Using My NCBI & My Bibliography


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  • Hello and welcome to our session on using My NCBI and My Bibliography. For those of you I don’t already know, my name is Tom Zucker-Scharff. I can be reached internally at x3512 or by email at I am, among other things, in charge of publication tracking for the Cancer Center.Today we will cover various aspects of compliance with NIH Policies, specifically the Public Access Policy. We will only briefly look at the various methods of submitting a publication to PubMed Central. The Library will be a giving a workshop addressing submission methods on April 9th – anyone who deals with this should attend that workshop.Since this is the fourth time that the Cancer Center is presenting this, we welcome any suggestions and, of course, any and all questions as they arise.
  • Since April 7th, 2008, the NIH has mandated that any award request, whether a renewal or competitive award, must list the Pub Med Central ID (PMC ID), instead of the PubMed ID (PMID) with each citation. Beginning on July 1, 2013, the NIH starting enforcing this policy: according to the NIH policy “Compliance with the NIH Public Access Policy is not a factor in the scientific and technical merit evaluation of grant applications. Non-compliance will be addressed administratively, and may delay or prevent awarding of funds.”In an attempt to make compliance easier, the NIH has provided researchers with several tools to monitor the compliance of each of their publications. These are eRA Commons, My NCBI, My Bibliography, and the NIH Manual Submission System (NIHMS).<start slides>In this session we will discuss:Creating a My NCBI accountLinking said account to your eRA Commons accountPutting any publications which are not already in your My Bibliography into it.
  • Linking publications to a funding sourceMaking publications compliant with the NIH Public Access PolicyAssigning delegates and what they can doNote that each one of these topics could be a session onto itself, so we will attempt to go over the most salient points. When we are finished you should be able to accomplish each one of these tasks with only minor assistance.
  • Since the NIH no longer allows manual entry of publications into eRA Commons,They have provided links to the places into which you should be entering your publications either through a pubmed search, manually entering them, or beginning the submission process in the NIH Manual Submission System. My NCBI has tools to help you track your publications and keep them compliant with NIH policies.
  • This is an explanation of who needs to include the PMCID in any citation in their grant application or progress report (example taken from the NIH website):Author A has no NIH supportAuthor B used Salary Support from his mentor’s NIH AwardAuthor C used her NIH award to support the researchAuthor B’s Mentor has an NIH awardAnother author (any other author other than the 4 mentioned) wants to cite the publicationThe first 4 MUST include the PMCID in the citation. Any other author does not need to include the PMCID.
  • Before going any further, it should be noted that much of what we are going to go over can be done by a delegate, BUT remember that someone who is an eRA Commons delegate IS NOT a My NCBI delegate. Once you have created a My NCBI account , you can assign a delegate in My NCBI separately (although it can be the same person). This delegate must also have their own My NCBI account (if they don’t have one they will need to create one in order to be a delegate), although they need not have an eRA Commons account.The way in which a delegate accesses and sees various items will be slightly different than the way in which a PI sees the same items. In this presentation I will, mostly, be looking at each item from a PI’s perspective. I will be happy to address any delegate questions.Briefly, how many people here already have a My NCBI account?
  • If you do not already have aMyNCBI account, you can register for one for free and link it to your eRA Commons account. To do this start the browser you normally use <next> and go to PubMed by typing in the location bar at the top <next>, then pressing enter. You will be redirected to PubMed homepage. <next> Click the Sign in to NCBI link in the upper right hand corner of the screen. <next> On the resulting page click the “Register for an NCBI account” link under the “Sign in” button.
  • Enter the information to create a new account (starred fields are required), <next>then enter the characters you see in the graphic (called a captcha) <next> In the box below the graphic and <next>Then click “Create account.”
  • <next>If you are successful you should see a confirmation screen<next>and then be redirected back to the Pubmedhomescreen, but you will be logged in<next> You will see the name you used to register in the upper right hand corner next to a “My NCBI” link and a “Sign Out” link.
  • All changes that are made in the My NCBI system will appear instantaneously in the eRA Commons linked to that account.Q:I entered my citation in the eRA Commons and not via My Bibliography. Why does my citation not display a grant-paper association status?A: Because My NCBI's My Bibliography is the primary location for PD/PIs [Program Director/Primary Investigator] to manage their bibliographies, and in the interest of maintaining accurate and complete data, eRA Commons does not allow a PD/PI to enter his or her citations directly into Commons. As such, grant-paper association statuses will appear only for citations added to a My Bibliography account that is linked with a eRA Commons account.
  • <next>When you are logged into PubMed, the name you used to register for MyNCBI appears in the top right corner<next>Click on your login name<next>In the following screen, <next> locate the Linked Accounts section. If your eRA Commons account is not listed, click the Change button to add it.
  • Once you click on the Change button in the previous screen you will be presented with a this search screen <next>In the “Search for account name:” box type in NIH (upper or lower case). <next> Then click on the first link.<next> When you are asked to login, enter your eRA Commons login name and password.<next> Under “Your Linked Accounts”, “NIH & eRA Commons” should now appear as one of the linked accounts.
  • If you want to be sure that the accounts are linked correctlyClick on the My NCBI link in the upper right hand cornerLocate the My Bibliography section click Manage my BibliographyIf you are a delegate, locate the Collections section and be sure that the person you are a delegate for has an entry there and click that linkIf the accounts are linked, an eRA Commons logo appears at the top of the page
  • First you should check to see if your publications are in your My Bibliography.If you are logged in and have clicked My NCBI, <next> the My Bibliography section will list how many publications are in your bibliography <next>If no publications appear, use the Search section just above the My Bibliography section to add publications to your bibliography.Note: you will NOT be able to add a delegate unless you have at least one publication in your “My Bibliography.”
  • To search for an authorJust enter the author’s last name, for example “scharff” or scharff[au] (denoting author)You can add a date or date range by using the word AND followed byOpen parentheses - (beginning date or yearOpen bracket - [dp for Date PublishedClose bracket - ]Colon to denote “between” - :ending date or yearOpen bracket - [dpClose bracket - ]Close Parentheses - )(2013[dp]:2014[dp]) denotes publications which have a “Date Published” ([dp]) between 1/2013 and 12/31/2014Scharff[au] AND (2013[dp]:2014[dp]) means publications authored by Scharff which also have a “Date Published” ([dp]) between 1/2013 and 12/31/2014<next>Once you click search you will be presented with the results page. On the far right side are the words “Send to:” followed by a down arrow to open a dialog box. Click the arrow next to “Send to:”
  • <next>Choose My Bibliography then click <next> Add to My Bibliography.<next>You are now given the choice to put the publications into My Bibliography or Other Citations. Or if you are a delegate, you will be able to choose the PI’s library.<next>Other Citations is generally used for citations that are not yours, but you wish to keep track of. Other citations:Other Citations is under “Collections”. PubMed “Collections” are NOT updated. So any citations put into “Other Citations” or a collection other than “My Bibliography”, or in a delegates case their PI’s bibliography, will be exactly the same as when you first saved them to one of your collections.
  • In order to see the “edit status” link or “add or delete award” link, or see the public access compliance status of a publication, you will need to be in awards view.First your account must be properly linked to your era commons account, this can be seen if you see an eRA logo on your My Bibliography page.The Display settings will usually be set to List view, Sort by Date, group by citation type
  • Next click the down arrow next to Display SettingsFinally click Award under View and click apply.When you are done the resulting words next to Display Settings should reflect the changes you made.
  • <next><next><next>Click Search once you have entered your search terms<next>In the resulting search, click the arrow next to the item you searched to select a specific grant. Put a check mark in any of the boxes next to the grant you wish to associate with the citation(s) in question<next>click “Save”
  • For example, in order to link publications to the Cancer Center core grant (P30 CA013330), which you should doif you use any of the Shared Facilities supported by the Cancer Center, or if the publication results from Cancer Center Pilot project fundingClick the Search/Add other awards tabIn the first name field enter, I. DavidIn the last name field enter, GoldmanClick the Search buttonIn the results box, click the first down arrowClick on the first box to put a check in itClick save to assign the CCSG as a funding source to the specified publication.
  • If, in your “My Bibliography”, no publications have been selected, then the buttons at top will be greyed out and unavailable.
  • Select publications to which you would like to assign awards by placing a check mark in the box next to the publications.
  • Click the “Assign Awards” button to bring up the Assign Awards dialog.
  • Choose the award(s) from your list, the Other Awards list, or do a search to find the correct award. When you are done and have selected the correct award(s) – by putting a check mark in the appropriate box(es), click save to assign them to the selected publications.It should be noted that if you try to associate a grant to multiple publications and one of the publications already has the same grant associated with it, you will not be able to make the association.
  • In my conversations with the NIH helpdesk, I brought up a rather frustrating problem for some of us. How can you easily find things on this page especially in the unsorted filters box?The answer is rather easy. To just do a find in the filters boxMake sure you click in the white area of the filters box, not checking any grantPress the Ctrl and F buttons on a windows machine or Command and F on a MACThe search box appears 3a. in the top left corner of Internet Explorer 3b. In the bottom left corner of FireFox 3c. In the top right corner of Chrome 3d. In the top right corner of Safari4. Type in the grant number or what ever you are searching for (p30 ca013330 for the Cancer Center Support Grant)5. It will find each instance of what you typedYou can do the same for the whole page if you are looking for instances of a certain grant or PMIDs.
  • This is essential since funding can and has been withheld if the publications are not compliant.Publications must be associated with said funding source, or ANY grant on which you wish to list them.If you have not already done so, reread the blast email Ed Burns sent out regarding the need to address compliance as soon as possible.
  • Actually making a non compliant publication compliant is a whole session onto itself (there will be a Library workshop on April 9th which will delve into more of the facets of this process). For now we will cover how to change the state of compliance for a publication that has already been submitted or is not supported by NIH funds.Using the “Edit Status” linkClick edit statusAnswer yes or no to whether the specified publication is supported by NIH fundsNO – click no and save and your publication will be marked as NAYES – click yesA dialog will appear asking for further informationChoose to begin submissionEnter existing NIHMSIDThe publication is being taken care of by the journalChoose why the NIH Public Access Policy does not apply
  • In My Bibliography, each publication listed in the award view will have the compliance status associated with it. The various different icons are outlined here. Any publications that have a question mark next to them (meaning there is not enough information to determine compliance) must have the status edited using the “Edit Status” link. Publications out of compliance should be ameliorated as soon as possible.Note that if you receive a PMCID it might take as long as 7 days to reconcile as in compliance in the My Bibliography view.
  • This chart shows the basic methods of submitting a publication to PubMed Central. This will be covered more comprehensively in the April 9th Workshop hosted by the Library.This particular chart is separated into sections by<next> What version of the paper is submitted to PMC<next> Who is responsible for depositing the publication<next> Who is responsible for approving the publication for processing<next> Who is responsible for approving the version that PMC will display<next> A list of journals/publishers which have agreed to each method<next> You can check out this link for the NIH’s overview of submission methods<next> And this will show you a step by step guide to submitting a publication
  • In order to add a delegate, who can do most of the tasks to meet compliance regulations, you must log into Pubmed. Once logged in, click on the My NCBI link. You will be directed to the page which contains the My Bibliography component. <next> Under My Bibliography, click on the settings link (you will only see this link if you have publications in your bibliography)On the settings page, there is a section called Delegates. <next> This section will list any delegates you already have in My NCBI and allow you to create new ones.Click the “Add a Delegate” link to add a new delegate (remember your delegate MUST have a My NCBI account in order for them to accept and use delegation). <next>Enter the email of the person you wish to add as a delegate, then click the “Add Delegate” button.
  • <next><next>Click save to save your changes.<next> An email will be sent to the email you entered in the previous page. In order to accept or decline the delegation request, the person must click the link in the email received from myncbiIf they do not have a myncbi account they will be asked to create one at this point.<next> The link will take them to a page where they can confirm or decline the invitation. <next> <next>Either action will generate information you will see in your account<next> Notice that by accepting a delegation request the delegator will now see a change from “Awaiting confirmation” to a listing of the person’s account
  • Using My NCBI & My Bibliography

    1. 1. USING MY NCBI AND MY BIBLIOGRAPHY Thomas Zucker-Scharff Phone: 718.430.3512 Cell: 914.275.1048 Email: April 4, 2014
    2. 2. Introduction • Creating a MyNCBI account • Linking your eRA Commons account to the MyNCBI account • Putting your publications into your MyBibliography There are several components to correctly using My NCBI’s My Bibliography. All of these must be done by October of 2014, when the NIH mandates that ALL awards MUST use My Bibliography. We will cover:
    3. 3. Introduction • Linking the publications to your grants/awards • Making publications compliant with the NIH Public Access Policy • Assigning a Delegate / the Delegate’s View
    5. 5. NIH Will Open the Research Performance Progress Report (RPPR) for All Type 5 Non-SNAP Progress Reports on April 25, 2014 Policy stating that PD/PIs will be unable to manually enter publications into eRA Commons Location of literature Citations
    6. 6. Who includes the PMCID? Author A has no NIH Support Author B has Used Salary Support from Mentor’s NIH Award Mentor Author C used her NIH award to support the research Including PMCID in citations (NIH) Anyone else who cites the paper Must cite using PMCID DOES NOT NEED TO INCLUDE PMCID
    7. 7. • Competing Applications • Non-competing Continuation Progress Reports • Final Progress Reports Where do I need to use PMCIDs?
    8. 8. Creating a My NCBI Account
    9. 9. • Open a browser (IE, Firefox, Safari, Chrome, etc.) • In the location bar at top type • Click “Sign in to NCBI” • Click “Register for an NCBI account” Click to Register
    10. 10. • Enter the information in the registration screen • click the “Create account”
    11. 11. • Once you have submitted the information successfully, you will see a confirmation page for about 5 seconds • The confirmation page will redirect you back to the PubMed’s main page, but you will be logged in
    12. 12. Linking your MyNCBI and eRA Commons accounts eRA Commons Frequently Asked Questions about My NCBI
    13. 13. • When you are logged into MyNCBI, your login name appears in the top right corner • Click on your login name • Under linked Accounts, if your eRA commons account is not listed, click the “Change” button.
    14. 14. Linking Accounts Con’t
    15. 15. Linking Accounts Con’t • To check that you have linked the accounts correctly, click on “My NCBI” in the upper right corner. • In the My Bibliography section, click the link that says “Manage My Bibliography” • If the accounts are linked, an eRA commons logo appears at the top of the page.
    16. 16. Putting your publications into My Bibliography
    17. 17. Putting Publications into “My Bibliography” • Check to see if you have publications in the bibliography by clicking My NCBI • The My Bibliography section will tell you if you have any publications and how many. • If no publications appear, in the Search section, just above the My Bibliography section, enter your name and click Search (you can also enter a date or date range).
    18. 18. Putting Publications into “My Bibliography” • From the results page, you can send the first 500 hits to your bibliography. Click the arrow next to “Send to:”
    19. 19. Entering Publications continued • You are now given the choice to put the publications into My Bibliography or Other Citations. Or if you are a delegate, you will be able to choose the PI’s library. • Other Citations is generally used for citations that are not yours, but you wish to keep track of. • Choose My Bibliography and click “Add to My Bibliography”
    20. 20. Entering Publications continued • Put all your own citations in My Bibliography, or your PI’s bibliography. • Your resulting screen will tell you that your items have been added to My Bibliography. • Click “Edit your bibliography” to go to My Bibliography.
    22. 22. Link Publications to funding
    23. 23. Link Publications to funding
    24. 24. Link Publications to funding • If, under funding, it says “No funding has been associated with this citation.” you can associate the grant that funded or partially funded the work that resulted in the citation by clicking “Add award.” • The Assign Awards dialog box will appear. Grants associated with your eRA commons account will appear under “My awards:”, other grants associated with publications in your library will appear under “Other awards:”
    25. 25. Link Publications to funding con’t • Use the “Search/Add other awards” tab to find any other awards in the NIH database. • In the search dialogue, search by Grant # or Grant name or by the Grantee (PI) name.
    26. 26. To link Publications to funding con’t
    27. 27. To link Publications to funding con’t You can assign a number of publications to one award at the same time.
    28. 28. To link Publications to funding con’t You can assign a number of publications to one award at the same time.
    29. 29. To link Publications to funding con’t You can assign a number of publications to one award at the same time.
    30. 30. To link Publications to funding con’t You can assign a number of publications to one award at the same time.
    31. 31. To link Publications to funding con’t You can assign a number of publications to one award at the same time.
    32. 32. MAKING PUBLICATIONS COMPLIANT WITH THE NIH PUBLIC ACCESS POLICY NIH Will Open the Research Performance Progress Report (RPPR) for All Type 5 Non-SNAP Progress Reports on April 25, 2014
    33. 33. • A result of NIH funding AND • Peer reviewed (i.e., not chapters) AND • Published after April 7th of 2008 AND • Written in a Latin based script Publications must comply with the NIH’s Public Access Policy if they are:
    34. 34. Publications must comply with the NIH’s Public Access Policy if they are: NIH Funding Peer Reviewed Published after 4/7/08 In a Latin Based Script
    35. 35. Changing Compliance Status • To change the Status of an article, click the Edit Status link. • You should be presented with a dialogue asking whether the publication is supported in whole or in part. If you designate yes you will be given more choices, otherwise you can click Save & Close and the publication will be designated as NA.
    36. 36. Green: Compliant Yellow: In-Process (by journal or at NIHMS) Red: Non-Compliant ?: Cannot determine status N/A: Not Applicable Changing Compliance Status con’t • The designations for publications are:
    37. 37. Changing Compliance Status con’t 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 Pub Med Central display? Not Applicable Not Applicable Author, via NIHMS Author, via NIHMS Participating journal/publisher Method A Journals Make arrangements with these publishers Check publishing agreement Check publishing agreement publishers Check this link for NIH overview of submission methods Awardee Task: An Example
    39. 39. INVESTIGATORS PLEASE NOTE -- It is important to acknowledge the supporting Cancer Center Shared Resources in all publications that include data derived from each facility. In addition, acknowledgments should mention the NCI cancer center support grant (P30CA013330), which partially supports all work conducted through the shared facilities. In results or methods section please thank the respective resource(s) for any help provided. Link the Cancer Center Support Grant (P30 CA013330) to your publication if it supported it in any way
    40. 40. Email header from OWA Full email from OWA (contains link to suggestion)
    41. 41. • When the recipient clicks the link (if they have a MyNCBI account) they will see the screen above • If they click the ADD button they will have added the citation to their bibliography • They will then receive the confirmation screen below
    43. 43. Delegate view of PI’s My NCBI / My Bibliography
    44. 44. When Accounts are correctly linked, you will be able to access the awards view • Click on the down arrow next to Display Settings • Under view you will be able to see “Award”
    45. 45. Summary • Create appropriate accounts – NCBI and link to eRA Commons • Make sure all your publications are in your My Bibliography – A Delegate can take care of your publications if you designate them as a delegate in MyNCBI (different from eRA Commons delegate) • Link your publications to funding sources • Make sure all your NIH funded, peer reviewed publications published after April of 2008 are compliant with the NIH Public Access Policy
    46. 46. Resources • Library Guide on NIH Public Access Policy • Library Guide on My Bibliography and Public Access Compliance • NCBI YouTube regarding My Bibliography and Public Access Compliance • NCBI YouTube on the My NCBI homepage • NCBI YouTube on My Bibliography • NCBI Help page on Managing Compliance • UNC YouTube on Managing compliance with My NCBI (part 3) (Parts 1, 2, 4) • Duke Compliance YouTube • Slide decks about compliance • Creating a delegate • NIH Public Access Policy Homepage • PubMedCentral ID (PMCID) Manual • Presentation on NIH Public Access Policy (Methods) • Slidedecks UCSD, UCSF, UWISC, UCSF-2, UMICH, UMICH -2, UMICH-3, UMICH-4, MDAndeson • Video of this publication • This Slidedeck • The Big Picture – How are they connected • Library guide from Himmelfarb Health Sciences of George Washington University • LSU Health Sciences Library PDF on using My NCBI • NIH eRA Commons Password Policy (PDF) • eRA Commons Frequently Asked Questions (FAQ) about MyNCBI • List of YouTube Videos
    47. 47. QUESTIONS?