Pubmed ID

aurimas · January 4, 2014

@adamsmith, you mean this is an issue in the csl style, right? I'm just confused by your pending patch (edit: to Zotero), which looks unrelated to this, and your use of "get" above.

If yes, then it is also worth mentioning (once this is fixed) that PMID and PMCID are supposed to be entered on separate lines in the Extra field

adamsmith · January 4, 2014

no, this is an issue in Zotero: Zotero will not parse PMCIDs from the extra field (that start with PMC (which is all of them). I.e. currently Zotero does not parse a PMCID from the extra field (and so doesn't pass on a PMCID variable to CSL)
PMID: 12345
PMCID: PMC12345
although it should. That's what my patch fixes and that would basically address tgliou's issue (though, as you say, the PMCID would have to be on a new line, not just space separated)

edit: the "whichever comes first" above is incorrect. It just doesn't properly parse PMCIDs.

dmilton · January 4, 2014

I'm not familiar with XML and cannot easily implement tgliou's fix. I gather that this is a replacement for the section <maco name = "pmcid"/> but it would be very helpful if the final version of the new macro were posted here so that I can copy it. Or, maybe a fix to the cls in the repository is in order for now - until Zotero is patched?

dmilton · January 4, 2014

I will keep an eye on this -- hope it is fixed soon. But, meanwhile, its back to Endnote. darn.

tgliou · January 5, 2014

@adamsmith: Thanks very much! The ability to parse both PMID and PMCID and choose between them is less important than getting the PMCID in there. NIH only penalizes for absence of PMCID. Without a word limit on the bibliography and reference section in the standard grant application, having PMID in there too doesn't hurt. But I agree that code that doesn't do what it is supposed to do is always a worry.

Is having PMCID on a separate line really a requirement? I didn't think the code as written really cared, just that it was supposed to be looking for the string "PMCID:". (Or is my lack of knowledge about XML showing?)

@dmilton I think that the next NIH due date is Jan 25 unless there is an special due date on a particular RFA or PA. I'm pretty confident that this will be fixed well before that. The crew at Zotero have always been quite responsive, so don't give up on Zotero!

I can share my clumsy patch with you, but it would probably be better to wait a little and see what adamsmith and friends come up with.

dmilton · January 5, 2014

I thought that the mention of separate line was just about how to enter data in the "extra" field, not how it would appear in the formatted reference. But, I could not get it to work regardless of how I entered it in the field.

@tgliou: granted this might be fixed soon, but I would much appreciate receiving your patch in the meantime -- there's enough anxiety surrounding writing applications, having a workable solution and not having one more thing to do just before the deadline would be a very good thing.

adamsmith · January 5, 2014

@dmilton:
see the general instructions here:
http://www.zotero.org/support/dev/citation_styles/style_editing_step-by-step
in particular, you want to make sure to edit the ID of the style once edited so it doesn't get overwritten on automatic updates.

Specifically, find

 <macro name="pmcid">
    <text variable="PMCID" prefix=" PMCID: "/>
    <choose>
      <if variable="PMCID" match="none">
        <text variable="PMID" prefix=" PMID: "/>
      </if>
    </choose>
  </macro>

and change it to

 <macro name="pmcid">
<text variable="note"/>
  </macro>

I can't change this on the style repository, as the same styles are used in various other reference managers, some of them have working PMID/PMCID support, so you'll have to hand patch it.

Re separate lines: To clarify the current problem - Zotero doesn't recognize the PMCID in the extra field as a PMCID. That has nothing to do with the citation style, which is correct. Even once my patch goes through (which I'd expect to be the case for the next Zotero release), it will only recognize PMCIDs (and PMIDs) that are at the beginning of a line. In other words
PMID: 12345
PMCID: PMC12345
will recognize both separately,
PMID: 12345 PMCID: PMC12345
will only recognize the PMID and
PMCID: PMC12345 PMID: 12345
will only recognize the PMCID. So the separate lines are required, but that's because of the way Zotero parses that field, not because of the citation style.

dmilton · January 5, 2014

OK, if I have the PMID and PMCID on separate lines, as will be necessary when your patch arrives, there is no space between them in the bibliography. e.g.

Environ Health Perspect. 2005;113:1516–1521. PMID: 16263505PMCID: PMC1310912

If I put them on one line with the space between them, then the style works:

Environ Health Perspect. 2005;113:1516–1521. PMID: 16263505 PMCID: PMC1310912

So, I'm beginning to see why I should wait for the update. But, I have a fall back now. Thanks!

However, the fact that Endnote automatically captures the PMID (as accession number) and PMCID (as a separate field) and can produce the properly formatted output from an appropriate style...

adamsmith · January 5, 2014

you could try putting a space behind the PMID in Zotero. I think that should work and it won't affect how this works once the patch is through. Obviously all of this is clumsy.
Once the parsing is working correctly, this works out of the box, though, since the pubmed central translator does import PMID and PMCID on separate lines.
I hope we'll finally get separate fields for both sometime this year so we can retire the extra field.

aurimas · January 5, 2014

I'd suggest just waiting a day or two. At the very least, you will be able to install a "beta" version of Zotero that will fix this.

you could try putting a space behind the PMID in Zotero. I think that should work and it won't affect how this works once the patch is through.

AFAICT, PMCID has to start on a new line and there cannot be spaces before it.

adamsmith · January 5, 2014

right, but a space at the _end_ of the PMID line wouldn't interfere i.e. in technical terms I'm suggesting:
PMID: 12345 \n
PMCID: PMC 12345

and I believe it would be rendered by variable="note" (though I haven't actually tested that).

dmilton · January 5, 2014

Yes, the space works. But, when I import references from PubMed that have PMCIDs assigned, only the PMID is being captured by my Zotero database. Thus, I don't see that the following statement is true: "Once the parsing is working correctly, this works out of the box, though, since the pubmed central translator does import PMID and PMCID on separate lines." Is there something in the setup that I need to change to capture the PMCID?

adamsmith · January 5, 2014

right, that only worked from pubmed central ( http://www.ncbi.nlm.nih.gov/pmc/ ). I've just added it to regular pubmed as well:
Your version of Zotero will automatically update within 24hs, or you can update manually using the "Update Now" button in the "General" tab of the Zotero preferences.

dmilton · January 5, 2014

Cool. And, you have it putting the extra space " " after the PMID too. Very nice!

tgliou · January 5, 2014

Sorry to be slow to respond to all of you. I seem to be working at the opposite end of the day!

@adamsmith, Thank you for addressing these issues so completely.

adamsmith · February 17, 2014

FWIW, the underlying issue in Zotero is fixed for 4.0.18, which should be out in the next couple of weeks. Those in a hurry can use the beta:
http://www.zotero.org/support/dev_builds#zotero_40_beta

Klortho · September 3, 2014

Saheli wrote:

> Hi, I was wondering if there is any progress on how to easily convert existing ID numbers (doi, PMID, etc) to PMCID if available?

adamsmith wrote:

> no there isn't - that part also won't happen very quickly.

PMC now has an ID converter API, documented here: http://www.ncbi.nlm.nih.gov/pmc/tools/id-converter-api/. I don't know if that is something you might be able to use in Zotero or not.

keithk900 · September 28, 2014

Sorry, Please delete. I corrected the issue by updating my Zotero.

Hey,

Using the National Library of Medicine (grant proposals with PMCID/PMID) style, I am able to only get PMIDs to import into my bibliography.

For example the following paper that imported into Zotero with both PMID and PMCID in the "Extra" area:

PMID: 24055765
PMCID: PMC3886931

Shows up as such:

Nebenzahl-Guimaraes H, Jacobson KR, Farhat MR, Murray MB. Systematic review of allelic exchange experiments aimed at identifying mutations that confer drug resistance in Mycobacterium tuberculosis. J Antimicrob Chemother. 2014 Feb;69(2):331–342. PMID: 24055765

As I understand the macro, it is only supposed to get a PMID if there is no PMCID present.

Is there a style that is actually pulling the PMCID from the Extra area of info in Zotero?

I am not sure what I am doing incorrectly.

b0c5 · August 10, 2017

Any progress on this??

adamsmith · August 10, 2017

What issue? Everything described in this thread has been solved

b0c5 · August 10, 2017

@adamsmith I was thinking about adding a field with common identifiers, DOI, PMID, PMCID, etc. Do something like the Authors, where you can add several authors, and select whether each is a collaborator, editor, etc.

In the current version of Zotero I do not see any field to input PMID, PMCID. "Extra" seems adhoc.

adamsmith · August 10, 2017

oh OK. New fields are slated for Zotero 5.1. They require (sync) support for Zotero 4 versions to be stopped. Extra is adhoc, but it works.

b0c5 · August 10, 2017

@adamsmith The new fields in Zotero 5.1 include PMID, PMCID, etc.? That would be nice.

adamsmith · August 10, 2017

I don't think we know exactly how we'll handle identifiers, but I'm pretty confident that we'll do DOIs for all item types and PM(C)IDs for all relevant item types. Given the number of potentially relevant IDs across fields (arXiv, ZMat, OCLC, NBN, etc.) I do think we'll have to go into the direction you describe (i.e. something like the author types as a menu) at some point, but no idea if that's going to be in 5.1 or later.

b0c5 · August 10, 2017

I see a DOI field in Zotero 5. But it stands by itself. It would look better unified with the other IDs, which should also include ISSN, ISBN of books, etc, like in the Author field.

Also ideally Zotero should fetch all these IDs automatically (currently I only get the DOI automatically).

Repoman21 · February 2, 2018

Thanks for making Zotero available. I'd just like to second the idea that it would be ideal if Zotero automatically fetched PMID, and stored it in a dedicated field.

bwiernik · February 3, 2018

When available, Zotero downloads and stores the PMID in Extra as:

PMID:12345

Also:
PMCID: 12334

These will get picked up and stored properly. Zotero 5.1 will have a dedicated PMID field.

adamsmith · February 3, 2018

but there's no way to fetch it for existing items, which I think is the request -- not unreasonable, but I don't think it'll happen any time very soon.

bwiernik · February 3, 2018

@adamsmith Does PubMed have an API that you know of?

adamsmith · February 3, 2018

yes, the have all sorts of APIs -- we use the eutils API for the pubmed translator already and I think there's dedicated PMID-->PMCID conversion APIs and maybe even a DOI --> API ones.