How to manage publications on a local computer

Question

I would like to find a better way of naming publications which I store on my local computer as PDFs. So far I have been doing something like this:

Albano R., Sole A., Adamowski J., Mancusi L. (2014) - A GIS-based model to estimate flood consequences and the degree of accessibility and operability of strategic emergency response structures in urban areas.pdf

This presents a couple of disadvantages:

• Titles can be extremely long. This causes problems in certain operating systems or software such as OneDrive. You can only have so many characters in a filename...
• Not all publications can follow this format. The above is OK for journal papers and theses, but not so much for books or other kinds of publications.

I would like to have a consistent way to manage such a database. I thought of keeping the publication metadata such as authors, date of publication, type of publication and type in a separate text or excel file and naming the PDF files by ID, like 1.pdf, 2.pdf, etc. This could work, but it would require referring to and managing a spreadsheet which would contain all the meta data.

Is there a simple method or perhaps lightweight software that I can use which can help me with this sort of task?

EDIT

I didn't really like the way @Jonas Stein's script is set up, though I do owe him the inspiration and indication to use JabRef. Here's my alternative script:

import bibtexparser
import os
from shutil import copyfile

filename = 'db.bib'
out_folder = 'out'

with open(filename) as bibtex_file:
    db = bibtexparser.load(bibtex_file)

for entry in db.entries:
    print(entry['file'])
    id = entry['ID']
    file = entry['file'].split(':')[1]

    copyfile(file, os.path.join(out_folder, id)+'.pdf')


print('done')

It's much more compact and does the job.

Answer 1

I manage publications with JabRef in a bibtex database. It is possible to add a link to the filename with JabRef in the bibtex database.

A python script pybibtexcleaner transcribes the special characters in the title and moves all sorted files to one folder with file names in the format

bibkey-title.pdf

The script will generate from a bib entry

@Article{Stein2017a,
  author    = {J. Stein and M. Baum and S. Holbein and T. Finger and T. Cronert and C. Tölzer and T. Fröhlich and S. Biesenkamp and K. Schmalzl and P. Steffens and C.H. Lee and M. Braden},
  title     = {Control of Chiral Magnetism Through Electric Fields in Multiferroic Compounds above the Long-Range Multiferroic Transition},
  journal   = {Physical Review Letters},
  year      = {2017},
  volume    = {119},
  number    = {17},
  doi       = {10.1103/physrevlett.119.177201},
  file      = {:../included/119.177201.pdf},
  publisher = {American Physical Society ({APS})}
}

the new filename

Stein2017a-Control_of_Chiral_Magnetism_Through_Electric_Fields_in_Multiferroic_Compounds_above_the_Long-Range_Multiferroic_Transition.pdf`

and copy the file to ../articles/ and also adjust the path in the .bib file.

It is very useful if the filenames start with the bibkey. You should always use all digits of the year.

The script can also transcribe chemical formulas in a readable way, if they are introduced with \ce as in \ce{H2O}.

You can keep track of your work with git and you can restore old versions or synchronize the literature database on your different systems.

ps: I use the old stable 3.8.2 version of JabRef, because the new versions 4.x were less stable when I tried them. The user has better control on the rename process with the short python script and can easily adjust it to the needs, but recent JabRef versions are shipped with similar functionality.

Answer 2

For the filename, I use a system that I plagiarised from my PhD supervisor:

aaaadd_xxxx_jjj.pdf

where:

• aaaa: name of the first author (variable length)
• dd: 2-digit year of publication (fixed length)
• xxxx: first word of title, minus articles and other small words (variable length)
• jjj: abbreviation of journal of publication (variable length, but short)

I then use the same without the .pdf as my bibtex key (with an added :).

For example:

T. Penguin et al, a Survey of Antarctic Leasure Activities, Journal of Improbable Results, 2025

would be

penguin25_survey_jir.pdf

with the bibtex key penguin25:_survey_jir.

I like this system because:

• I'm used to it
• Filenames remain compact and UNIX shell friendly
• The encoded information is usually enough for me to identify the paper

It doesn't cover tagging or categorising.

This applies well to journal articles. For conference proceedings articles or books, the journal acronym is replaced by an acronym of the conference or the publisher, or perhaps the full name of the publisher; I'm not fully consistent there. But I don't usually have entire books as PDFs anyway.

Answer 3

There is lots of software out there which can help (e.g., Mendeley). I used this (and others) but found it would take more management than I would care to give.

Personally, I just had a publications folder with nested sub-folders for different topics. I would then simply name the .pdfs using the last name of the first author and the year of publication, that is: lastname_2019.

I found this had several advantages:

1. It's easy to remember. In discussion with peers I could easily refer them to a paper by lastname in 2019. It's great to be able to do this easily and helps your reputation. The alternative is discussing with peers who just vaguely remember the contents of a paper but can't remember the title or authorship.
2. It's easy to search for the paper using (for example) spotlight in macOS. I just typed in the last name and all their papers would come up. Also helps in memorising the authors last name. I relied on this heavily and never really searched the publications folder.
3. If using LaTeX, I could easily remember what papers I wanted to cite and as I set the bib reference to the lastname_2019 format, I had no more information to remember.

Of course, if a person publishes multiple papers in a year, I would just append a letter to the add. To be honest, I think I only had to do this once or twice for my field.

Answer 4

I use mendeley with automatic folder scanning. I download a paper with a filename like SI90234023499-II.pdf dump it into one of my watched folders, and it is automatically sorted into ~/Literature/FirstAuthor/Year/Journal/Title.pdf and added to the Mendeley database. You can customise the directory location from any combination of metadata, but for me is doesn't reallly matter because I only ever access stuff via the Mendeley App anyway, so I rarely handle the PDF files directly.

Answer 5

For books you can use Calibre, which is a free e-book management program. Easy to use.

Answer 6

How about plain old Excel.

• Start by naming your PDF documents using a naming scheme like what @gerrit has suggested (or some other mechanism that results in manageable/recognizable file names).
• Create an Excel worksheet document. Make Column A very wide. Each row will represent a single file
• Select a cell. Choose the Insert tab and press Link
• Paste in the full name of the document (in whatever format you want) into the "Text to Display" field
• Navigate to your PDF file in the file browser, select the right file and click OK

You now have a searchable document that contains your publication titles and clickable links to your documents

If you want to be fancy, you could have several columns (publication date, authors (or maybe primary author and other authors), title, etc.). Put some column headings in. Now, it's not only searchable, but it's sortable and filterable (particularly if you create it as a Table (play with the Table button on the Insert tab.))

Answer 7

I recommend you name the papers as you say 1.pdf, 2.pdf, and have corresponding metadata files 1.txt, 2.txt which you can structure however you want.

Then the crucial part is this: use grep (available for both Linux and Windows) to search through the content of all the text files in that folder. This will find you which txt files contain the searched terms.

Searching is as simple as this (this will show which text files in the current folder contain the word "Adamowski"):

grep -r "Adamowski" .

I think this is the simplest way.

Answer 8

Is there a simple method or perhaps lightweight software that I can use which can help me with this sort of task?

Although it is a bit over the top, JabRef can maintain bibliography and rename files:

Renaming of files is now part of the “Cleanup Entries” feature (brush button in the toolbar or Ctrl + Shift + F7). Then, you can rename attached files based on the BibTeX key. You can change the format (pattern) under Options → Preferences → Import, by altering the pattern under “Default PDF file link action”.

And the patterns are diverse, and it is possible to consistently abbreviate journal names, titles, and combine author names, for example:

Author-related key patterns

• [auth]: The last name of the first author
• [authors]: The last name of all authors
• [authorLast]: The last name of the last author

Title-related key patterns

• [shorttitle]: The first 3 words of the title, ignoring any function words (see below). For example, An awesome paper on JabRef becomesAwesomePaperJabref.
• [veryshorttitle]: The first word of the title, ignoring any function words (see below). For example, An awesome paper on JabRef becomes Awesome.
• [camel]: Capitalize and concatenate all the words of the title. For example, An awesome paper on JabRef becomes AnAwesomePaperOnJabref.
• [title]: Capitalize all the significant words of the title, and concatenate them. For example, An awesome paper on JabRef becomes AnAwesomePaperonJabref.

Modifiers Generally, modifiers are applied in the order they are specified. In the following, we present a list of the most common modifiers alongside a short explanation:

• :abbr: Abbreviates the text produced by the field name or special field marker. Only the first character and subsequent characters following white space will be included. For example:
  • [journal:abbr] would from the journal name “Journal of Fish Biology” produce “JoFB”.
  • [title:abbr] would from the title “An awesome paper on JabRef” produce “AAPoJ”.
  • [camel:abbr] would from the title “An awesome paper on JabRef” produce “AAPOJ”.

Answer 9

My method is to name each PDF file as:

year, authors, title.pdf

E.g.:

2020, Abc Def Ghi, The letters of the alphabet.pdf

I work with Ubuntu and never had problems with these filenames, although they contain spaces and commas.

Putting the year first makes it easy to sort papers by year in the file explorer.

Putting the title in the filename makes it easy to immediately see in file explorer what the file is about.