meta data for scholarly journal articles?

[somewhat]

Hi,

I have some articles from journals that I'd like to keep in Calibre. These documents have detailed metadata associated with them for citation purposes but it doesn't seem like it is getting through to Calibre.

Files obtained from PubMed seem to have Title and usually Author done properly but not the published date, publisher, series, abstract/description. The files from JSTOR portal typically have zero meta data.

Unsurprisingly, downloading metadata from the amazon etc sources that are available does not work since these are not books.

Scholarly articles often have a DOI associated with them which allows finding of metadata for example in crossref.

So I'm looking for:

• A metadata source that would be able to grab the details from a database somewhere, or
• A reasonably streamlined way to import individual citation files

example

In case anyone is interested in taking a crack at this but isn't familiar with the systems:

Here is a pubmed search for articles whose full text is freely available online that contain to word "cats".

One finding: Identification of separation-related problems in domestic cats: A questionnaire survey links to the fulltext on PLOS ONE where citation is available in different formats.

JSTOR is a walled garden you must have access to usually via an institution. I get it thru the public library. But I can't link to anything usefully. However it provides the following formats to save the citation (aka metadata): "NoodleTools, RefWorks, EasyBib, RIS file (For EndNote, ProCite, Reference Manager, Zotero, Mendeley…), (For BibTex)"

Citation manager software

I know that there are integratino plugins for Zotero and Mendeley. Zotero for example has the facility to pull metadata for articles. But I'm not actually an academic and I've never managed to work out citation managers as they always seem to be overkill for my needs. The documentation for the plugins that I found assume you already know how to use the citation manager and have it going. I don't know if it's the only way to patch the meta data through. I am hoping there is a more direct way. Because I don't actually need to manage citations.

any thoughts on this or related strategies to amange these kinds of documents are appreciated.

[kovidgoyal]

Look throught the list of metadata ources in the plugins sub forum. I vaguely recal there being one or two for scholarly articles. If so you can install and use them in calibre.

[somewhat]

Thanks I tried to look to for this but couldn't find anything.

I am not sure if I am using the search function properly tho because I got many hits where the search term didn't seem to be present using ctrl-F find in page (including opening "spoilers"), or using the "search this thread" option at the top. I don't know if the search is indexing something I can't see or maybe it has a thesaurus as some engines seem to these days?

At any rate, for use of others, below are the results for the 3 searches I could think to run which were "journal", "scholarly", and "doi" each followed by the most relevant mention. All I can find is a couple other people asking if it is possible and speculating about maybe how it could be done.

Search: Keyword(s): journal ; Forum: Plugins and child forums

2017: [GUI Plugin] FanFicFare

Does this mean it could be possible to add journal/html sites if someone built an index/metadata-hub?

2011: Plugin ideas... add yours here

I wonder whether Calibre is capable of retrieving the metadata for journal articles. For these you do not have an ISBN, but (as explaiend in the opening message) a DOI.

Search: Keyword(s): scholarly ; Forum: Plugins and child forums

(nothing)

Search: Keyword(s): DOI ; Forum: Plugins and child forums

2015: [GUI Plugin] Consolidate All Library Metadata (CALM): A Calibre Add-on

Version 2.0.19 -2016-06-24 Compatibility improvement for use with Linux and OSX; now does not delete any Identifiers that start with a 'z', nor 'doi'.

I don't know if not deleting them means anything other than not deleting them.

[GUI Plugin] Search the Internet

tried http://dx.doi.org/{identifiers:select(doi)}

I don't know what this person was trying to do.

[kovidgoyal]

well if there isn't one then unless you are willing to write one, you are out of luck.

[BetterRed]

See ==>> Index of plugins <<== click.

Scroll down and you'll get to the Metadata Source plugins. If you need it again, the thread is stuck to the top of the Calibre.Plugins subforum.

BR

[DaltonST]

So you want someone to write a plugin for Calibre to replace Zotero because you don't want to even slightly use it? Not likely to happen.

However, with no new software, here is how you easily do what you are requesting:

[1] Install Zotero 5.0. Customize it so its sqlite database is on a local drive (e.g. C).

[2] Wherever you create your Citation RIS files, do so. Example I used to test what I am telling you now:

Spoiler:

TY  - JOUR
T1  - Ethics and Resource Scarcity: ASCO Recommendations for the Oncology Community During the COVID-19 Pandemic
AU  - Marron, Jonathan M.
AU  - Joffe, Steven
AU  - Jagsi, Reshma
AU  - Spence, Rebecca A.
AU  - Hlubocky, Fay J.
Y1  - 2020/04/28
PY  - 2020
N1  - doi: 10.1200/JCO.20.00960
DO  - 10.1200/JCO.20.00960
T2  - Journal of Clinical Oncology
JF  - Journal of Clinical Oncology
JO  - JCO
SP  - JCO.20.00960
PB  - American Society of Clinical Oncology
SN  - 0732-183X
M3  - doi: 10.1200/JCO.20.00960
UR  - https://doi.org/10.1200/JCO.20.00960
Y2  - 2020/04/29
ER  -

[3] Import the RIS files into Zotero using "File > Import > RIS".

[4] When it finishes, since you do not want to use Zotero for anything, export the newly created Zotero items using "File > Export > CSV". Do not delete them yet; wait until everything has been imported into Calibre via ZMI to purge Zotero of items.

[5] Run Calibre.

[6] Create a "workbench" a.k.a. "intake" a.k.a. "in-process" Calibre Library, and switch to it.

[6] Install the "Zotero Metadata Importer" plugin. Restart Calibre.

[7] Set the Options for ZMI via its Options Tab. You want to be able to import anything, including .html files, and also items with no file attachments.

[8] Restart ZMI.

[9] Hover your mouse on the first Tab to read all of the ToolTips.

[9] Let ZMI automatically create its 26 Zotero metadata custom columns. Restart Calibre.

[10] In ZMI, use the top pushbutton to import your Zotero export .csv file. Finish processing them per the other pushbuttons per their ToolTips.


Now, you will have in Calibre all of your citation metadata from Zotero that came from your .ris exported Citations that you selected on the internet.

ZMI has thousands of users who also use Zotero for their thesis or dissertation or (in the case of university professors) their saved research documents, and who want the Zotero PDFs and metadata in Calibre as "ebooks".


Questions? Read the images attached to the ZMI Original Post, and all of the ToolTips. The answers to all of your questions are in the former.


Good luck.




DaltonST

[catsknit]

Honestly, I use Zotero for writing papers for my masters and it is really easy to use, and it's free. I'm now also using it for Genealogy stuff after finding someone who wrote a book about using it for that. But it's quite simple. Install zotero, add the plugin for your browser (i use firefox) and then go to the site where you got your article. There will be a zotero button on your browser if you installed it. Click on that and it will save all the metadata as well as a pdf copy if available (zotero must be running while you do this). Or you can go into zotero and use the magic wand button and enter the DOI and it will pull it in that way. Easy peasy.

[Fiat_Lux]

Originally Posted by catsknit

Honestly, I use Zotero for writing papers for my masters and it is really easy to use, and it's free.

I ended up using Calibre as my citation manager, because both Calibre and Zotero require me to add all of the metadata needed to correctly format citations, and since I was using Calibre as my digital library, I didn't see the point of doing that work, twice.

Or you can go into zotero and use the magic wand button and enter the DOI and it will pull it in that way.

If one starts out with Zotero, or a citation manager that can be imported by Zotero, and consistently adds potential references to it, it works fairly well.

When one has to manually add every citation to it, and all of the related metadata, especially when one already has a core list with a couple of thousand citations, migration becomes a perilous task, made even more daunting by maintenance issues.

About half the material I cite in my non-fiction, lacks DOIs, ISBNs, or ISSNs.