Pubmed Entry saved but not wanted

rickogorman
Lately (I don't think this happened in the distant past, ie, 6+months ago) when I save items to Zotero from online databases (Science, PNAS) the entry that is created includes a 'Pubmed entry' that I don't want and can't figure out how to stop Zotero creating. Have I missed something? I'm using Zotero standalone, but saving via the Zotero location bar icon in Firefox.
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  • adamsmith
    what do you mean by a pubmed entry? It's supposed to add the PMID in the extra field, is that what you're talking about?
  • rickogorman
    Under title, the items there have drop-down arrows. If there is a pdf attached, this is where it shows. Lately, there will also be an item called 'pubmed entry'.
  • adamsmith
    does any of those items (the top level items, not the attached Pubmed entry) have something in the URL field? Could you post the URL(s) here?
  • aurimas
    What is your reasoning for avoiding these links? They don't count towards your storage quota, if that was your concern.
  • rickogorman
    edited December 13, 2013
    @adamsmith: yes. An example (from Science AAAS): http://www.sciencemag.org/content/330/6000/33.1

    It happens with some journals (e.g., Science, Proc R Soc B) but not others (e.g., Oxford journals). I see that it's saving the PubMed entry right when I click the zotero save item icon in the location bar and the Zotero save pop-up shows up; the PubMed entry shows up whenever it is there to be saved and before the pdf is confirmed saved (or not). I also have Zotfile, Zutilo and Zotero Scholar Citations installed, but I can't see anything there to cause the issue.

    @aurimas: I use Zutilo to send pdfs to my tablet for later reading and the PubMed entry always prompts a 'cannot save' or such error for the PubMed item. And I don't use PubMed or care a whit about it. And I'm sure there was a window of time where these pubmed entries did not appear so it seems to me that this was added in or is a bug, though I concede that I may have missed it somehow all along. And I'm a minimalist. I turned off 'automatically take snapshots' for example because I only want the pdfs (where I can) and the database item details. And Zotero allows reasonable control over such details, so I am hoping that I either somehow am missing the box to untick or, as already noted, it's a bug. It's also inconsistent (not all journals provide it).
  • aurimas
    edited December 13, 2013
    I wouldn't call it a bug in Zotero. This was introduced consciously about 5 months ago. Though it does seem like a bug in Zutilo (not ZotFile?). It would technically be possible to add a hidden preference to disable this, but in general we want to avoid such preferences as much as possible. So if this was fixed in Zutilo/ZotFile, would it still be a problem?

    Regarding inconsistencies, we're attaching the link wherever possible. Not all pages supply PubMed ID's, so it's not possible to attach these everywhere.

    Edit: Ooops, meant ZotFile.
  • rickogorman
    Thanks Aurimas for the info. No, if it was added intentionally than I wouldn't call it a bug either. :)

    But I can't fathom why it would be foisted upon users, as opposed to optional? I guess the developers (not clear whether you are a fellow user or developer) thought it was costless as it doesn't count toward the space limit, but I don't see why I need it. As I said, I don't use PubMed, I don't even know why the PMID could be useful for me. I don't care that the PMID is stored in the set of info for a particular item, I can ignore it easily. If I have to live with the separate PubMed entry then I guess it's not a dealbreaker :) but I just find it's clutter, as well as right now giving me error messages in Zotfile (presumably that will get sorted in due course).
  • dstillman
    For many users being able to get back to the PubMed page is extremely important. The PMID is also fairly important metadata that could have useful applications in Zotero in the future (such as uniquely identifying a given item).

    It's true that the attached link is a bit cluttering if you don't actually need it, but it's the only place to put these for now. In the future Zotero will likely gain extensible ID support, which will allow the PubMed ID to be placed in its own metadata field (which will function like URL and DOI, allowing you to click the label to get to the relevant site).
  • rickogorman
    @Dan: I've no doubt that for those who use PubDed the link is valuable. If it's of value to enough other users, I can live with it. I guess no-one else has objected to it; I was going to suggest a note somewhere (I couldn't find anything about this being added, maybe its in the release notes) but if no-one else is fazed then little point I suppose. :)

    I look forward to it becoming like DOI/URL though.
  • qbilius
    I second @rickogorman. I cannot stand these PubMed entries precisely because they clutter my otherwise very precisely organized Zotero library. For me, this is redundant and useless information that also makes me think there is a note attached to a given item. I can see why others would like to have this option but it would be great to have an option to disable saving these PubMed links too (can be in advanced preferences if you don't want to expose it). I can't see why developers would want to avoid this as much as possible, as @aurimas said? At least until the new metadata field is introduced.
  • adamsmith
    edited January 1, 2014
    Too many preferences are a bad idea. They add GUI clutter, they create confusion for people starting out with the software etc, even when you turn them into hidden prefs they make troubleshooting a nightmare and hidden prefs only benefit a tiny fraction of users.
    (edit: as for "Note attached to an item" - you can turn on a "Note" column for the middle panel that shows whether and how many notes are attached).
  • hhng
    yea, I'm running into this "feature" as well. Right now I manually delete all of the PMID. This is mainly because it shows there is an "attachment" in the attachment column (with a blue dot).

    If the PMID is not going away, is there a way to at least differentiate the attachment color? Right now there is a blue dot if there is anything (note, PMID, PDF). Since I'm mainly interested in the PDF attachments, it would be nice to be able to make that priority and if there is a PDF, for it to be a certain color.
  • adamsmith
    I think having a separate attachment-dot color for PDFs would be nice. I doubt it'll happen any time very soon.
    As a workaround to deal with unwanted PubMed entry attachments, you could create a saved search with
    Title --> is --> PubMed entry
    and then just periodically go into the saved search and select all (ctrl+a) and then right-click --> move items to trash.
  • aurimas
    I do think that the blue dot indicator should probably not be triggered by a web link attachment, since half of the purpose that the dot serves is to indicate attachment availability, which is only relevant for stored/linked files.
  • adamsmith
    That's actually better than treating PDFs different, yes.
    It already doesn't get triggered by notes.
  • adamsmith
    @Dan - would you be OK with that?
  • dstillman
    edited May 2, 2014
    I do think that the blue dot indicator should probably not be triggered by a web link attachment
    It isn't, at least for me. Is it for you?
  • adamsmith
    uh - you're right, it doesn't.
  • aurimas
    Dan, you're right, it doesn't trigger. Yay for not checking before posting (I'm going to play my "writing from mobile" card on this one).

    I'm confused then @hhng is experiencing a bug of if there is another attachment for the item in question.
  • adamsmith
    edited May 2, 2014
    I'm confused then @hhng is experiencing a bug of if there is another attachment for the item in question.
    I'd assume a snapshot, since most pages that create PubMed links also attach a snapshot (e.g. the science page that rickogorman links to above)
  • aurimas
    well, yes, but presumably deleting the PubMed Link (referred to as PMID, though... so maybe not) clears the blue dot...
    Right now I manually delete all of the PMID. This is mainly because it shows there is an "attachment" in the attachment column (with a blue dot).
    @hhng, if you're still following this thread, could you confirm one way or another?
  • cricketbird
    +1 for getting rid of the ghost PubMed "attachments". Drives me nuts - I always delete them. Can it just go into a field, like DOI or URL?
  • adamsmith
    see above.
  • cricketbird
    I can delete them (with or without a saved search), but it would be nice for them to not even be generated (or to be placed in a field like the other metadata). I didn't see an option for that in the thread above.
  • adamsmith
    it can't currently be done, will be in the future, see Dan's comment from December last year.
  • hhng
    @aurimas, it does trigger it for me for PubMed entry as well as notes... I didn't know this was not suppose to happen. I'll reinstall Zotero and report back
  • dstillman
    No, please don't waste your time reinstalling.

    It's almost certainly triggering for you on a snapshot, not a linked URL. If you really think that's not the case, take a screenshot, upload it somewhere (Dropbox, imgur.com), and provide a link.
  • hhng
    hi Dan, thanks for posting that before I had to redo everything. I did verify and it is like you and Adam said - the pubmed entry coincided with papers I could not download the PDF (but it took a snapshot anyways).

    And thanks Adam for the suggested search, I still want to get rid of Pubmed entries as I have no use for them and it is nice to declutter.

    cheers
  • bp_216
    I add my support for an option to get rid of Pubmed links. To me they are also useless clutter, and it is tedious to have to delete them manually, which is what I have to do at the moment.
  • adamsmith
    I don't think there's any willingness to remove the link before there's is a dedicated (and clickable) PMID field, sorry. We want users to be able to get back to the Pubmed entry as Dan says above.

    It's obviously possible (if probably a bit daunting for most users -- though it's not terribly hard to do) to custom-modify the translator in your Zotero data directory to not save the link.
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