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Old 10-09-2013, 07:58 PM   #1
Rhialto
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Scientific papers downloadable as epubs - Calibre management?

I am an immunologist by profession;

The below link describes an option at PubMed.gov to download academic papers as epub files. I was able to open the files in Marvin reader app on my iPad.

I assume I could import these epubs into Calibre and use Calibre to manage these papers. Has anyone else tried this use of Calibre?


http://www.ncbi.nlm.nih.gov/pmc/about/pubreader/
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Old 10-10-2013, 01:53 AM   #2
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Rhialto,
I cannot recall anyone else mentioning that they're using calibre for this reason. However, since the files are epubs, it should not be a problem having calibre manage them. Obviously you're going to be a bit more hands on with regards to the metadata (you cannot simply download it from Amazon), but otherwise you're fine.
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Old 10-10-2013, 05:50 AM   #3
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Quote:
Originally Posted by Rhialto View Post
I am an immunologist by profession;

The below link describes an option at PubMed.gov to download academic papers as epub files. I was able to open the files in Marvin reader app on my iPad.

I assume I could import these epubs into Calibre and use Calibre to manage these papers. Has anyone else tried this use of Calibre?


http://www.ncbi.nlm.nih.gov/pmc/about/pubreader/
I downloaded one of the test papers as an epub and put into a vanilla Calibre library. I got the title, the tags, the synposis, the publication date and an ID that links back to the nih page automagically, but couldn't see how to get the authors or the publisher (but I didn't try very hard) - so I copy/pasted them from the text.

The 1st screen shot is the result as far as the library is concerned

The 2nd screen shot is what I see in the calibre epub viewer, the links to the bigger views of graphs and expanded table seem work

One thing you will need to be aware of is that Calibre will truncate file names in the library - this is not a problem per se, but initially it can be disconcerting.

Start slowly with a few articles to get a feel for calibre and its capabilities. Calibre is very flexible, almost to a fault, and there are normally several ways to 'tackle ' the same issue - the trick is to find the one that suits your needs.

BR
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Old 10-10-2013, 04:54 PM   #4
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BetterRed; thanks very much for your testing. I am mainly wondering if I really need to collect papers in a personal library as epubs. These days, provided you are at an academic institution, clicking on reference links in online publications opens papers as .pdfs on publishers sites pretty quickly.
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Old 10-10-2013, 06:10 PM   #5
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Originally Posted by Rhialto View Post
BetterRed; thanks very much for your testing. I am mainly wondering if I really need to collect papers in a personal library as epubs. These days, provided you are at an academic institution, clicking on reference links in online publications opens papers as .pdfs on publishers sites pretty quickly.
@Rhialto: for me the advantages are a) fetching texts from a wide variety of sources into a single 'catalogue', b) ability to search across the texts via author, keywords etc in Calibre and via full text search tools outside of calibre c) ability to read things off line - at weekends I'm often on a satellite link, d) some of my sources are unreliable - i.e. just because something was there yesterday doesn't mean it will be there next week

My areas of interest are economics, finance and law.

BR
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Old 10-10-2013, 07:16 PM   #6
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@Rhialto: if you are an author as well as a reader, you might want to consider an using academic bibliography manager that can automate citation formatting in your papers, something calibre cannot and will never do. I have used bibTeX (and associated tools), endnote, and zotero. My opinion: bibTeX is useful only if you are a laTeX user. Zotero was good, but I haven't used it since it was "cloud-enabled" so I can't say that it is still good. My institution paid for endnote so I ended up using that, allowing easy sharing of bibliographic databases with my coauthors.
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Old 10-11-2013, 11:47 AM   #7
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Yes, I use Endnote X6 for writing and managing citations. The support for Word is excellent. It also allows you to manage .pdf collections, though I admit I haven't used this feature much. I am not enthusiastic about reading paper .pdfs on the iPad; the screen seems too small, which is one reason a epub system is potentially interesting.


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Originally Posted by chaley View Post
@Rhialto: if you are an author as well as a reader, you might want to consider an using academic bibliography manager that can automate citation formatting in your papers, something calibre cannot and will never do. I have used bibTeX (and associated tools), endnote, and zotero. My opinion: bibTeX is useful only if you are a laTeX user. Zotero was good, but I haven't used it since it was "cloud-enabled" so I can't say that it is still good. My institution paid for endnote so I ended up using that, allowing easy sharing of bibliographic databases with my coauthors.
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