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NIH Public Access: Helping Researchers ComplyOliva Smith, Division of Sponsored ProgramsJune 12, 2013

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https://becker.wustl.edu/sites/default/files/nih_resources_chart.pdf page 1

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The NIH Public Access PolicyThe Policy . . . . states: The Director of the National Institutes of Health shall require that [Who] all investigators funded by the NIH submit or have submitted for them to the National Library of Medicine’s [Where] PubMed Central an electronic version of their [What] final, peer-reviewed manuscripts [When] upon acceptance for publication, to be made publicly available no later than 12 months after the official date of publication . . . consistent with copyright law. http://grants.nih.gov/grants/guide/notice-files/NOT-OD-08-033.html

When = TIMING(1) request/arrange for the manuscript to get to the NIHMS-PMC

system as soon as possible.(2) Designate the article to be viewable in PMC a year, (or less*) from

date of publication [publication date = print date].* This delay or ‘embargo’ period is specified by the journal/publisher. 4

Why you need the PMCIDFor non-competing continuation grant awards with start date July 1, 2013 or beyond:• NIH will delay processing of an award if publications arising from it

are not in compliance with the NIH public access policy. http://grants.nih.gov/grants/guide/notice-files/NOT-OD-13-042.html

• Compliance = Publication must be in PubMedCentral PMC database (tho possibly not viewable until after embargo). Paper in PMC is designated with PMCID.• BOTTOM LINE: must have PMCIDs to get $$

• Investigators will need to use My NCBI to enter papers onto progress reports. Papers can be associated electronically using the RPPR, or included in the PHS 2590 using the My NCBI generated PDF report. 5

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Getting the publication into PMC depends on Journal/Publisher: Four Methods

Method A Method B Method C Method D

Version of Paper Submitted

Final Published Article

Final Published Article

Final Peer-Reviewed Manuscript

Final Peer-Reviewed Manuscript

Task 1: Who deposits the paper?

Publisher direct to PMC

Publisher direct to PMC

Author or designee, via NIHMS

Publisher, via NIHMS

Task 2: Who approves paper for processing?

Not Applicable

Not Applicable Author, via NIHMS

Author, via NIHMS

Task 3: Who approves paper for PubMed Central upload?

Not Applicable

Not Applicable Author, via NIHMS

Author, via NIHMS

Participating journal/publisher

Method A Journals have agreement with NIH

Make arrangements with these publishers charge $$

Check publishing agreement

Make arrangements with these publishers

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http://publicaccess.nih.gov/submit_process.htm

If the publication appears in a journal on this list = Method A.

Journal submits to PMC without author involvement.

http://publicaccess.nih.gov/submit_process_journals.htm

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Submission “Method A” Journals

• Method A: The journal has a formal agreement with NIH to deposit all final published articles in PubMed Central PMC without author involvement.

• Use PMCID in citation to indicate in PubMed Central PMC; • To find PMCID: search PubMed (use Hardin Lib link or google

PubMed) by title of article abstract with PMID lower left, PMCID lower right (if available).

• if the PMCID is not available from “Method A” journals (ONLY those listed on the link as Method A journals (search for the title in PubMed) can use "PMC Journal - In Process”

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Submission “Method B” Journals

• Method B: Author makes arrangements for publisher to deposit a specific final published article in PMC, for a fee.

• These publishers also have a FREE option. (Method C or D)• These journals do not automatically deposit every NIH-funded

paper into PMC; author chooses the journal’s fee-based open access option for publishing specific article.• Examples: Springer “OpenChoice” $3000• Elsevier “Open Access” $500 - $5000 depends on journal• SAGE “Choice” $3000• Taylor & Francis “iOpenAccess” $2950• Wiley-Blackwell “OnlineOpen” $3000

• To cite articles from “Method B” use PMCID if available; if not: "PMC Journal - In Process” because you paid $3000 for it!

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Submission “Method C” Journals

• Method C: “Author information” on the journal’s webpage instructs author to deposit final peer-reviewed manuscript into the NIH Manuscript Submission NIHMS-PMC System. (which is why you need to keep copy of manuscripts)

• Author must complete all steps in NIHMS Manuscript Submission system to get the article through NIHMS to PMC PubMedCentral PMCID.

• Timing: NIH awardees are responsible for ensuring manuscripts are submitted to the NIHMS upon acceptance for publication. • Set embargo/delay when uploading into NIHMS-PMC system, so full-

text may not appear in PMC before one year = publisher happy.• NIHMS ID is temporary - only valid within 3 months of publication

date---after that must have PMCID. 11

Submission “Method D” Journals

• Method D: “Author information” on journal’s webpage says journal/publisher will deposit final peer-reviewed manuscript into NIHMS-PMC system.• Usually author must request—or should request so publisher does

this ASAP. Set embargo when uploaded to NIHMS.• Author must complete all remaining steps in NIHMS system for

the article to get to PMC PMCID.• http://publicaccess.nih.gov/select_deposit_publishers.htm#d

• Timing: NIH awardees are responsible for ensuring manuscripts are submitted to the NIHMS upon acceptance for publication. • Set embargo/delay when uploading into NIHMS-PMC system, so full-text

may not appear in PMC before one year = publisher happy.• NIHMS ID is temporary - only valid within 3 months of publication

date---after that must have PMCID.

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PMCID – PMID: what’s the dif?

• PubMed Central PMC (since 2000) full-text biomedical journal articles, assigned the PMCID; articles freely accessible (w/o going through publisher’s site).

• PMCID = article is in PubMed Central PMC = complies with NIH Public Access policy.

PMCID: PMC7654321 PMC + 7 numerals (so far)• PubMed assigns PMID to citations & abstracts from

MedLine, life science journals, books, etc. PubMed does not contain FULL TEXT – unless library links $$.PubMed has nothing to do with NIH Public Access.

PMID: 23314567 eight numerals14

Hardin Library’s PubMed url to take advantage of this service. http://www.ncbi.nlm.nih.gov/pubmed?otool=uialib

Costs $4 million for UI Libraries to provide links to journals for full text from PubMed.

PMCID assigned

For us in academia, PubMed works great because our libraries link citation record to the full text; if use PubMed

from home you are not linked to the full text.

Article not available in PMC but has PMCID, i.e.

honoring the Blood’s 12 month delay/embargo.

PMID

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Common Questions

• Is the paper under this policy?• How do I know how if the journal submits to

PMC, or should author submit it?• How do I find if article is in PMC, has a PMCID?• What if article not in PMC and should be?• How do I submit the article to the NIHMS?• What if article is stalled in NIHMS-PMC system?

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Is the paper under this policy?• Peer-reviewed;

• Reviews, editorials, commentaries, conference proceedings are exempt. (designate N/A in MyNCBI)

• Must be Latin script. Russian, Japanese, etc. exempt.

• Accepted for publication in a journal on/after April 7, 2008; Use the Hardin PubMed link http://www.lib.uiowa.edu/hardin/ to find full text article, title page often includes date accepted.

• And, arises from:• Any direct funding from NIH grant or cooperative agreement

active in Fiscal Year 2008 or beyond, or;• Any direct funding from NIH contract signed on/after April 7,

2008, or;• Any direct funding from the NIH Intramural Program, or; • An NIH employee.

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How do I know if a journal submits to PMC?• First check if it is Submission Method ‘A’ (slides 7, 8). (Use

google.com) http://publicaccess.nih.gov/submit_process_journals.htm

* If yes, [horray] = no author involvement. * Cite with PMCID or “PMC Journal in process.”

• If No: need to find out journal’s author info.1. Find journal’s webpage “author information.”2. Or use google.com to find [ Sherpa-Romeo ] = db of publisher info http://www.sherpa.ac.uk/romeo/ .3. Or U of Toledo link http://mulford.meduohio.edu/instr/ for journals in health sciences.

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How do I find the PMCID?

• Use PubMed to find the abstract with PMID lower left and PMCID lower right if it has one.

• Converter Link: Use PMID to find PMCID or NIHMSID: http://www.ncbi.nlm.nih.gov/pmc/pmctopmid/

Use google.com to find: PMCID converter • If is has a PMCID add it to citation.

• If has NIHMSID (temporary id) => in the NIHMS-PMC system. Can use NIHMS id for up to 3 months after date of publication, by then supposed to have PMCID.

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What if article not in PMC or the NIHMS-PMC system?• Check journal’s policy: do they send or does author (i.e.

Method C or D)?• If journal (Method D), contact and request they do this asap.

• OR ask journal if YOU can submit manuscript (not .pdf of the article) to NIHMS-PMC yourself—so you know it is done (esp if the article is a year or more from date of publication).

• Submit to NIHMS-PMC system http://nihms.nih.gov/help/faq.shtml

• Manuscript – not a .pdf of the article as it appears in the journal (which is the property of the journal) 20

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NIHMS NIH Manuscript Submission System

• Submitting the paper into PubMed Central begins with the NIHMS NIH Manuscript Submission System http://nihms.nih.gov/help/faq.shtml

• Manuscript – not a .pdf of the article as it appears in the journal (which is the property of the journal)

• ALWAYS login via “NIH & eRA” route; I use google to find “NIHMS login” link.

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Log into NIHMS

Athttp://www.nihms.nih.gov/db/sub.cgi

Or use google to

find NIHMS login.

Includes overview of manuscript submission

process (next slide)

ALWAYS log in via “NIH & eRA” route

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Make any corrections in web approval; only errors that

affect accuracy of the article, since they have to retag it.

1.

2.

3.

Step 2 Approval generates NIHMSID = ok to use within 3 months of publication date.

Takes ~4 weeks

between Steps 2 & 3.

Step 3 Approval will

generate PMCID.

What if article is stalled in NIHMS?

• If publication sitting in NIHMS longer than a month, it may be stalled (somewhere between steps 1, 2 or 3).

• Author check if STALLED in NIHMS system. Log in to NIHMS http://www.nihms.nih.gov/db/sub.cgi • Check for articles under Stalled Tab• Search for manuscript with NIHMS or PMID and Watch or

Claim it. (see NIHMS FAQs http://nihms.nih.gov/help/faq.shtml#q16 )

• Must be an author or PI to Claim a record.

• If you suspect article Stalled—contact me and I can look in the “Public Access Compliance Monitor” PACM = an Excel file listing articles for UIowa. 25

Log in to NIHMS

http://www.nihms.nih.gov/db/sub.cgi or use google: NIHMS login

Find stalled article(s) in Stalled tab in Manuscript List.

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FAQs & Help

NOTE: due to volume, NIHMS says it will take 7 - 10 business days to

answer your emails.

If I one of the authors for an article that is stalled and the first author is not available to “unstall it” I can “claim” it (must be an author).

I do so by putting the NIHMS ID or the PMID in the search box and “Find Manuscript”.

Claiming an article to move it

through the NIHMS system

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Must be one of the authors (which I am not), but if wanted to Claim click “Watch

Manuscript” then supposed to get the Claim Option

Claiming an article to move it

through the NIHMS system

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FAQs & Help

https://becker.wustl.edu/sites/default/files/nih_resources_chart.pdf page 1

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What is My NCBI?

A tool integrated with PubMed (not PubMed Central) to track literature searches, collections of citations, and public access compliance. http://www.ncbi.nlm.nih.gov/books/NBK3842/

• ALWAYS log in to NCBI via NIH & eRA Commons log in.• Must link eRA Commons accounts and MyNCBI • Once linked, users can associate publications with NIH grants.• Tracks NIH Public Access compliance Award View.• The only way to enter publications into RPPR progress report.• Creates the publications section (Section E) of PHS 2590s for U01

which still uses paper.30

Use eRA Commons

Not here

31If you “Sign in directly to NCBI” it

creates a duplicate account = more confusion!

To LINK My NCBI with

eRA Commons,

click username

If publications in eRA Commons do

not match up with papers in

MyNCBI-MyBib—must link eRA to

MyNCBI.

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Common Q: Are your NCBI and eRA pages linked?

If not linked, would click here to Link.

May need to log out/back in---but now eRA Commons and NCBI My Bib publications should be same list.

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Want to see PA status for each

publication.If you do not see this view

with blue-shaded “Public

Access Compliance

Status” go to next slide . . .

Will not work in old version

of Internet Explorer

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Designees can not see this Award View.

Common Q: How do I see this view: “Award View”

How do I get to the Award

View? If you see this

view, i.e. without blue

shaded PA status after

each citation, click “Display

Settings.”

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In View Column Select: AwardSort by: Public Access Compliance

Grouping: by citation type.

Then click “Apply”37

Now you see Award View,

with blue shaded area after each citation.

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Icon = Linked

Needs PMCID

Add/delete award

Can change only those with yellow icon. Gray “lock” icon = LOCKED & cannot disassociate award from publication.

NOTE: if PI associates grant with publication it is LOCKED and takes email to

NCBI to disassociate. PIs must be sure they want publication associated with

grant.

Red Dot = needs attention!

NIHMS is only “good” w/i 3 mo.

of pub. date.

Add Award: See NLM Tech Bulletin: www.nlm.nih.gov/pubs/techbull/ja12/ja12_myncbi_new_features.htm

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To sort by how papers got into MyBib

Making bib public

generates url to share with

others.

“Edit settings” to Add delegate. NOTE: the delegate does not have access to same functions as PI.

Add more publications

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Want to include paper but it is

exempt from PA Policy: how to denote this to

prevent red flag?

Exempt: accepted before April 2008; not peer-reviewed; not Latin script;

or not supported by

NIH.

Click “Edit Status”

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Select option. Non-peer-reviewed

papers are designated here also:

editorials, reviews, letters, conference

talks, poster sessions.

Save & Close.

Citation will have green N/A.

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Generating Award

Compliance Report PDF for

your bibliography..

Select “Linked to my awards”OR select check boxes next to publications. 43

Checking compliance of each article.

What to do about flagged

article?Biochem J2012 July

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What to do about flagged article?1. “Edit Status” if article is exempt:

non-peer-reviewed; accepted for publication prior to April 7, 2008.

2. Check in PMCID converter to see if PMCID is assigned.No PMCID but has NIHMS id so in NIHMS-PMC system.

3. Author/PI can log in to his/her NIHMS and look for Stalled Tab.• PI can CLAIM the article if it is STALLED.

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Checking compliance of each article.

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Edit Status

Want to include paper

but it is exempt from

PA Policy: how to denote this to prevent red

flag? Edit Status asExempt: accepted

before April 2008; not

peer-reviewed; not Latin script; or not supported

by NIH.

What to do about flagged article?1. “Edit Status” if article is exempt: non-peer-reviewed; accepted

for publication prior to April 7, 2008.

2. Check in PMCID converter link to see if PMCID is assigned. [google PMCID converter]No PMCID but has NIHMS id so in NIHMS-PMC system.

3. Author/PI can log in to his/her NIHMS and look for Stalled Tab.• PI can CLAIM the article if it is STALLED.

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No PMCID

http://www.ncbi.nlm.nih.gov/pmc/pmctopmid/ [or google PMCID converter]

NIHMS number tells us it is in NIHMS-

PMC system

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1. Enter PMID

What to do about flagged article?1. “Edit Status” if article is exempt: non-peer-reviewed; accepted

for publication prior to April 7, 2008.

2. Check in PMCID converter link to see if PMCID is assigned. [google PMCID converter]

No PMCID but has NIHMS id so in NIHMS-PMC system.

3. Author can log in to his/her NIHMS and look for Stalled Tab.

• PI can CLAIM the article if STALLED.49

Log in to NIHMS

http://www.nihms.nih.gov/db/sub.cgi

or to find login use

google.comNIHMS login

If I am the first author of the article, or the author who approved the initial upload into the NIHMS system, I will find the stalled article here in my

Manuscript List.If I an author other then the first or other than the initial approving author, or if

I am the PI, I can get the stalled article going by ‘claiming’ it. (next slide)50

If I am one of the authors (or PI) for an article that is stalled and the first author is not available to “unstall it” I can “claim” it (must be an author or PI).

I must first find it using NIHMS ID or the PMID in the search box and click “Find Manuscript”.

Claiming an article to move it

through the NIHMS system

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Must be one of the authors. If want to Claim click “Watch

Manuscript” then will to get the Claim Option, which prompts the system to

send first author email asking if you can claim—if no response, you get email

indicating it’s yours to approve and move through the system.

Claiming an article to move it

through the NIHMS system

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Research Performance Progress Report RPPR

• http://grants.nih.gov/grants/rppr/index.htm • RPPR: required for all awards issued under the Streamlined Non-

competing Award Process (SNAP), and all F awards with budget start dates on/after July 1, 2013. U01 mechanism still uses paper 2590.

• Publications cannot be manually added in RPPR—must go via My NCBI-My Bibliography. ALWAYS log in via NIH & eRA login.• MyBib use check box to populate RPPR’s Products/Publications

section.• If not all papers appear in NCBI MyBib, but are in eRA—must LINK

(slides 28-29)

• RPPR lists Public Access compliance status; • if no PMCID = “NONCOMPLIANT” 54

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http://dsp.research.uiowa.edu/files/dsp.research.uiowa.edu/files/NIH%20RPPR%20Basic%20Guide.pdf

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Edit

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Research Performance Progress Report RPPR

• Part C - Products = Publications

• “Are there publications or manuscripts accepted for publication in a journal or other publication during the reporting period resulting directly from the award?”

• If Yes - select from list provided—if not all publications are there:• Login to My NCBI - check box next to title to

associate/transfer publication to this progress report. ALWAYS log in to NCBI with eRA & NIH login.

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Research Performance Progress Report RPPR

• RPPR: Step-by-Step Guide http://dsp.research.uiowa.edu/files/dsp.research.uiowa.edu/files/NIH%20RPPR%20Basic%20Guide.pdf

• RPPR FAQs http://grants.nih.gov/grants/rppr/faqs.htm

• Progress Report Additional Materials PRAM - used to add PMCIDs if you get them after initial RPPR sent.

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Avoid Delays in Compliance

• Find journal’s policy, start process as soon as accepted.

• Keep copy of manuscripts.

• NCBI: (1) Link NCBI to eRA Commons; (2) Display Settings ->Award View; (3) Associate appropriate paper(s) with appropriate award(s).

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Avoid Delays in Compliance

• NIHMS: log in http://www.nihms.nih.gov/db/sub.cgi • ALWAYS log in via “NIH & eRA” link.

• Set up manuscript• Approve pdf receipt (be sure to go through all the

steps) assigns NIHMS (temporary), and • After ~ 4 weeks, approve web version =>PMCID.• Investigators see only articles in NIHMS-PMC system;

if article has not started in NIHMS, not in your Manuscript Summary page.

• Stalled articles -- see “Stalled” tab; use search box to find articles to Watch or Claim. 62

I hope I helped make this graphic a little more clear.

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We are here to help you

• I will send monthly reminder notices to PIs with non-competing renewals due the following month.

• DSP’s NIH Public Access webpage http://dsp.research.uiowa.edu/nih-public-access-policy

• Hardin Library Public Access Policy Guide http://guides.lib.uiowa.edu/nihpublicaccess

• Janna Lawrence janna-lawrence@uiowa.edu, liaison for Public Access, will assist with answers to your questions.

• Hardin Library also will submit to the NIHMS-PMC for authors http://guides.lib.uiowa.edu/content.php?pid=6167&sid=38874

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Thank you

• I am happy to answer questions and/or provide training sessions or work with you one-on-one.

• Please feel free to contact me with questions.Oliva Smith Division of Sponsored Programs DSPoliva-smith@uiowa.edu 335-3708

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