@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
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.
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?
@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.
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.
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.
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...
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.
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?
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.
> 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.
@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.
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.
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).
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.
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.
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.
Upgrade Storage
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.