Pubmed ID
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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
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.
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.
@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.
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.
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...
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.
PMID: 12345 \n
PMCID: PMC 12345
and I believe it would be rendered by variable="note" (though I haven't actually tested that).
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.
@adamsmith, Thank you for addressing these issues so completely.
http://www.zotero.org/support/dev_builds#zotero_40_beta
> 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.
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.
In the current version of Zotero I do not see any field to input PMID, PMCID. "Extra" seems adhoc.
Also ideally Zotero should fetch all these IDs automatically (currently I only get the DOI automatically).
PMID:12345
Also:
PMCID: 12334
These will get picked up and stored properly. Zotero 5.1 will have a dedicated PMID field.