Switching to Zotero from Papers
I've been interested in using Zotero for a while as a number of colleagues have rated it highly. However, I've been stuck on Papers 3 for some time and don't know what it would take to transfer my entire library—citations, PDFs, tags, etc—to Zotero. Is there a simple tool that allows users to import from a Papers library (sort of like the ReadCube Papers import tool, which mostly works fine)? Anything that requires manually importing each paper and recreating collections/tags seems like a huge barrier for those with large libraries who are coming from other reference managers.
(With regard to collections, I can probably just give all the items in the collection the same tag and later create the collections in Zotero based on the tag, assuming the import is successful and all the tags are transferred over as well).
1. Exporting to an RIS file works, but it's less than ideal because some information seems to go missing while irrelevant/incorrect information is added. For example, if a book in Papers is listed as being published in 2019 (no month or day) and in its second edition, upon import the publication date given will be January 1, 2019 and the edition data will be gone. The same is true of journal articles. If a journal article only has year information (e.g., 2009), on import it will also have New Year's Day for that year listed as well (January 1, 2009).
This probably isn't a huge issue, except for those who regularly use citation styles that require giving year, month, and day (if available).
2. This problem doesn't seem to arise when exporting/importing with BibTeX. However, I've had problems with importing websites with BibTeX.
3. This problem also doesn't arise when exporting/importing with XML. There are also no issues with importing websites when using XML. However, it's messy—for each item that gets imported a note is automatically generated in Zotero that reads "The following values have no corresponding Zotero field:label: r17379". That's every single item.
Currently it looks like importing via BibTeX is the most promising solution. However, all of the methods above have allowed me to transfer my tags, which is great.
If there isn't, could you open the XML with a text editor and look at how the title looks there? If the XML has
'Zotero should import this just fine (just tested). If the XML has
&apos;it won't, but again, that should be an easy fix.
1. With the **XML method**: Seems to treat book chapters in edited books as edited books by omitting the book title (1a). Also, when dealing with an edited book by itself, converts editors to authors (1b). See examples below:
(1a). Incorrect (APA): Gibb, R., & Kovalchuk, A. (2018). Brain development (R. Gibb & B. Kolb, Eds.). London, UK: Academic Press.
Correct (APA): Gibb, R., & Kovalchuk, A. (2018). Brain development. In R. Gibb & B. Kolb (Eds.), *The Neurobiology of Brain and Behavioral Development* (pp. 3–27). London, UK: Academic Press.
(1b). Incorrect (APA): Gibb, R., & Kolb, B. (2018). *The Neurobiology of Brain and Behavioral Development*. London, UK: Academic Press.
Correct (APA): Gibb, R., & Kolb, B. (Eds.). (2018). *The Neurobiology of Brain and Behavioral Development*. London, UK: Academic Press.
2. With the **BibTeX method**: Omits edition from chapters in edited books (2a). Also, does not import abbreviated journal names (2b). See examples below:
(2a). Incorrect (APA): Baron, I. S. (2010). Maxims and a model for the practice of pediatric neuropsychology. In K. O. Yeates, M. D. Ris, H. G. Taylor, & B. F. Pennington (Eds.), *Pediatric neuropsychology: Research, theory, and practice* (pp. 473–498). New York, NY: Guilford.
Correct (APA): Baron, I. S. (2010). Maxims and a model for the practice of pediatric neuropsychology. In K. O. Yeates, M. D. Ris, H. G. Taylor, & B. F. Pennington (Eds.), *Pediatric neuropsychology: Research, theory, and practice* (2nd ed., pp. 473–498). New York, NY: Guilford.
(2b). Incorrect (AMA): Shapiro-Mendoza CK, Lackritz EM. Epidemiology of late and moderate preterm birth. *Seminars in fetal & neonatal medicine*. 2012;17(3):120–125
Correct (AMA): Shapiro-Mendoza CK, Lackritz EM. Epidemiology of late and moderate preterm birth. *Semin Fetal Neonatal Med*. 2012;17(3):120-125.
(An aside: I another difference I noticed that is the XML method will import author initials with periods, while the BibTeX method strips periods).
It's certainly frustrating that Papers is so inconsistent/lossy with its various export formats.
[removed — D.S.]
ETA: I failed to anticipate that this Zotero website would render some of this code as HTML! You can see the clean version of this script as a Github gist over at:
JSON.parse: expected ',' or '}' after property value in object at line 1 column 1251 of the JSON data SyntaxError: JSON.parse: expected ',' or '}' after property value in object at line 1 column 1251 of the JSON data
There are a bunch of other errors listed but that is listed first and a bunch of times in the Debug Output.
Any idea what could be wrong and/or how to fix this?
You should start from scratch with a fresh import. You can delete all the imported items by sorting by Date Added in the items list.
1. Some characters didn't import properly, notably "&", quotation marks, and the symbol ">".
2. Some Greek letters imported properly, while in other instances they did not.
3. Italics did not import properly.
4. Some supplemental files did not transfer over. I know Papers3 sometimes removed the extension of supplemental files when importing them into Papers3. I wonder if this caused Zotero to fail to import them.
Script is here in case it's of use to anyone else: https://github.com/lastbroadcast/Papers3-to-Zotero
*From Papers3, export as 'EndNote XML v8 or higher'
*Customise the script to make the modifications you want. I did:
-'%20' character changed to a space
-I was using Parallels to run Papers3, so I needed to remove a specific string from all path names
-several XML tags that are not recognised by Zotero are removed
*Import into Zotero
Note that folder/sub-folder structure is not retained by the XML export.
*I created some scripts to transfer the collections/folders from Papers3 to Zotero. Run these scripts after doing the XML export. See readme file for info on how to use them.
*I found that Zotero and Papers categorise parent/child items differently. After using these scripts I found that papers were filed in parent collections if they were also present in child collections. If you want to eliminate papers from parent collections if they are also in child collections, use this script:
Note: back up your Zotero database before you use these. I am not a professional programmer, so things could go wrong!
Are you trying to open papers using macOS Catalina or higher? If so, this is probably the issue. Catalina and higher only support 64-bit apps, and papers is 32-bit. The app might open OK, but won't function properly.
I got around this issue by downloading Parallels and used the free trial period to install macOS Sierra (also downloaded for free) to open papers and export the library as xml.
The whole thing was a faff - I still have a few more days left on the trial period, so if you're quick, you could try to send me your library (if it's not super large) and I'll export it and send it back to you.
*Edit: send me a private message through the forum
thank you for your suggestion and help ! I don't know what does mean "a faff" but I accept your help ! how do I send you a private message ?