PubMed Central Identification Number

The PubMed Central Identification Number (PMCID) does not import from the PubMed Record to the EndNote Journal Article type. I’ve emailed PubMed tech support to create a datafield for PMCID that would import into EndNote, etc. I’ve not yet heard from PubMed, and would welcome others to reqeust PubMed to support PMCID import. The data has to be there before EndNote can import it.


The PMCID is now an important data element, because NIH has mandated that articles from NIH funded research be placed in PubMed Central and that future grant requests and articles cite the PMCID. 


The PMC is not to be confused with the PubMed ID #, which imports into the EndNote Accession Field of the Journal Article type.

From what I’ve heard, EndNote will be releasing a new PubMed filter soon. The PMCID will now map to the accession number field. And the PMID will be lumped into Notes.  

Currently, PubMed does include the PMCID in the MEDLINE format. It’s just that EndNote doesn’t yet know what to do with it. 

After scrutinizing quite a few results at PubMed, I am having a very hard time finding a record that provides the PMCID number in the MEDLINE format.

Would you be so kind as to provide the PubMed ID for one of these records, that I might have a look?


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The easiest way to find records with a PMCID is to use the Limits tab and select the PubMed Central subset after you’ve done a search in PubMed.

For example, PMID 18401448 has a PMCID.  

The NLM Technical Bulletin that discusses the PMCID and MID is at

The new PubMed filter I’ve seen now puts the PMID in the Notes field. Won’t that be confusing to have some records with the PMID in the accession number field, and then now have the PMCID in the accession field instead? Every PubMed citation has a PMID, but not all of them will have a PMCID.

Message Edited by jaysonlf on 04-18-2008 08:35 AM

Message Edited by jaysonlf on 04-18-2008 08:46 AM

I have solved this problem by using a Custom field and editing the pubmed import filter to send the PMCID to the custom field. But I worry for my patrons who are not as EndNote savvy.

If EndNote changes the filter to send the PMCID to the accession number field, where will the PMID go?

Also you may want to do a Change Move Field action to move all PMID’s already in the accession field to another field. However I think users will want both the PMID and the PMCID available.

I believe the PMID will now go into the Notes field. I’d prefer to have both fields available too.

Fortunately, the PMCID is prefaced with PMC so we can tell the difference. 

At least some of these issues should be resolved by following the instructions on this FAQ:

If you follow the steps there, are there still things that appear not to be importing, or are importing incorrectly?

Message Edited by gilliann on 05-22-2008 11:16 AM

Thanks for officially supporting the PMCID. Now…we need the MID field to import into it’s own field (custom 3?) because if a manuscript does not have a PMCID assigned to it yet, we’ll need to include the NIHMSID in the NIH reports.

Take a look at the U of Wisconsin’s modifications: 


Message Edited by jaysonlf on 05-22-2008 10:11 AM

Hello, Jaysonlf:

Could you provide me an example of a record from PubMed that has the NIHMSID? You can either attach an exported file, or provide me with an author name, year, and title and I can search for it.

I would need to see how PubMed exports it, and then from there I can direct you how to make the appropriate changes. If this is a standard NIH requirement, I can also alert our Content group that it needs to be altered in the public filter as well. 

Here’s the PMID of a citation that has an NIHMSID, 16930585.

Here’s the FAQ regarding the NIH policy that we are trying to comply with


Hello, Jaysonlf:

I see the field you’re referring to, and it shouldn’t be a problem to send it to a custom field. I will provide instructions on that down below.

As a side note, though, I do have a related concern. According to your link, the requirements for including the NIHMS ID in documents seem to be conditional… IF there’s no PMCID, THEN add the NIHMS ID instead. This isn’t a problem for import, but it is a style issue; EndNote doesn’t really have a way to include things in the bibliography on a conditional basis. It’s either there in the bibliography all the time, or it’s not included. You will have to decide whether it makes more sense to edit your style to always include the NIHMS and then later take out any that aren’t needed, or if it’d be easier to just manually add them later where they are needed. 

That said, let’s return to our import issue. Here’s how to manually edit your filter to bring in the NIHMS ID:

  1. In EndNote, click Edit>Import Filters>Open Filter Manager.
  2. Find PubMed (NLM) and highlight it. Click Edit
  3. Click on Templates.
  4. Scroll to the bottom of the templates and put your cursor after the last character of the last line.
    Hit the Enter key to make a new line.
  5. Enter the tag in question in the Tag box of the new line. In this case, if you look at a text file downloaded from PubMed in Medline style, you’ll see the tag for that is     MID-
  6. Hit your tab key to get to the next box, and then use the Insert Field pull-down at the top of the screen to select the field in EndNote that you’d like the NIHMS ID to be imported into.
  7. Click File>Save and then try the import again. What happens?

Hi Gillian.

Yes, that modification seems to work. However, I’d prefer the NIHMSID to be included as a separate field, such as custom 3, so that there is a spot to include it and use it, if necessary.

Maybe conditional logic in styles can be an enhancement for EN X3. 

Hello, Jayson:

You should be able to do that with the instructions I gave. When it you select your Field in the template window, you can select whatever field you like… including Custom 3.

If you can’t see Custom 3 in your records even after making that change, you may need to edit your journal reference type to show Custom 3. Instructions on modifying reference types is found on page 392 of the EndNote X1.0.1 manual for Windows.  

One workaround I have used for this kind of thing, is to create a new reference type which has an output with the alternative information in the style for that ref type. 

Search library for a blank in PMCID and ref type “journal article” (probably add year range, for recent) and then change the reference type to the alternative reference type where the style will output the NIHMS ID instead. If an article gets a PMCID assigned, you wil need to alter the record to include that information and you can then also alter the ref type at the same time. 

I know this goes a little beyond the scope of EndNote, but here is some information on the NIHMSID (MID as you called it) and why it doesn’t show up in PubMed.  The NIHMSID is assigned when the article is submitted through the NIH Manuscript Submission System (by the author) or sent in an email to the author after the journal sends it to the NIH Manuscript Submission System. Since the article is not necessarily available to the public in PubMed Central right away, the NIHMSID does not appear in the citation in PubMed. The NIHMSID will appear in PubMed Central after it is released (up to 12 months later) but at that time the PMCID is also given, so it’s not much help.

Just fyi as of May 30, the PMCID appears in that record now too, so I do see the MID in the MEDLINE format or the record.  I have never seen PubMed list the MID without the PMCID, so I’m not sure they list it before the record has a PMCID.  Please correct me if I am wrong as I am the Instruction Librarian for my campus and need to know how to correctly follow NIH guidelines.

That’s a good point about the order in which the ID numbers are assigned. I may not worry so much about importing the NIHMSID, but I can see the value of having a separate EN field for users to record the NIHMSID to use for reporting until the PMCID is assigned.  In reality, I may just be over-thinking this.  ;-)