managing publications with ncbi-my bibliography

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Managing Publications with NCBI-My Bibliography

Oliva SmithDivision of Sponsored Programs DSP

oliva-smith@uiowa.eduSpring, 2014

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National Center for Biotechnology

Information (part of NIH National Library of

Medicine NLM)

• Includes PubMed, PubMed Health, PubMed Central PMC,

NIH Manuscript Submission System NIHMS.

• Dozens of databases - genetics, proteins, DNA/RNA,

biochemical structures, viruses, etc.

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https://becker.wustl.edu/sites/default/files/nih_resources_chart.pdf

Created by:

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https://becker.wustl.edu/sites/default/files/nih_resources_chart.pdf

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What is NCBI Bibliography?

It is a tool integrated with PubMed to track literature

searches, collections of

citations and public access compliance.

Always NIH/eRA log in

Not here

May be helpful

Does not work with Internet Explorer 7; must be IE 8 or higher; Firefox is fine.

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Setting up your NCBI account.

Go to (or google) PubMed http://www.ncbi.nlm.nih.gov/pubmed

In far upper R of the PubMed homepage, click:

Sign in to NCBIto bring up this page

Log in using eRA/NIH log in.

Click “By email”

Then you must confirm the email from NCBI.

Finally, click “here” to continue to MyNCBI

From http://libguides.library.umkc.edu/content.php?

pid=493199&sid=4049213

First-last@uowa.edu

First-last@uowa.eduFirst-last@uowa.edu

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Why use NCBI Bibliography?

(1) It automatically tracks

public access compliance - includes

*NIHMSID/**PMCID.(2) It is the only way to get

citations into RPPR Progress Report ‘Products.’

(3) Create .pdf report of publications for non-RPPR

reports.(4) Automatically adds

publications to Biosketch.

Always NIH/eRA log in

*NIHMSID = manuscript in NIH Manuscript Submission System which

accepts manuscripts, converts to PMC/web format, sends to PMC after final web approval; temporary until

PMCID is assigned.

**PMCID PubMedCentral ID = article is in PubMedCentral PMC, the NIH’s full

text, publically available (free) database of NIH funded research articles.

Article must have PMCID (NIHMSID if w/i 3 months of publ date) to indicate

PA Compliance.

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The PMID = citation is in PubMed (1996).

PubMed does not contain full articles—only the citations /abstracts (22 million) that go back to

1966, with some from the 1800s.

The PMCID = indicates the full text article is in PubMed Central PMC (along with ~ 3 million

others). PMC started in 2007.

PMID and PMCID are different

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Sign in with eRA login as the Investigator (Owner)

OR as the Delegate.

Delegate invitations are initiated by the

Owner/PI.(handout 17).

the PI must set up their NCBI-Bib first and then assign

delegates.

Sign in

Not here

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http://www.ncbi.nlm.nih.gov/books/NBK53595/

Using this Guide :(1) Add citations from PubMed PMID or type in manually

Collections: My Bib and Other

(2) Sort by Award View to indicate compliance to Public Access PA Policy

Edit statusAssign award

(3) Create .pdf report for non-RPPR reporting.

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Sign in to NCBI Bibliography

https://www.ncbi.nlm.nih.gov/account/?back_url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fmyncbi%2F I use google.com to find NCBI login

Always use eRA/NIH login

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Screen shot of my “fake” NCBI

Biblio

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Screen shot of my “fake” NCBI

Biblio

Or here: To see the whole biblio

This is a record of the various searches I have done in PubMed recently—has nothing to do

with My Bibliography—I should just disable this.

See whole biblio

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Clicked “Manage my Bibliography” to get to this

page.If no eRA icon =

NOT LINKED. Must link

MyBiblio to eRA Commons. Click log in

name/email at upper right.

Icon = linked to

eRA Commons

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What you should see linked.

To return

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“Add Citations” NCBI Biblio. (pp. 1 - 4 of handout)

Indicates linked to eRA Commons

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(most common) “Go to PubMed” to

(1) search by PMID or title to add single article.

“Manual citation” for papers that are not in PubMed, such as

recently submitted or still “in press” that don’t have PMID

yet; or papers from journals not indexed in PubMed.

Use Manual Citations to add non-journal

types of publications if they don’t have a

PMID (book chapters, conference papers, meeting abstracts).

They will get put into category “Meeting

Abstract” etc.

OR (2) search by author, select relevant citations and add in one batch.

Handout p. 2

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Manual citation for an article: Required

fields - Title- Last Name

- Journal- Year

This way, if paper has just been

submitted can include this paper in MyBibliography.

“Forthcoming” = submitted + accepted

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Here it is

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Adding new items using Manual Citation puts

Meeting Abstracts,Presentations,

Book Chapters, etc. in separate categories in

MyBibliography (following the list of publications)

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Add a citation using

the PMID.

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1 PMID or title 2

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5

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23Handout p. 2

Select citations

Search by author in PubMed

Send to MyBibliography

Add Many Citations to NCBI- MyBib at once

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“My Bibliography” is for articles authored by you.

“Other Citations” Collection is to create an additional

bibliography, e.g., items you did not author/not your grant but on which you contributed.

Progress Reports: Only publications listed in MyBibliography are loaded

into the RPPR module (i.e. not “Other”).

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Default Sort by date = newly

added citation [year 2010] is

in the middle of the list

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To Add a Delegate to enter citations to your NCBI-MyBib, click Edit Settings (p. 17 handout)

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Click and enter delegate’s email on the next window.

Your delegate will:- receive an e-mail notifying them of access.- click a link in the e-mail to activate access.- be invited to register if he/she does not have a My NCBI account.

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Click

(p. 7 - 9 handout) Manage NIH PA compliance: Sort citations by Clicking “Display Settings” to View = Award; Sort by = PA Compliance; Group = By citation type. “Apply” [Delegates cannot see this view] **does not display in browser IE7.

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Add/delete Awards (handout 10 – 14).

(1) Associate awards that directly funded the

research. Gray lock =associated via

eRA Commons and “cannot be disassociated.”

Yellow lock =“contact NIHMS-Help” to

disassociate.

(2) if someone other than PI (such as trainee) adds

the award, notification at the top of PI’s My

Bibliography. **I am not demo’ing how to

add awards on my “fake” biblio because I am not PI on

any grants.

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NCBI-My Bibliography: Determine Applicability

• Is peer-reviewed; • And, is accepted for publication in a journal1 on or after April 7, 2008;

– 1 A journal is defined as a publication that is published in successive parts for an indefinite time frame and has an ISSN (International Standard Serial Number).

• And, arises from: – Any direct funding2 from an NIH grant or cooperative agreement active FY 2008 or

beyond, or any direct funding from an NIH contract signed on or after April 7, 2008

• 2 "Directly" funded means costs that can be identified specifically with a particular sponsored project, or that can be directly assigned to such activities relatively easily with a high degree of accuracy

• Written in Latin scripts; scripts other than Latin (e.g., Russian, Japanese, or videos) cannot be processed by the NIHMS

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Direct Funding

• If a grant provides access to core facilities at a decreased fee, this is a direct cost = the grant should be associated when core facilities generated data for the paper.

• The PI is responsible for ensuring all articles that are directly funded from that grant are compliant, whether or not the PI is an author.

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Edit Status

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NIH Public Access Policy Does Not Apply To:use “Edit Status” in NCBI MyBibliography

• Reviews of the literature usually are NOT considered research articles since they do not talk about the work on YOUR specific grant;

• Others not peer-reviewed/not directly funded/non-research/non-journal -- invited papers, letters, editorials, commentaries, book chapters, conference proceedings are all exempt;

• Articles from work funded by non-NIH funds;• Accepted before April 7, 2008—find acceptance date

on .pdf of the published article (search via Hardin’s PubMed).

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Manually-entered Meeting abstracts and Presentations are automatically designated N/A since NIH PA does not apply to this type

of correspondence.

Papers accepted for publication prior to April 7, 2008 are N/A.

Citation with Green = has the PMCID and is In Compliance with PA Policy.

You have: Added the Award(s)

And (if applicable) Edited Status

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Pages 8-10 handoutCitation with Yellow = “In Process”

with temp. NIHMSID within 3 mo. of publication (print),

OR published in “PMC journal.”

PMC Journals have formal agreement with NIH to send final article directly

to PMC (free of charge). NOTE: most journals are NOT

“PMC journals.” (google NIH Submission Method A );

Most journals submit the manuscript to NIHMS (if requested

and/or NIH funding indicated) author must approve initial receipt

and web version= Not “PMC journals”

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What to do with citation with Red dot?

Exempt? = Edit Status (p. 9).Or does it fall under the PA Policy and need to get into the NIHMS-PMC system?

We’ll return to this in a few slides . . . .

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For non-RPPR reports: (p 16 of the PHS 2590 instructions) http://grants.nih.gov/grants/funding/2590/phs2590.pdf E. Publications Report publications resulting directly from this grant that you have not previously reported, including manuscripts accepted for publication. (If there are no publications to report, include such a statement.) Using My Bibliography provide a My NCBI generated PDF list of publications (see

http://www.nlm.nih.gov/pubs/techbull/nd12/nd12_myncbi_pdf.html for instructions). My Bibliography will display the correct text format, and if available, include the appropriate reference number (PMID, PMCID, or NIHMSID), and compliance status. If a publication is not compliant with the public access policy NIH staff will contact the PD/PI and business official to inform them that the award will be delayed until a reply to the email is received with evidence of compliance . . .

In NCBI-Bibliography - Add citations manually

for manuscripts submitted and

accepted(p. 3 handout).

Creating Award Compliance Report - for non-RPPR

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1. Select appropriate grant.

2. Click “Apply Filters” to bring up

list of citations assoc with that grant.

3. Check each citation to include in

it the report.

4. Click “PDF report” button at top.

(pp. 13-14 handout)

Preparing NCBI-Bibliography- generated report of publications,

as per PHS 2590 instructions (non-RPPR)

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3

2

1

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Preparing NCBI-Biblio generated list of publications, as per PHS 2590 instructions (non-RPPR)

Once you have checked each citation, click “PDF report”

button, fill out to save, and

Download PDF.

Questions?

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RPPR Instructions for Section C- Products (i.e. publications) start on p. 55

http://grants.nih.gov/grants/rppr/rppr_instruction_guide.pdf or use google.com

RPPR Instructions

42http://grants.nih.gov/grants/rppr/rppr_screen_shots.pdf

Screen shot of RPPR

C. Products.Publications

assoc. with this grant are

automatically drawn from

NCBI-MyBiblio.i.e. the only way to report papers

in RPPR is via NCBI-MyBiblio

Select citations in

lower table, then

“Save” [Save button

appears after you select] to

refresh the screen and

move citations

into upper table to

associate with this project. Questions?

Reporting publications in RPPR progress report

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NCBI Collections-those listed in My Biblio and

associated with a grant go to the RPPR;

-those listed in Other Citations do not go to the RPPR.

Publications listed in My Bibliography also

populate the SciENCV Biosketch.

Publications in Biosketch

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“Show/hide entries” to select for

inclusion in BioSketch.

PMCIDs are included if

available, but otherwise no Public Access compliance

alerts.

- SciENCV = Biosketch

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Review: NCBI-My Bibliography

– Set up/Sign in to NCBI using NIH/eRA login– Confirm NCBI and eRA are linked– Add citations: via PubMed or manually

• Edit Status if applicable• Add delegate(s) if you want assistance

– Associate awards with citations– Confirm Public Access status of citations– Generate .pdf list of publications for non-RPPR– Associate papers in RPPR progress report– Include citations in SciENCV NIH Biosketch.

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NCBI-My Bibliography• NCBI-MyBib

– manages bibliography for progress reports, biosketch – indicates public access compliance lists PMCID or the temporary

NIHMSID • Adding the citation to NCBI-MyBiblio does not get the paper

into the NIHMS-PMC system.• Citation flagged with red dot:

– Has NIHMSID = manuscript likely* is in the NIHMS-PMC system. . . . You can find out if is stalled.

– Has neither NIHMSID nor PMCID = manuscript not yet in the NIHMS-PMC system and needs to be uploaded.

• * flaw: assigns temp NIHMSID before files are uploaded.

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Red Dots: Determine why they do not have the PMCID

(or at least the temporary NIHMSID).

Red Dots in NCBI-MyBib = Noncompliant

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NCBI-MyBibliographyNon-compliant papers (red dots)

• Does citation have a NIHMSID? The only place to find NIHMSID is in NCBI-Bibliography.– YES => it is somewhere in the NIHMS system, but

temporary NIHMSID is “not legal” > 3 months from publication date (print date).

• Log in to NIHMS system (with NIH/eRA login),– Use search box in upper right to search by

NIHMSID (or by PMID).

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NIHMS login (use google.com) http://nihms.nih.gov/db/sub.cgi

How to upload, approve initial and web versions

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Confirm it is not waiting on files or approval from the authors:TWO COMMON PROBLEMS:- Awaiting manuscript files (when authors upload themselves) - unfortunately this system generates the (temp) NIHMSID before any files are uploaded .

- “Awaiting author approval for PDF receipt” = 4 steps ending with “Agree” in lower R easy to miss. NOTE: when publishers upload the manuscript—that is all they do; one of the authors must approve PDF receipt to get this process started.

Search by NIHMSID (or

dropdown for PMID)—but

more successful by NIHMSID.

Google NIHMS login; use NIH/eRA

login

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Need to contact author and ask they login and approve PDF receipt

immediately (Attention tab in Manuscript list); if

that author is not available, click “Watch

Manuscript” then “Claim Manuscript.”

System sends email to first author—if no reply in 7 days, they give you

approval rights.

Confirm it is not waiting on files or approval from the authors:- Awaiting author approval for PDF or approval of final web version; initial approval of PDF receipt is 4 steps ending with “Agree” in lower R—easy to miss.- NOTE: when publishers upload the manuscript—that is all they do; corresponding

author must approve PDF receipt to get this process started . . .

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It is going through the system.

Corresponding author waits for the email from NIHMS-

Help asking to approve final Web

version.

It takes approx. 8 weeks in the NIHMS: from uploading the files and initial approval of PDF receipt, to web markup, to final

approval of web version, before the PMCID is assigned.

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It takes approx. 8 weeks in the NIHMS: from uploading the files and initial approval of the PDF receipt, to web markup, to approval of web version,

before the PMCID is assigned.

Corresponding author waits for the email from

NIHMS-Help asking to

approve final Web version.

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Sometimes the NIHMS staff

determine the article is not under PA policy,

and stops it. Need to “Edit status”

in MyBiblio to indicate PA Policy not

applicable N/A.?? Maybe this was

this a Review, or letter to editor, or not

directly funded since 2008?

= why is helpful to see actual full article

(search via Hardin PubMed)

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Why did NIHMS stop processing article?

Use Hardin’s PubMed to find full text article -> determine if it is N/A

under Public Access, as a review of the literature,

editorial, etc. (i.e. not directly funded)

Search by PMID or title from Hardin’s site.

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Hardin Library pays ($4M) to access full text journal

articles

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Submitting to NIHMS

• Upload manuscripts—never the final article as it appears in the journal = property of the journal.

• NIHMS Manuscript Submission System http://www.nihms.nih.gov/help/

– Submit manuscript to NIHMS-PMC system/set embargo http://www.nihms.nih.gov/help/PI-NPMC/PI-NPMC.pdf

– Approve initial PDF receipt http://www.nihms.nih.gov/help/PI-PDFAPP/PI-PDFAPP.pdf ;– Review/approve final web version http://www.nihms.nih.gov/help/WA/WA.pdf

• Hardin Library Assistance http://guides.lib.uiowa.edu/content.php?pid=6167&sid=38874

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NIH Manuscript Submission System NIHMS

• Manuscript uploaded to NIHMS (either by publisher or author) where it is converted to web version and finally loaded into PubMed Central PMC and the PMCID is assigned. **publisher owns the final article as it appears in the journal—so use the manuscript.

• Once assigned, the PMCID is automatically added to the citation in NCBI-MyBibliography. (may be a delay or a day or two)

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Publisher Policies

• Many publishers (Elsevier, Wiley, Springer, LWW, others) will upload final manuscript to NIHMS, if NIH grant acknowledged - may need to remind them. – Remember: immediately after publisher uploads:

corresponding author receives email from NIHMS-Help asking to approve PDF receipt to get it going in the NIHMS-PMC system—or it sits forever.

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Publisher Policies

• Do NOT upload to NIHMS yourself until you determine publisher’s policy; search for information for authors, or publisher policy toward NIH PA mandate on publisher’s website.

• If it is several months from publication and the publisher still has not uploaded to NIHMS, ask/insist YOU do it to make sure it is done.– When in doubt, set embargo for 1 year from date of

publication (print date).

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NIHMS login (use google.com) http://nihms.nih.gov/db/sub.cgi

How to upload, approve initial and web versions

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“Help and FAQ” link in lower left of

NIHMS login page:

How to submit and approve initial and

web versions.

http://www.nihms.nih.gov/help

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Use the NIHMS NIH Manuscript Submission systemto (1) check status of papers with NIHMSIDs and (2) upload manuscripts and approve versions for

inclusion in PubMed Central

Log in

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We’ve covered a lot:

• Using NCBI to manage citations for PA, for progress reports, for Biosketch.– Edit Status if Exempt; Associate Grants; Download pdf list of

citations• Noncompliant: Is paper is stuck in NIHMS? = check

NIHMS and/or Compliance monitor PACM (I can for you).• Noncompliant: Paper is not in NIHMS-PMC system and

needs to get started so it gets a PMCID• Get the manuscript into NIHMS-PMC system -

Request/urge Publisher - Author upload manuscript/set embargo

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Thank you

• Please feel free to contact me about – using your NCBI Bibliography – determining applicability for articles – finding publisher policies re: submitting to NIHMS– reporting publications in progress reports– Finding where/if manuscripts are stuck in NIHMS– questions or would like me to demo in your office

Oliva Smith Oliva-smith@uiowa.edu 335-3708

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What to do about the non-compliant papers

• No NIHMSID—try looking up NIHMS via the PMID and may it find NIHMSID . . . but unlikely.

• Better (if no NIHMSID) = PACM: Public Access Compliance Monitor (email era@uiowa.edu to get PACM rights). Log in as for NCBI.– Google [nih pacm] or http://www.pubmedcentral.nih.gov/utils/pacm/

– Search by PMID in upper right.– Tells who is the corresponding author follow up/remind

them to check NIHMS and approve.

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PACM Public Access Compliance Monitor is a “look up” tool. Email era@uiowa.edu to request PACM rights. Log in as for NCBI.

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PMID

PACM lists the publisher, whether it is a Method A/PMC journal—meaning no action is required to get the article to PMC.

IS THE ARTICLE STALLED? Lists when files uploaded to NIHMS and by whom; Date of initial PDF approval and by whom; Date tagging complete, Grants acknowledged in the article (= not “officially linked” as in NCBI)

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PACM is probably the best way to find where the article is if it is stuck in the system.

But not all articles in the PACM are under the NIHPA Policy.