Managing Publications with NCBI-My Bibliography

1. Managing Publications with NCBI-My Bibliography Oliva Smith Division of Sponsored Programs DSP oliva-smith@uiowa.edu Spring, 2014

2. 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.

3. https://becker.wustl.edu/sites/default/files/nih_resources_chart.pdfhttps://becker.wustl.edu/sites/default/files/nih_resources_chart.pdf Created by:

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

5. 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.

6. Setting up your NCBI account. Go to (or google) PubMedhttp://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 MyNCBIFrom http://libguides.library.umkc.edu/content.php?pid=493199&sid=4049213 First-last@uowa.edu First-last@uowa.eduFirst-last@uowa.edu

7. 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.

8. PMID and PMCID are different 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.

9. 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

10. 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 status • Assign award • (3) Create .pdf report for non-RPPR reporting.

11. 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

12. Screen shot of my “fake” NCBI Biblio

13. Screen shot of my “fake” NCBI Biblio See whole 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.

14. Clicked “Manage my Bibliography” to get to this page. Icon = linked to eRA Commons If no eRA icon = NOT LINKED. Must link MyBiblio to eRA Commons. Click log in name/email at upper right.

15. To return What you should see linked.

16. Indicates linked to eRA Commons “Add Citations” NCBI Biblio. (pp. 1 - 4 of handout)

17. “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. (most common) “Goto PubMed” to (1) search by PMID or title to add single article. OR (2) search by author, select relevant citations and add in one batch. Handout p. 2

18. Manual citation for an article: Required fields - Title- Last Name- Journal • YearThis way,if paper has just been submitted can include this paper in MyBibliography. • “Forthcoming” = submitted + accepted

19. Here it is

20. Adding new items using Manual Citation puts Meeting Abstracts,Presentations,Book Chapters, etc. in separate categories in MyBibliography(following the list of publications)

21. Add a citation using the PMID.

22. 1 PMID or title 2 3 4 5

23. Add Many Citations to NCBI- MyBib at once Search by author in PubMed Send to MyBibliography Select citations Handout p. 2

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

26. Default Sort by date = newly added citation [year 2010] is in the middle of the list

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

28. 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 registerif he/she does not have a My NCBI account.

29. (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. Click

30. Add/delete Awards (handout 10 – 14). 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.

31. 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 funding2from 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

32. 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. 

33. Edit Status

34. 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).

35. You have: Added the Award(s) And (if applicable) Edited Status Citation with Green = has the PMCID and is In Compliance with PA Policy. Papers accepted for publication prior to April 7, 2008 are N/A. Manually-entered Meeting abstracts and Presentations are automatically designated N/A since NIH PA does not apply to this type of correspondence.

36. 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”

37. 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 . . . .

38. Creating Award Compliance Report - for non-RPPR In NCBI-Bibliography - Add citations manually for manuscripts submitted and accepted (p. 3 handout). For non-RPPR reports: (p 16 of the PHS 2590 instructions) http://grants.nih.gov/grants/funding/2590/phs2590.pdfE. 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 . . .

39. Preparing NCBI-Bibliography- generated report of publications, as per PHS 2590 instructions (non-RPPR) 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) 4 3 1 2

40. 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?

41. http://grants.nih.gov/grants/rppr/rppr_instruction_guide.pdfor use google.com RPPR Instructions RPPR Instructions for Section C- Products (i.e. publications) start on p. 55

42. Reporting publications in RPPR progress report 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? http://grants.nih.gov/grants/rppr/rppr_screen_shots.pdf

43. Publications in Biosketch NCBICollections -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 SciENCVBiosketch.

44. - SciENCV = Biosketch “Show/hide entries” to select for inclusion in BioSketch. PMCIDs are included if available, but otherwise no Public Access compliance alerts.

45. 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.

46. 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.

47. Red Dots in NCBI-MyBib = Noncompliant Red Dots: Determine why they do not have the PMCID (or at least the temporary NIHMSID).

48. 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).

49. NIHMS login (use google.com)http://nihms.nih.gov/db/sub.cgi How to upload, approve initial and web versions

50. Search by NIHMSID (or dropdown for PMID)—but more successful by NIHMSID. Google NIHMS login; use NIH/eRA login • 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.