publications, manuals, etc. and how does it compare to reference management software like Zotero. For example when I put a document into Zotero it will get from the Web the metadata for it. I've tried to do the same with Calibre via a plugin ("Google Scholar") but I got an error. This plugin is no longer maintained. I haven't found any other working plugins.

What do you think about it? Does anyone use Calibre for other kind of documents apart from books and magazines? Does anyone had success with downloading metadata automatically for them and how?

Thanks in advance!

AFAIK the only rule is that Title - Author need be unique to avoid the 'Duplicates trap'
One way for Regularly published Magazines is to include the Issue number or date as part of the title (field). Tags and Series [index] are additional tools for further orginazation

As always:
Having a consistently implemented PLAN is the key to success

[excaliber]

@Joanna: thanks for your quick response. I suppose you enter all the information you need manually.

@theducks: thanks for your quick response. OK, but my main question is if calibre has still some advantages over tools like Zotero.

For me the automatic extraction of metadata and the downloading of metadata are now the most important features otherwise I have to enter all metadata manually and that takes time.
For testing purposes I have entered some documents into calibre with "read metadata from file contents rather than the file name" enabled. The same documents I have entered into the PDF metadata extractor PDFMtEd (I use mainly Linux). In PDFMtEd I can see all metadata correctly. I have no idea how calibre extracts metadata but they are only a few and seem to be inaccurate.

[DaltonST]

@excalibur:

If your PDFs have an ISSN, the Library Codes plug-in can retrieve a lot of metadata. It can first extract the ISSN if there is one, of course.

See the attached image.


DaltonST


n.b. if you wonder how the attachment GUI colors got to be that way, see: https://www.mobileread.com/forums/sho...4&postcount=94

[BetterRed]

Originally Posted by Joanna

I use Calibre occasionally for research articles and manuals (and regularly for lots of other stuff, such as audiobooks and language learning materials) but wouldn't go with it as my main tool for research. Right now, I'm pretty happy with my simple and slightly chaotic way of organizing scientific publications in regular folders on my hard drive but if I wanted to get a more systematic solution, I would certainly use something like Zotero, Mendeley or Citavi (not only because of metadata download features but also the simplicity of generating references).

- if I was engaged in formal research with an eye to the publish or perish phenomena I would use something like the tools Joanna has mentioned, I've had a look at those and a couple of others - but for me they were too rigid. But my so-called research doesn't claim to follow standard practices, and it targets a very specific (and private) audience.

I use Evernote to supplement Calibre (and vice versa) - see Calibre and Evernote.

More recently I've been adding OneNote .ONE files to books as a place to keep book specific notes.

BR

[chaley]

FWIW: I am in full agreement with BR and Joanna, especially if the research process includes writing as well as reading. I can't imagine writing papers and articles without a real academic citation and bibliography manager. The pain is too great. For example, changing all the citations of a paper to match what the publishing venue required took far more time than I was willing to spend (think ACM vs IEEE vs Springer publishing styles). Having automatic citation generation makes that problem go away.

Another point: research bibliographies require specific information that calibre doesn't deal with very well. For me the largest problem is people and roles, for example authors, editors, translators, organizers, reviewers, and the like. A person can have multiple roles in the same time paper. In some publishing venues, the role controls how the name is to be displayed. A bibliographic data manager can deal with this.

During my 8 years or so as a writing researcher I tried Bibtex, Endnote, Zotero, and a product that no longer exists. BibTeX lost out because I decided not to use LaTeX. Zotero worked quite well but was still in its infancy back then (may be better or worse now). I ended up using Endnote because it worked beautifully, was what my coauthors used, and was supplied by my university.

[excaliber]

@DaltonST: thanks for the tip. I have installed the plugin and tried over ISSN but none of the documents I tried had an ISSN.

@BetterRed: thanks for the tip. Linking notes to docs is great. I have tried the combination Evernote and Calibre for adding notes and it's awesome. Unfortunately Evernote runs only in Windows and I use mostly Linux. I tried Evernote over Wine but without success. I have found though another tool in Linux similar to Evernote called KeepNote which provides the link functionality.

@chaley: thanks for your input. Things like inserting citations is for sure something for bibliography managers but where to keep docs organized? Storaging docs and enriching them with metadata are things both calibre and bibliography managers share.

BTW, I have tested again the importing of metadata in calibre. Most of them were OK. But apparently calibre is not able to write PDF metadata so any metadata modifications must be done before importing them.

It would be great if calibre would offer synchronization of databases with tools such as Zotero or JabRef or at least importing and exporting.

[DaltonST]

@excaliber:

Have you tried exporting from Zotero using Zoteroexport http://zoteroexport.mozdev.org/index.html and then importing that exported file into Calibre?

[excaliber]

@DaltonST: thanks for the tip. Firefox does not let me install "Zoteroexport" because it's not signed. I have tried with "Zotero autoexport" to export in csv and import it in calibre but that didn't work for me either.
I have also tried CalibreImportRDF but I get errors.

I have found some previous posts related to my problem:
https://www.mobileread.com/forums/sho...d.php?t=108952
https://forums.zotero.org/discussion...ibliographies/

Glad to see it's not only me! The posts are from 2010 and 2013.

[DaltonST]

@excaliber:

I had a few minutes to spare, so I installed Zotero for Firefox. I then exported my library to a CSV file. See the attached image.

Would it be possible for you to export to a CSV file some representative items with an itemType of "pdf", and Private Message that to me? Perhaps add a "real" PDF file that is referenced near the top of that CSV file so I can figure out how to link a row in the CSV to the real PDF file?

I'm just putting the tip of a toe into the water long enough to scope out the feasibility of using a Zotero CSV export file as an interface source for Calibre ebook metadata. No promises. Just looking...just scoping.


DaltonST


DaltonST

[DaltonST]

@excaliber:

I got your CSV and the PDF that was represented by a row in that CSV. I can work with that. I will get back with you later in the week after I have a new plug-in for you to test on your "real" data.

Thanks.



DaltonST

[excaliber]

@DaltonST: Great! This is awesome! I am very excited about it! Thanks!

[BetterRed]

Originally Posted by excaliber

...But apparently calibre is not able to write PDF metadata so any metadata modifications must be done before importing them.

@excaliber - FWIW the calibre Embed Metadata tool will write metadata to unprotected PDFs, it writes it as XMP data so you need a PDF something for Linux that will access the embedded XMP. On Windows I use PDF Exchange, viz:



Added 1 : IIRC Phil Harvey's ExifTool (runs on anything) will see embedded XMP in PDFs, and maybe even allow modification.

Added 2 : Just remembered there's also this ==>> Import Mendeley Documents. Looks like its not working - might be worth asking the PI 'author' if its fixable.

BR

[excaliber]

@BetterRed: thanks for your tips! I have tried again to save metadata in calibre with "edit metadata" into an unprotected .pdf but it doesn't work for me. I have checked it with PDFMtEd (uses ExifTool) and PDF Exchange or you mean something else with "calibre Embed Metadata tool"? How did you do it?

I won't even try with Mendeley because it couldn't get metadata like Zotero.