Adding PMC ID

sut2006

Hi, I need to include PMCID to my grant application. I followed the instructions to modify (https://forums.zotero.org/discussion/54495/looking-for-style-w-pmcid-all-authors-and-simple-superscipt/) but it did'nt work. I am using APA 6th edition style. Can someone help me figure this out?

Thanks,
S

bwiernik

If you want APA 6th edition with PMCID added, this will be the easiest way to modify the apa.csl style:

Find the following lines in bibliography section of the style (at the end of the code):
<text macro="access" prefix=" "/>
<text macro="original-date" prefix=" "/>

Add the following line immediately after:
<text variable="PMCID" prefix=" PMCID: "/>

General instructions for changing styles at
https://www.zotero.org/support/dev/citation_styles/style_editing_step-by-step
Make sure you don't miss the part about changing title/id.

sut2006

Hi, I did this but nothing changed.. Is it possible that the PMC ID's are not included in the refs to begin with and thus cannot include in final document? Anyway to fix this?

sut2006

Correction: Some papers have their PMCID. others don't. anyway to ensure that all after 2000 do?

sut2006

Also any way to include PMID and doi if PMCID is not available?

bwiernik

Whether or not they are included will depend on whether they are in your data in Zotero (they can't be shown if they aren't in the metadata).

Currently, the style as modified shows the DOI for all items and then also the PMCID if available. If you want it to prefer the PMCID over the DOI, then you'll need to modify it differently.

Start from the original non-modified apa.csl style. Find these lines:
<choose>
<if variable="DOI">
<text variable="DOI" prefix="http://doi.org/"/>
</if>

Change them to:
<choose>
<if variable="PMCID">
<text variable="PMCID" prefix="PMCID: "/>
</if>
<else-if variable="DOI">
<text variable="DOI" prefix="http://doi.org/"/>
</else-if>

If you want the order of preference to instead be PMCID -> PMID -> DOI, instead change it to:
<choose>
<if variable="PMCID">
<text variable="PMCID" prefix="PMCID: "/>
</if>
<else-if variable="PMID">
<text variable="PMID" prefix="PMID: "/>
</else-if>
<else-if variable="DOI">
<text variable="DOI" prefix="http://doi.org/"/>
</else-if>

Again, PMCID and PMID can only be shown if they are in your Zotero data (in the Extra field formatted as PMCID: XXXXXXXX).

sut2006

Hi, great, is there a way to "refresh" the citations in zotero to pull the PMID, PMCID and doi IF they are not already there?

DWL-SDCA

Is there any way to refresh...?

Short answer is No.

Mostly, PMID and PMCID are only available through the National Library of Medicine websites. Some other specialty databases include these IDs but only for items that have them. There are many records in PubMed that are not available on PubMed Central (a repository for selected open access publications). Articles from journals that are not indexed in PubMed will not have these identifiers.

I know of no easy way to automate getting the PMID or PMCID from an article title or a DOI. For articles that are included in PubMed you can use the PubMed "Single Citation Matcher" and search by article title. That utility return a list of likely matches. You can then add the appropriate IDs to your Zotero record by hand.

The issue becomes a bit more complicated if you 1) obtained the original item from a source other than PubMed and 2) have already used that record as a citation in your application or manuscript.

Because of this, I am careful to _always_ only get articles from PubMed if the journal is indexed in PubMed. Sometimes this means waiting a week to ten days before the item reaches PubMed. Some publishers are quite slow to ship their metadata to the NLM. Having a PMID in the record allows me to automate the process of updating ePub ahead-of-print articles with volume, issue, and pagination when that info becomes available. (The ability to do this requires a license from the NLM that allows a special connection to the database. The license number must be used with each connection/query. There are strict limits to the frequency and quantity of requests. This access is not designed for the general public but primarily for systems such as my SafetyLit database -- a free service presented without advertising.)

bwiernik

Someone could write a Lookup engine to pass an item's DOI to the PMCID lookup API (http://www.ncbi.nlm.nih.gov/pmc/tools/id-converter-api/). Then you would only need to copy the result to the item. This would also be possible to write a plugin to do each step (lookup, copy to item, save), but that would be more involved.

mkerppola

Hi! I'm trying to add the PMCID -> PMID -> DOI code listed above to the American Medical Association 11th edition style, but I'm getting the following error: "Error parsing style: Error: File is not valid XML".

I tried replacing:
<choose>
<if variable="DOI">
<text value="doi:"/>
<text variable="DOI"/>

with:
<choose>
<if variable="PMCID">
<text variable="PMCID" prefix="PMCID: "/>
</if>
<else-if variable="PMID">
<text variable="PMID" prefix="PMID: "/>
</else-if>
<else-if variable="DOI">
<text variable="DOI" prefix="http://doi.org/"/>;
</else-if>

dstillman

(@mkerppola: Note that you have to add <code></code> tags if you want code to show up here. I've added them to your post.)

adamsmith

If this is actually from your code,
<text variable="DOI" prefix="http://doi.org/"/>;
then the semicolon at the end of the line is the problem.

The rest looks good, but would have to see the entire macro (or ideally the entire style -- post to pastebin.com or hastebin.com and link to from here) to say more.

mkerppola

I ended up finding the following style to work for what I needed:

National Library of Medicine (grant proposals with PMCID/PMID)

Thanks!

ajpodge

Hi, I'm having a related problem. I'm using the National Library of Medicine (grant proposals with PMCID/PMID) style, just like mkerppola. I have some references whose PMID is showing up in my reference list. Others whose PMCID is showing up in the reference list (but not the PMID even though both are listed in the Extra field). And some whose PMID is not showing in the reference list, even though the PMID is in the Extra field within Zotero. Anyone know what's going on here, and how I can fix it?

adamsmith

The way that style is written it uses either PMCID (which is preferred) or PMID.
There should not be any case where a PMID is in Extra and neither PMID nor PMCID are printed -- could you double check on that case? It wouldn't be very hard to modify the style to print both when they're present. What's that for?

enozkan

This style stems from the NLM style, with a modification for grants as explained here: https://grants.nih.gov/grants/how-to-apply-application-guide/format-and-write/format-attachments.htm#citations

It is used by all faculty, students, postdocs and other staff ever applying for a research grant in the US in biomedical sciences from NIH. That's a huge chunk of people.

NIH says it does not care which style is used as long as a PMCID is added to the end (see link above). It was interpreted to include PMCID when available, but fall back on PMID when not. I find that a very reasonable choice, and I've seen that in many grant proposals.

NIH says that if you don't know what style to use, the NLM style would be a reasonable one (which is here: https://www.ncbi.nlm.nih.gov/books/NBK7256/).
I just checked the journal paper entry for NLM at that source, and the current csl style for "National Library of Medicine (grant proposals with PMCID/PMID)" does appear to follow NLM + PMCID (and if not present, PMID). That looks correct to me.

(There may be some minor mistakes in the NLM csl style due to recent updates to the style, but that is another issue.)