PMID, PMCID in "Extra" column

Mlocr
For several years now, I have been able to quickly display the PMID, and PMCID, number in the "Extra" column. These numbers are essential to know if a publication is peer-reviewed and in Compliance with NIH mandates for grants.

Now, the new update does not display any of those numbers when I add the "Extra" column.

How can I display these two numbers so they appear fast in Zotero. I have a multitude of publications for several principal investigators.

Thank you
  • dstillman Zotero Team
    PMID and PMCID are now real Zotero fields, so the identifiers have moved there. Those fields aren't currently available as columns, since we generally limit columns to human-readable fields. If you want to find items without those values, you can use an empty "does not contain" condition in a saved search. (We'll be adding a more explicit way to search for empty fields in Zotero 10.)
  • adamsmith
    You can't display them in a column (Extra was always a shaky way of doing that since it also took other values).

    You can, otoh, much more ready filter for the presence/absence of these variables using advanced search (and saved searches if you want to).

    E.g.
    PMID -- contains -- [empty field]

    Shows all item with a PMID

    PMID -- does not contain -- [empty field]

    Shows all items without a PMID

    (If you use the Zotero Beta version 10+, this works even more smoothly because Advanced search now works like a filter on the main view)

    Does that work for your use case? If not, what exactly would you need?
  • Mlocr
    Thank you very much, dstillman. I see the numbers automatically appear when I create my desired bibliography. This is a wonderful update.

    Thanks a lot again.
  • Mlocr
    Thank you also to you, Adam.
  • iagogv
    I also asked for this (https://forums.zotero.org/discussion/130190/allow-to-include-new-item-fields-as-columns-in-main-middle-pane)

    And added a Pull Request: https://github.com/zotero/zotero/pull/5831

    But not merged.

    The added value of visualizing this in columns is the ability of sorting items per PMID, so one could identify quickly an item without the need of a search.
  • Mlocr
    @iagogv. True. That is a great request because I used to sort also by PMID. When you have hundreds of publications, sometimes is very useful. I second your request.
  • dstillman Zotero Team
    edited 7 days ago
    Again, since these identifiers aren't human-readable, a column doesn't provide any value beyond seeing whether the field is empty. In Zotero 10, you'll be able to do that trivially by clicking the advanced-search filter button and choosing "PMID" "is empty" from any items list.
  • iagogv
    Let me disagree and insist on my point
    The added value of visualizing this in columns is the ability of sorting items per PMID, so one could identify quickly an item without the need of a search.
    When writing a draft, some coauthors tend to identify papers to be referenced by their PMID. If I want to look quickly if I have a specific item by its PMID, but for many items, the fastest way is having a collection or library sorted by the PMID, with the option of looking to all of them simultaneously. So that PMID aren't human-readable is not completely true, at least in practice.
  • dstillman Zotero Team
    If you're looking for a specific PMID, why can just paste it into the search bar.
  • RamonMi
    If you do need to add those two columns, just use zotero-pmcid-fetcher or implement a custom script via Actions and Tags for Zotero.
  • iagogv
    edited 6 days ago
    @dstillman it is not a specific PMID. It is quite big number of them, quoting myself
    a specific item by its PMID, but for many items
    @RamonMi Regarding the first, I prefer not installing plugins just for one (not so every-day) feature. Regarding the second, if it was easier...
  • Mlocr
    I work with many collections for complex grants and many publications within each collection. The automatic PMID and PMCID in the Extra column have helped me immensely in finding publications that need to be added to the grants and progress reports.

    Copying and pasting these numbers in the Extra column is too time-consuming when deadlines are coming quickly, and looking for a specific PMID can help in specific occasions, but not like having these numbers in the Extra column.

    I love all the improvements in Zotero 9, and I appreciate the work of so many people for a free software, but this is removing the ability to automatically have the PMID and PMCID from the Extra column has greatly hindered my work.
  • dstillman Zotero Team
    If I want to look quickly if I have a specific item by its PMID, but for many items, the fastest way is having a collection or library sorted by the PMID, with the option of looking to all of them simultaneously.
    @iagogv: I can't say I really understand this. You're saying you're scrolling up and down an items list — with potentially thousands of items — looking for many PMIDs in succession by finding them sorted in numerical order? And that's faster than just pasting a PMID into the search bar and immediately seeing if it's in your library?

    In any case, PMIDs and PMCIDs, as plain integers, are somewhat more sortable and human-readable than identifiers like DOIs, so we could consider adding them as columns.
  • Mlocr
    @dstillman. Thank you, but how do I sort a collection by PMID since it doesn't automatically appear in a column? That is exactly what I used to do when PMIDs were in the Extra column automatically.
  • Mlocr
    BTW, thank you so much for considering adding these numbers as columns.
  • dstillman Zotero Team
    @Mlocr: I'm not sure what you're asking. I'm saying we can consider adding a column, and that I also genuinely don't understand how sorting is faster than searching.
  • Mlocr
    Sorry, I realized now that you copied text from iagogv.

    With sorting, I can visually browse many publications without knowing the PMID. By searching, I have to type every single PMID and know the number to be able to type it in a library with about 2,000 publications.
  • dstillman Zotero Team
    But why are you visually browsing? For what purpose?
  • Mlocr
    Duplicates in the same collection that are ok in different collections and PMIDs that have PMCIDs as time passes.

    I used to be able to touch one publication and see in what collections it was, but I cannot find the feature now.
  • dstillman Zotero Team
    https://www.zotero.org/support/kb/collections_containing_an_item
  • dstillman Zotero Team
    edited 6 days ago
    But if you have duplicates in your library, you should merge those, not use a random column to determine that. And if you want to find items with a PMID that don't have a PMCID, that's a search, even a saved search.

    (Requesting that duplicate detection take PMIDs and PMCIDs into consideration in addition to DOIs would be an appropriate feature request for a new thread.)
  • Mlocr
    Thank you! that really helps
  • Mlocr
    Ah! posts crossed. Thank you for the location link.

    With what you said, I don't need a new location feature.

    Is it that difficult to add a column for PMID or use the Extra column for showing PMID/PMCID automatically as before?
  • dstillman Zotero Team
    edited 6 days ago
    No, of course not — but every column we add makes it harder to find and toggle other columns quickly, and it seems to me that essentially every use of this column expressed so far is likely better served by other features. That's part of the reason we push back on requests like this — we want people to use Zotero in the most efficient way, not just stick to habits they might have adopted from other tools or earlier versions of Zotero with fewer features.

    (And the fact that you're still mentioning Extra at this point suggests some confusion here. Again, PMID and PMCID are real fields now, so they have nothing to do with Extra, which is just a catch-all field where unknown data fields were dumped in previous versions — and in a random order that made it unreliable for using as a sortable column anyway. It has absolutely nothing to do with any future solution here.)
  • Mlocr
    That would depend on the user's preference for columns. For instance, I work only with Creator, Date, Date Added, Tittle, and in previous versions, Extra for PMIDs. I see that PMIDs and PMCIDs have their own fields now, but no columns, which is the feature I need. This is why, erroneously, I have been mentioning the Extra column. I care about the column with PMIDs and PMCIDs.
  • mjthoraval
    edited 6 days ago
    @Mlocr: As mentioned by RamonMi, the PMID and PMCID columns are already provided by the PMCID Fetcher plugin:
    https://github.com/retorquere/zotero-pmcid-fetcher
    It is written by a long time Zotero plugins developer, and works well from my testing.
  • iagogv
    edited 6 days ago
    @iagogv: I can't say I really understand this. You're saying you're scrolling up and down an items list — with potentially thousands of items — looking for many PMIDs in succession by finding them sorted in numerical order? And that's faster than just pasting a PMID into the search bar and immediately seeing if it's in your library?
    @dstillman Well, I did this with a collection far from thousand of items; a better approximation is a collection for saving the references for a draft. For the rest, you have understood perfectly. It is faster, because I do not have to copy and paste every single PMID for around than 20 PMID's in the draft or more, and every time I paste in the Zotero search wait for its identification. Further, for pasting the next PMID, either I have to remove before the previous copied PMID, or I have to select it for pasting over it, which slows down the process.
    In any case, PMIDs and PMCIDs, as plain integers, are somewhat more sortable and human-readable than identifiers like DOIs, so we could consider adding them as columns.
    I would be deeply grateful
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