importing from Papers3 into Zotero4

I was able to export the collection information from Papers3 mac version using the BibTeX complete format but it doesn't include collection information; the only other issue is that a small number of pubmed articles (126/4k) had blank title/abstract fields in zotero even though the few I checked had them in the BibTeX file; otherwise the import into Zotero was successful.

FYI I used BibTeX complete because I read somewhere that BibTeX was the only option that supported PDF path and supported by Zotero.

thanks for any help
PS Hopefully not repeating but couldn't find this topic elsewhere and I am zotero newbie so please point to other threads if previously discussed.
  • Unfortunately it won't be possible to transfer collection information. There currently is no standard data format for bibliographic data that includes collections, so this tends to be a problem going from one reference manager to another.

    If you post a sample bibtex where Zotero import is missing data we can take a look, shouldn't happen.
  • thanks Adam for the prompt response,
    this is the particular record missing title and abstract in zotero standalone 4.0.19

    author = {Adetunji, Adedotun A and Achenbach, Chad and Feinglass, Joseph and Darin, Kristin M and Scarsi, Kimberly K and Ekong, Ernest and Taiwo, Babafemi O and Adewole, Isaac F and Murphy, Robert},
    title = {{Optimizing Treatment Switch for Virologic Failure during First-Line Antiretroviral Therapy in Resource-Limited Settings.}},
    journal = {Journal of the International Association of Physicians in AIDS Care (Chicago, Ill. : 2002)},
    year = {2012},
    month = nov,
    doi = {10.1177/1545109712463733},
    pmid = {23128403},
    language = {English},
    read = {Yes},
    rating = {0},
    date-added = {2013-01-26T02:10:06GMT+00:00},
    date-modified = {2013-10-29T21:26:00GMT+00:00},
    abstract = {We evaluated adult Nigerian patients with antiretroviral switch to second-line treatment with ritonavir-boosted protease inhibitor (PI/r)-based regimens due to virologic failure (confirmed HIV-1 RNA viral load [VL] >1000 copies/mL) during first-line antiretroviral therapy. Proportion of patients with VL >400 copies/mL and characteristics associated with nonsuppression during second-line treatment are described. Approximately 15% of patients (34 of 225) had VL >400 copies/mL at 1-year after treatment switch to PI/r-based regimens. In adjusted analyses, VL ≥5 log(10) copies/mL at treatment switch (odds ratio [OR] 2.90 [confidence interval (CI) 1.21-6.93]); duration of first-line treatment after virologic failure >180 days (OR 2.56 [CI 1.0-6.54]); and PI/r regimen adherence <90% (OR 3.27 [CI 1.39-7.68]) were associated with VL >400 copies/mL at 1 year of second-line treatment. We therefore recommend that the maximum permissible time between suspicion of virologic failure and completion of antiretroviral treatment switch should not exceed 6 months when patients develop first-line antiretroviral failure in resource-limited settings.},
    url = {},
    local-url = {file://localhost/Applications/Papers2/Articles/2012/Adetunji/J%20Int%20Assoc%20Physicians%20AIDS%20Care%20(Chic)%202012%20Adetunji.pdf},
    file = {{J Int Assoc Physicians AIDS Care (Chic) 2012 Adetunji.pdf:/Applications/Papers2/Articles/2012/Adetunji/J Int Assoc Physicians AIDS Care (Chic) 2012 Adetunji.pdf:application/pdf}},
    uri = {\url{papers2://publication/doi/10.1177/1545109712463733}}
  • works for me. If you copy the above (from @ to the last }) and then select "import from clipboard" in Zotero, does that import correctly?
  • just saw that "import from clipboard" feature, it is great!
    and yes that did work for me, even if I include the previous record.

    Could it have happened because I was transferring almost 4k records with pdfs at once? thanks again
  • It really shouldn't have, but I guess that's the best explanation.
    If you can reproduce this with smaller bits of the bibtex we'd be interested in taking a look at those (you can post longer bibtex files to as a public gist).
  • I will try that and keep you posted
    thanks again
  • Based on that key suffix and the number of records you indicated, you might also check to see if there are duplicate records in the larger BibTeX file describing this (or a similar) resource in case you snagged the wrong one....
  • good point. That's actually a lot more likely as an explanation.
  • I searched for "{Adetunji" in the BibTeX file and there is only one match ...
    Another thing that comes to mind is that it is consistent (I did twice, once on a mac and another on a PC) so it is probably not due to the number of records or I would expect it to be more random ?

  • thank you all for your help, I was looking at the unmodified BibTeX file. I incorrectly got rid of all the lines with "uri" instead of "uri =" or "\url".
  • I made the adjustments and all 3,983 references imported correctly with a title.

    thanks again for the great tool!
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