Update: There seems to be a way how to get it from API now, see this comment below for more details.

New version from user Jason UX is here (see the comments). Additionally, with version 1.19.1, there is an encryption make this script obsolete (see here).

According to my previous posts, I decided to use Mendeley as an annotation software and reference manager.

Unfortunately, I was really frustrated by two things with Mendeley.

No UTF-8 in PDF export

Mendeley has ability to export annotations along with PDF in such a way, that when you want to export them, you just choose "Export PDF with annotations". Then you can choose if you want to export original PDF with annotations at the end of file or just annotations as PDF.

Unfortunately, Mendeley currently (Mendeley Desktop v1.11) doesn't support UTF-8. It really drives me crazy, since there is absolutely no reason not to support this. Shame on Mendeley's developers. It was my first lessons about strings when I learned programming... On the other hand, as a reaction to my question I sent them my incriminated PDF and they assured me that they are working on that.

Export only to PDF format

As mentioned earlier, annotations could be exported as PDF (with or without original document). The problem is that the PDF format is the only option.

Since there are several requests to have this functionality (export annotations to different formats) without any serious answer, I decided to do it myself. By the way - again, that is ridiculous that there is not feature like this, since it took me about 20 minutes to export it on my own. The only reason I can think of is that developers just want to make people use only Mendeley for sharing annotations.

Solution

I'd found where Mendeley stores it's annotations and decided to export them through a python script. It didn't take long and here is solution (you'll need to install pandas - can be installed by pip install pandas.

Click to download mendeley_notes.py

import sqlite3 as lite  
user_mail = "example@mail.com"  
path = "/home/USER/.local/share/data/Mendeley Ltd./Mendeley Desktop/{0}@www.mendeley.com.sqlite".format(user_mail)

con = lite.connect(path)  
cur = con.cursor()

cur.execute("SELECT id, title FROM Documents")  
documents = cur.fetchall()

cur.execute("SELECT id, documentId, page, note, createdTime, modifiedTime FROM FileNotes")  
notes = cur.fetchall()

import pandas as pd  
df = pd.DataFrame(data=notes, columns=["id", "documentId", "page", "note", "createdTime", "modifiedTime"])

documents = dict(documents)  
df.documentId = df.documentId.map(documents)

def to_string(df, *filename):  
    """
    Returns notes in nice formated string

    If filename is given, it saves string to this file
    """

    vyslstr = ""
    for name, note in df.iterrows():
        type(note)
        vyslstr += """
ID: {0}|File: {1}|Page: {2}  
{3}
        """.format(note.id, note.documentId, note.page, note.note)

    if filename:
        with open(filename[0], mode="w", encoding="utf-8") as fout:
            fout.write(vyslstr)
    return(vyslstr)

def to_csv(df):  
    "Detailed output to csv file"

    df.to_csv("notes_mendeley.csv")

to_csv(df)  
to_string(df, "notes_mendeley.txt")  

as stated in the original script, you need to find out two things:

1. Where Mendeley stores it's files - on my Arch Linux laptop I've found this here: /home/USER/.local/share/data/Mendeley Ltd./Mendeley Desktop/
2. Your user email which you use to sign in to Mendeley. When you know this, now locate sqlite database file: example_email@somwhere.com@www.mendeley.com.sqlite.

If you find this file, it's all you need. Now just edit the script accordingly and you can export your notes to csv or txt (by default both). This can be of course converted to any other format then :) .

My contribution

If you want, I can edit the script so it should be more convenient to use for those who do not know how to use it. Leave a comment here :) .

I can also tweak the script so it could be possible to just choose just some notes, highlights or so.