[internet] inserted to REF row

Hello.
I have been a Zotero user for years. I recently prepared a paper for Brain journal and I noticed that a lot of the references have "[internet]" and then "cited from...." added to the reference row, after the journal. I tried to change the REF style, but it was still there. Apparently it is only a Zotero problem, since endnote got this right. It's a good thing I checked before submitting the manuscript... I suggest that every Zotero user double checks their references. What I eventually did was erasing the "URL" and "accessed" fields from all of the Zotero items.
This was aggravating... I'm afraid I'm not gonna work with Zotero anymore. Switched to Endnote.
  • edited July 16, 2018
    This is what is recommended by the style for online-only articles, which Zotero detects when there is a URL but no volume/page numbers. In general, Zotero/CSL styles tend to follow journal guidelines much more accurately than Endnote.

    If you have page numbers, you can prevent Zotero from including a URL at all by checking the box in the Cite pane of Zotero preferences.

    Generally, very little about using Zotero requires any manual labor, so if you are doing something that is taking a lot of steps, you are probably not doing it in the intended way. It is always better to ask a question here before spending a lot of time on something.
  • edited July 16, 2018
    I checked and the checkbox is checked (meaning zotero should not add urls when there are page numbers). It adds them anyway.I also tried to uncheck it. No difference. There are page numbers. The url comes after. Again, this is only a Zotero problem. Endnote does it fine.
  • edited July 16, 2018
    No, you need to have the box UNCHECKED.
  • ? what do you mean?
    It's not a question of style. I tried several...
  • The preference needs to be UNchecked to omit the URL from paper articles (those with page numbers).
  • When the box is unchecked, Zotero doesn’t include the URL in the item data it passes to the citation formatter (exactly the same as if you delete the URLs from the data, but that’s not necessary to do manually).
  • I tried that. It doesn't delete it for some reason. and yes. I refreshed the bibliography... It's really weird. Also, why do they even have the option of adding a url?
  • Can you test in a fresh document?
  • I just did. It makes no difference whether the checkbox is checked or not.
  • I cannot replicate what you are saying is happening. With the Brain style and the URL for paper articles option unchecked, then articles with with page numbers will not show the URL and articles without them will show the URL. This is what the style guide asks for. If this is not the behavior you are observing, please change your export style to “CSL JSON”, copy an item with page numbers and the preference unchecked, and paste the code here.

    Please also confirm what version number of Zotero you are using.
  • Handojoseno AMA, Gilat M, Quynh Tran Ly, Chamtie H, Shine JM, Nguyen TN, et al. An EEG study of turning freeze in Parkinson’s disease patients: The alteration of brain dynamic on the motor and visual cortex [Internet]. IEEE; 2015. p. 6618–6621.[cited 2018 Mar 1] Available from: http://ieeexplore.ieee.org/document/7319910/

    This is the item. What code? I exported as you requested but can't copy here (except for the bibliography item. Is that what you meant?
  • edited July 17, 2018
    Which citation style is this?

    Yeah, so this happens because these are conference papers. Not sure how you import them, though. If imported from http://ieeexplore.ieee.org/document/7319910/ , this doesn't get a URL in Zotero, which means you don't get it in the reference list. Did you import the references from Endnote?
  • I inserded the DOI to zotero. That's how I imported the items. And my Zotero version is 5.0.23
  • I later exported all of my items to endnote. There it works fine. No URL.
  • This isn’t likely the issue, but your version of Zotero is out of date. Upgrade to the current version 5.0.54.

    As adamsmith mentioned, the issue here is that this item is a conference paper, not a journal article. The style needs to be adjusted. I've made a pull request for that change, and you can download that style file from here:
    https://raw.githubusercontent.com/bwiernik/styles/2915479b4aafe5c7a8cadaebfcc42459bdb0ba58/brain.csl

    Thanks for reporting the style issue.
  • If there are styles for other journals you'd like to use where the URL is being shown for paper items where it shouldn't, please make another post, and the styles can be easily adjusted. It is planned to remove the URL checkbox from Zotero and code this logic into the CSL styles: https://github.com/citation-style-language/styles/issues/2495
  • edited July 19, 2018
    Thank you, I'll check it out. However, this is not unique to that specific style. I tried to change to Annals of Neurology and also to Nature. The same problem. It appears that this is not a style problem but rather a Zotero problem.
  • You really are mistaken there, please trust me. This is an issue with styles coded to include the URL if provided at all, rather than based on the presence of page numbers. That is a change planned to be made across styles.

    Please believe me that this is an issue with the programming of styles (further references to Zotero versus Endnote really aren’t needed; we do understand what is happening).
  • (well, but it is an issue that's pretty widespread across styles, so whether it's styles or Zotero is mostly semantic)
  • This is very likely unrelated - but this made me look at the Zotero style repository webpage, and hovering over the Brain entry (and several other styles in the repository) shows the [internet] tag for the Hisataka reference, which (I assume) is a journal article, and has volume and page numbers.

    Here is a screenshot: https://www.dropbox.com/s/69wu0nss7cp6c0w/Brain_screenshot.png?dl=0

    Same thing with Molecular Brain, Behavioral and Brain Functions, and others. I don't think this is expected behavior on the repository webpage, but I may be totally wrong. Sorry, if I am hijacking this thread.
  • yeah, that's because the repository defaults to behavior that mimicks having include URLs checked.
  • edited July 19, 2018
    ... but both Brain and Nature have the same citation data, but Brain shows [internet] and URL and Nature doesn't on the repository webpage?

    I assume that this is only for styles (like Brain) that on occasion might display a URL (for webpages or online journal articles according NLM's uniform requirements style), but not other styles?

    I checked that and that didn't appear to be true, so I am confused by the difference between, say, Brain and Nature, even though both can show URLs depending on item type according to their styles.

    edit: I realize that this is just about the behavior of only the repository webpage, and is not important at all, so ignore at will.
  • For Nature, URLs are only shown for webpages (if you look at the style code, the section with the URL is preceded by
    <else-if type="webpage" variable="URL" match="all">

    For Brain and many other styles, URLs are always printed when they're in the data. However, by default (with "include URLs" unchecked) Zotero treats articles with pages as if they don't have a URL even if they don't. That last bit is different on the repository, not for particularly strong reasons, but simply because it hasn't been implemented.
  • I understand how the webpage and Zotero app behave differently now, although I will just say that parity might be a good thing to avoid confusion for users who would appropriately check the online repo first. And also, the Zotero behavior is the correct one for Brain.

    Looking at Nature's citation style at https://www.nature.com/nature/for-authors/formatting-guide

    "References to web-only journals should give authors, article title and journal name as above, followed by URL in full - or DOI if known - and the year of publication in parentheses."

    Looking at Brain, they do not include URLs on their webpage on any of the examples they give (https://academic.oup.com/brain/pages/General_Instructions).

    They further refer to NLM's uniform requirements style for more details, and even there, standard journal articles (item 1) get no URLs: https://www.nlm.nih.gov/bsd/uniform_requirements.html

    Now, "Journal article on the internet" (item 36) has URLs. But that doesn't even apply to "published on the Internet ahead of the print version" (item 18) and the other optionals cited there. But then, Nature asks for URLs for online-only articles, as I cited above. In practice, neither journal uses them much at all.
  • edited July 21, 2018
    The best solution would be to change the relevant styles to print the URL only conditionally. Based on the requirements you are describing, testing for the presence of a page number (and perhaps also status, but that would likely only ever be entered manually by users, so it seems not worth it) seems to be the most appropriate way to distinguish between print and online-only journals.
  • Thanks for the input. This is not an important point, and to be honest, I should leave the interpretation of the multi-page style descriptions to the experts. I do agree that the testing for page numbers is a good way to figure out what to do.
  • Returning to the original post, can someone please send a link of a paper that cites a conference paper in the Zotero format? (i.e., [internet], cited from.....) I have never seen that anywhere!
    Until I see it, considering that endnote does not generate such a format, I have to conclude that Zotero is a risky citation manager to use if I want to publish in respected journals... Please people send me one example.
    Thanks.
  • The journal guidelines state that online articles and chapters should be cited with the URL and access date. Zotero reasonably infers that an article or chapter (including conference papers which are essentially chapters) is a paper copy if it has page numbers and online-only if it does not. The "[Internet]" label comes from Vancouver style, which Brain and most other biomedical journal styles are based on, and there are several examples where it is used in Brain.

    Here are search results showing numerous examples of internet-based sources with the [Internet] label:
    https://academic.oup.com/brain/search-results?page=1&amp;q="[internet]"&amp;fl_SiteID=5367&amp;SearchSourceType=1&amp;allJournals=1

    And several specific papers:
    https://academic.oup.com/brain/article-abstract/141/2/e11/4683985?redirectedFrom=fulltext
    https://academic.oup.com/brain/article/139/9/2441/1744887?searchresult=1
    https://academic.oup.com/brain/article/138/7/2059/254068?searchresult=1
    https://academic.oup.com/brain/article/136/6/1687/621356?searchresult=1

    (In general, I think you are worrying a bit too much here. Brain and most other biomedical journals are not particularly concerned about citation formatting; they have quite a bit of variation in their published articles. Any minor deviations that the publisher does want to change will be corrected by the typesetters. My experience with biology and neuroscience journals is that they really don’t care much about the specific citation style used in submissions. The inlcusion of "[Internet]" in particular is something that the typesetter will just delete if the publisher does not want it there.)
  • Thank you.
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