My NCBI Help. My NCBI Help My NCBI Help My NCBI Help My NCBI Help. What Is My NCBI? Getting Started

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1 What Is My NCBI? Getting Started Accessing My NCBI My NCBI saves searches and results from multiple Entrez databases, and features an option to automatically update and search results from your saved searches. My NCBI users can save their citations (journal articles, books, meetings, patents and presentations) in My Bibliography and manage peer review article compliance with the NIH Public Access Policy. My NCBI includes additional features for highlighting search terms, storing an address, filtering search results and setting LinkOut, Document Delivery Service and Outside Tool preferences. My NCBI is a tool that retains user information and database preferences to provide customized services. It allows you to save searches, select display formats and filtering options, and set up automatic searches that are sent by . My NCBI users can save their citations (journal articles, books, meetings, patents and presentations) in My Bibliography and manage peer review article compliance with the NIH Public Access Policy. My NCBI includes additional features that allow for setting up preferences for highlighting search terms, storing an address, displaying and filtering search results and setting LinkOut, Document Delivery Service and Outside Tool preferences. To use My NCBI, your Web browser must accept cookies and allow pop-ups from NCBI Web pages. Section Contents Accessing My NCBI Registering with My NCBI Signing into My NCBI If You Forget Your My NCBI Username or Password Changing Your My NCBI Password The My NCBI link appears at the top right of the screen on all databases pages. To display the My NCBI box from the NCBI homepage, choose a database from the Search pull-down menu and click Search.

2 Page 2 Registering with My NCBI Note: Signing into My NCBI 1 Click on the My NCBI link in the upper right hand corner of the page. 2 Enter a username (3 or more characters) and a password (6 or more characters). Usernames and passwords are case-sensitive. 3 Choose a security question and answer so you can use them to reset your password if you forget them. 4 Below the Security Question, you will see an image with 5 characters. This step is to help us prevent automated programs from registering accounts. 5 Enter an address if you want to receive updates of search results periodically. 6 When you provide an address with your registration, you will need to confirm by clicking on the link that is provided in the confirmation from NCBI. This address will be used for both automatic updates and the Send to E- mail feature in PubMed. 7 After confirming your address, which you will receive in an , you can start setting up automatic s for search alerts. More information on automatic e- mails is provided in Setting Up Automatic Updates. Only one address can be associated with each account. Record your username, password, and answer to the security question in a safe place for future reference. There are two ways to sign into a My NCBI account: using a direct My NCBI username and password or using a username and password associated with a partner organization. Partner organizations include research organizations and commercial Web sites using either an InCommon or OpenID standard to authenticate users. To see a list of all participating partner organizations, click See expanded list.

3 Page 3 To Sign in using your My NCBI username and password: Note: 1 Enter your username and password. 2 Check the Keep me signed in box to automatically activate My NCBI each time you use any Entrez databases. You can sign out at any time by clicking on Sign Out in the My NCBI box. A checked Keep me signed in box saves your My NCBI preferences on your computer in a persistent cookie file. It will also retain your password so that you do not need to sign in again. If the Keep me signed in box is not checked, you will be automatically signed out when you close your Web browser. Using My NCBI without your username and password means that after eight (8) hours of inactivity on PubMed or other databases, all history and preferences will be lost. To Sign in using your partner organization account: 1 Select an organization, and then click Sign in. The system will link you to the partner organization s login page. 2 Enter your username and password. 3 Link to your existing My NCBI account or create a new My NCBI account. After the accounts are linked, you should be able to access your My NCBI account while signed into your partner organization s account. In My NCBI, your linked accounts will be listed under

4 Page 4 Common Preferences. To remove a linked account, click on Linked Accounts under Common Preferences and click the next to the account that you wish to remove. If You Forget Your My NCBI Username or Password In case you forget your username: 1 Click I forgot my username on My NCBI s Sign In page. 2 Enter your address. 3 Click Send Reminder. 4 An will be sent to the address you provided with your username information. In case you forget your password: 1 Click I forgot my password on My NCBI s Sign In page. 2 Enter your username. 3 Click Next. 4 Answer the security question. Note: Answers to the security question are no longer case-sensitive. 5 You will be instructed to set up a new password. 6 Confirm password in the text box for Repeat Password. 7 Click Finish. 8 Sign into My NCBI with your username and new password. Changing Your My NCBI Password 1 Make sure you are signed in to My NCBI. 2 Click on Preferences in the left blue sidebar entitled Table of Contents. 3 Click Password under Common Preferences. 4 Enter your old and new passwords. 5 Click Save. Saving and Managing Searches Section Contents

5 Page 5 Saving a Search in My NCBI Setting Up Automatic Updates Changing the Schedule of Your Updates Running Saved Searches and Checking for New Results Sorting Searches Deleting a Search Changing a Search Saving a Search in My NCBI 1 On any database page, run a search make sure you are signed in to My NCBI. 2 Click on Save Search, located above the search text box. (Figure A in image below.) 3 You will be guided to your MyNCBI page. Click Save when prompted. (Figure C in image below.) You m ay edit the name of the search. The maximum size for the search name is 100 characters. The name of the saved search will be included in the Subject line of the automatic update messages. 4 You will be prompted to set up your automated preferences at this time. This can be done at a later time. Note:

6 Page 6 To save a search from the My NCBI home page, run a search by clicking on the link with the number of Saved Searches under My Saved Data. (If you click on the My Saved Data tab on the left side of the page underneath Table of Contents, you will need to click Manage next to Saved Searches, and then on the create some saved searches link.) You may use History numbers in your search, however, PubMed processes from left to right so order your search statement numbers with this in mind, or use parentheses for nesting. Your saved searches will be listed in the My Saved Data section of My NCBI, which can be accessed by clicking on My NCBI, located at the top right of any major Entrez database page (Figure B in the image above). Searches are grouped per database and listed by the date and time they were saved for the first time. Saved searches cannot be edited but they may be changed. See Changing a Search for more details. You can now save searches through the Recent Activity section in MyNCBI. Setting Up Automatic Updates In most Entrez databases*, when you click on Save Search (A in the image above) you are asked if you would like to receive updates of new search results automatically. Automatic updates of search results are then sent according to the frequency you selected when saving your search in My NCBI (none, once a month, once a week, or everyday). You can also choose format, optional text(up to 200 characters), and change the number of items to be sent. See an example of creating updates from your favorite journals here. The text, which appears in the body of your updates, can be used to create a title for your search or any specific information you want. You may enter up to 100 characters for the search title. The name of the saved search will be included in the Subject of your automated update messages. If you have trouble remembering the name of your original search word or phrase(s), hover over the search term with your mouse in My NCBI s My Saved Data. It will display the original search word or phrase(s). Automatic updates can only be sent to addresses that have been confirmed. See Registering with My NCBI for more information. Automatic updates that bounce back three times will no longer be sent and the address will be invalid. In the rare case of technical problems, updates may miss some citations. Users receiving automatic updates should use the option to link to view complete results to minimize the risk. *The databases that support updates are: PubMed, Protein, Genome, PubMed Central, Taxonomy, SNP, PubChem Compound, PubChem BioAssay, 3D Domains, GEO DataSets, CDD, Structure, NLM Catalog, PubChem Substance, Nucleotide, PopSet, Est, GSS Note: Links to Related Articles cannot be saved in My NCBI Dates and date ranges are not advisable for saved searches Saved searches cannot be edited (see Changing a Search) If an update bounces back (cannot be delivered) three times, the address will be changed to invalid.

7 Page 7 Each My NCBI account can only have one address In the event an update is not sent out on schedule or is incomplete, the next scheduled update will include the omitted items, if any updates may be affected by filtering SPAM software. Consider adding nih.gov domain to your safe list Changing the Schedule of Your Updates To change or create a schedule for a saved search select My Saved Data, click the Saved Searches Manage link, and then click Settings next to the search name. Click on the Saved Search you want to change. You will be pointed to the same box where you first saved the search and set up the schedule. You can then change the schedule or any other settings you want. To unsubscribe from an update, click on the link that is provided in the update sent to you. Running Saved Searches and Checking for New Results When signed in to My NCBI, click on My NCBI at the top right of the screen. Then click My Saved Data from the blue sidebar and then Manage Saved Searches. Click on the name of your search to run the saved search in its respective Entrez database. This will not change the date displayed in the Last Searched (A in the image below) column. To see the exact date when a search was last run on a database, place your mouse over the date shown under Last Searched. If you have set up an schedule for receiving search updates, this information is displayed in the Schedule (B) column. For searches that you have not set up a schedule or which were run in databases that do not offer this feature, you will see none displayed in the Schedule column. To check for new results, select a search by checking the checkbox and click on Show What s New (C). A hyperlinked number is displayed indicating how many new items were found. Click on this hyperlink to view the new items. This action will update the information in the Last Searched column. If you do not click on the hyperlink to see the new items, the date and time of your search in the Last Searched column will remain the same.

8 Page 8 My NCBI search strategy to find new citations (for searches with untagged terms and searches that do not use Limits):

9 Page 9 Note: My NCBI "remembers" the date and time you last retrieved new items from your Saved Search(es). For strategies without search tags, it also considers whether citations that were in-process (not yet indexed) the last time you updated have since had MeSH terms applied, and are now retrieved by your strategy My NCBI saved searches that include search field tags or selections from the Limits page use an abbreviated Show What's New search to ensure that all citations are retrieved Searches that include the PubMed search field tags FAU, IR, 1AU, LASTAU, CN, AU, PS, IP, TA, LA, PG, TI, TIAB, LID, JID, TT or VI use the strategy: Search AND T1 : T2 [EDAT] Searches that include search field tags other than the ones listed above, use the strategy: Search AND T1 : T2 [MHDA] The My NCBI Show What s New feature will not retrieve citations for articles that were available in PubMed more than one year ago. To retrieve all new citations regardless of publication date, do not use either the updates or Show What s New options for My NCBI Saved Searches. Rather, run the saved search and combine it with a Create Date range. Use the format yyyy/ mm/dd: yyyy/mm/dd [crdt]. For example: "lyme disease"[mesh Terms] 2009/11/24:2010/02/24[crdt]. For further information on searching by date see Searching by Date Not all databases support automatic updates. In this case, the option Show What s New will not be available After running and saving your first Saved Search in My NCBI, you will only need to run and save the search directly in its Entrez database (e.g. PubMed) to add future additional searches

10 Page 10 Sorting Searches Deleting a Search Changing a Search Collections To sort My Saved Searches, click on the column name, and then on the small blue arrow to change the descending or ascending order. The order of the columns can also be changed by drag and drop. Searches can be sorted: alphabetically by name by date last updated by schedule 1 Go to the My Saved Data section of your My NCBI page. Click on Manage next to Saved Searches. 2 Check the box next to the name of the search you want to delete. 3 Click Delete [Database Name] Searches. The button name will include the name of the database. Saved searches cannot be edited in My NCBI; save a new search with your changes and delete the old one. To change a saved search: 1 Make sure you are signed in to My NCBI. 2 Under My Saved Data; click the name of the saved search you want to change. 3 The saved search will run in PubMed without any date limits, and the search will display in the search box. 4 From there, you can edit, change or correct the search by making changes in the search text box. Click Search to run the revised search. 5 Click the Save Search link next to the search box and follow the steps to save the revised search. 6 Delete the old saved search. Search results from databases can be saved in My NCBI using the Collections feature. Section Contents Creating Collections Viewing Collections Sorting Collections Merging Collections Editing Collections

11 Page 11 Sharing Collections Deleting Collections Creating Collections To save search results to a collection: 1 Make sure you are signed in to My NCBI. 2 Run a search. 3 From the search results page, click the check box next to the item number for items you want to save; if you do not select any items all results up to 5,000 items will be sent to collections. An automated message will confirm Add the first 5,000 items. 4 After selecting items you wish to save, select Collections from the Send to pull-down menu, as shown in the image below. Click Add to Collections. The browser will open with My NCBI s Collections page. Note: The maximum number was recently increased to 5,000 from 500. If you have saved any Collections prior to February 2009, then these will remain with 500 as the maximum number unless you recreate the Collection again. 5 A Save Collection page will display. Create new collection will be selected by default (A in the image below). 6 My NCBI will create a default collection name using the number of items you are saving in the collection unless you decide to select the first 5,000 items (B in the image below). You should rename your collection using a short, yet meaningful, title. Be careful when naming Collections. Identical names for different Collections are allowed and may cause confusion. 7 Click Save to finish (C in the image below).

12 Page 12 Viewing Collections From My NCBI Home, click on the hyperlink with the number of Collections. Then click on the Collection name. This will display the Collection search results in its database. You may also display a Collection search by clicking the Collection s name in My Saved Data. Make sure you are signed in to My NCBI. Additionally, if you are Editing a Collection, a quick way to access the search results is to click on the magnifying glass icon located on the Actions toolbar. Like saved searches, saved collections will be grouped by database.

13 Page 13 From this screen, you can sort your collections, view Collection Details, or view the Collection in its source database. Click the check box on next to Name to select all Collections. Sorting Collections Merging Collections Editing Collections Click Edit to view collection contents, change the name, or delete individual items within a collection. To sort Collections, click the descending or ascending arrow next to the column headings on the Collections screen. A blue arrow indicates the currently selected sort option. Collections can be sorted: alphabetically by name by date last modified by number of items in the collection To view the Collection s results, click on the Collection Name and it will appear in its respective database. To merge Collections, select the Collections you want to merge by clicking the checkbox next to the Collection name on the Collections screen. Click the Merge PubMed Collections button. You will see the Merge Collections screen. Name the merged Collection using a short, yet meaningful, title. To remove the original, separate Collections, click the checkbox next to Delete collections being merged? If you would like to keep the original Collections in addition to the newly Merged Collection, remember to select Keep them. Click Merge Collections button. To change the name of a Collection:

14 Page 14 Make sure you are in the My Saved Data section of My NCBI. Click on the Edit link next to the Collection Name you would like to rename. Click on the blue Folder icon next to Actions at the top (as shown in the image below). Enter the new name for the Collection in the Collection Name text box. Then click Save. Appending Search Results to Existing Collections: To add search results to an existing collection, follow steps 1 5 under Creating Collections. On the Save Collection page, select Append to an existing collection (A in the image below). The window will change to display a Choose a collection pull-down menu with your collections listed (B in the image below). Choose the collection you want to add items and click Save (C in the image below). To delete items from a collection:

15 Page 15 Click Edit next to the Collection which you wish to modify. Click the checkbox next to items you want to delete and click the Red X icon,. Sharing Collections My NCBI collections and bibliographies are now set as either "Private" (the default) or "Public." A collection set to Public can be shared with others. Steps for changing a collection from Private to Public: Notes: 1 Access your collection in My NCBI: From the My NCBI homepage, click on My Saved Data, then click on Manage for Collections. 2 On the screen listing your collections, the "Sharing" column indicates the setting for each collection. Click on the Private link for the collection you want to share. 3 Under Collection Sharing, click the radio button for Public. Notice that a URL and an HTML code are provided. You can use the URL to share with others and the HTML code to post onto a web page. 4 Click Save. Any time someone uses the URL or the link created by the HTML to see the collection, the retrieval will include the citations currently in the collection maintained by the user of the My NCBI account. Adding or deleting items in the collection does not require an update to the URL/HTML

16 Page 16 If a collection is changed back to Private, the URL/HTML will no longer work. Be sure to use the Save button after making changes This feature is available for any database that has collections (currently: PubMed, Journals, NLM Catalog, and PubMed Central ) Deleting Collections My Bibliography 1 Under My NCBI My Saved Data, click the Collections Manage link 2 Click the column headings to sort alphabetically by name, last modified date, or by the number of items in each collection 3 Use the check boxes to select collections to delete and then click Delete PubMed Collections My Bibliography and Other Citations are available to save your publications (journal articles, books, patents, presentations and meetings) using a search template and manage your peer review articles compliance with the NIH Public Access Policy. Whether you are an author and want to populate your papers from PubMed, or you are a user who would like to populate specific searches by author, utilize My Bibliography to easily access these citations. A new feature, Awards View, allows users to see whether their journal articles comply with the NIH Public Access Policy, to start the compliance process for journal articles, and to associate their publications to NIH extramural awards. Section Contents Creating Bibliographies Creating Bibliographies Viewing and Downloading Citations Sorting Citations Managing Compliance with the NIH Public Access Policy Deleting Citations Editing My Bibliography Settings To populate a My Bibliography Collection with author-specific items, make sure you are signed in to My NCBI so that your preferences are saved with your username. 1 Make sure you are in the My Saved Data section of My NCBI. 2 Click on the link My Bibliography under Collections. Click on the blue plus icon on the Actions toolbar.

17 Page 17 3 Select how you want to search for an item. Adding items by existing PubMed journal articles is the default search filter, but you may select the search filters for adding journal articles manually. New search filters include books and chapters, meeting abstracts, presentations, patents, and non-standard citations. 4 After selecting a search filter, click continue. When searching by citations in PubMed, enter an author name (or select from autocomplete listing). You can also search citations by Title Words. For even more filtered search options, click on the tab More Options where you can search by Author, Title Words, Years Published, Journal, Grant Number, Affiliation, and PMID. When selecting search filters other than articles in PubMed, after clicking continue, make sure to fill in all required fields in order for the search to have results. All required fields will be denoted with a red asterisk.

18 Page 18 5 After the results of the search are displayed, click next to the items you Note: want to save to your my Bibliography. Make sure have selected any items. After you have completed all selections, click save them to your Bibliography collection. is displayed after you Use the Other Citations link in My Saved Data to create additional Bibliography collections using a saved search form. Click View results in PubMed icon to display your bibliography in PubMed To add more items to My Bibliography, simply follow steps 1 5 above Viewing and Downloading Citations To quickly view your My Bibliography citations in PubMed, make sure you are in My Bibliography from the My Saved Data section in My NCBI. All Bibliography items that are in PubMed are hyperlinked click on the title of the paper and it will go directly to the citation. You can also select multiple items and then click the magnifiying glass icon located in the Actions toolbar. To download citations from My Bibliography, select the citations you wish to download and click downloaded in the MEDLINE format.. On the pop-up window click Save. The Citations will be to

19 Page 19 Note: Sorting Citations The default View in My Bibliography is the Summary View,. This lists Bibliography items with hyperlinked titles linking to its citation in PubMed. To view your Bibliography items without PubMed or PMC IDs, and hyperlinks, you may view items in the Print View,. Here is an example of the difference in Views for one citation the top example is the default Summary View, the bottom of the Print View: Jackson SP, Yap CL, Anderson KE. Phosphoinositide 3-kinases and the regulation of platelet function. Biochem Soc Trans Apr;32(Pt 2): PubMed PMID: Jackson SP, Yap CL, Anderson KE. Phosphoinositide 3-kinases and the regulation of platelet function.. Biochem Soc Trans Apr; 32 (Pt 2) : When adding citations manually to My Bibliography, there will no hyperlink in the title unless it does exist in PubMed. If not, the citation will be displayed with a pencil icon, however, for you to edit if necessary. There are three ways to sort the order for Bibliography or Other Citations items: by publication date, first author, title. To sort by date, click on the icon with the number 15,. Dates are sorted by earliest to most recent from top to bottom. These are not sorted by Entrez date but the date the citation was published. To sort by author, click on the icon, in alphabetical order. To sort by title, click on the icon,. This will sort publications by the first listed authors. This will sort titles alphabetically. Note:

20 Page 20 The default setting for the Sort option is to Group by: Type of Citation. You may use the drop down menu to Sort by the various methods of Sorting items in My Bibliography as well as to modify the Grouping option. Please note that when selecting the No Grouping option, citations will be listed in one list. Meeting abstracts have two different dates: conference date and publication date. When listed in My Bibliography with sorting by Date and No Grouping, please note that the publication date will be used to determine the sort date. When a publication has both a print date and Epub date, the print date will be used for sorting dates. Managing Compliance to the NIH Public Access Policy From the Awards View era Commons users are able to see whether their publications are compliant with the NIH Public Access Policy and to start the compliance process. The Awards View is only available to era Commons users with active grants in their portfolios who have linked their My NCBI account with their era Commons account. To see whether your publications are compliant or not, go to My Bibliography and click on the Awards View icon This icon is only visible to users who have linked their accounts.

21 Page 21 On the resulting screen each citation is marked with visual clues the peer review article compliance status. that indicate Peer review articles that are compliant with the NIH Public Access Policy are marked with a green dot and have the PMCID number listed. Articles newly submitted to the NIH Manuscript Submission system are considered in process and are marked with a yellow dot. Note that the NIHMS ID number is listed. A red dot indicates that the article is non-compliant. The compliance process can be started by clicking on Citation not in NIHMS or PMC Articles that were accepted for publication prior to April 7, 2008 are not covered by the NIH Public Access Policy. These citations are marked as not applicable. A question mark indicates that compliance with the NIH Public Access Policy cannot be determined without additional information. Click "Edit Status" to start the compliance process.

22 Page 22 To begin the compliance process for non compliant journal articles, click on Citation not in NIHMS or PMC and follow the steps provided by the pop-up wizard. The Public Access Policy wizard allows users to associate their awards to a peer review article and provides a list of choices that address NIH Public Access compliance. or

23 Page 23 To associate your NIH extramural awards to your publications, click the NIH Funding link. Deleting Citations Alternatively, you may click on to associate several citations with awards at once. To delete items, go to My Bibliography under My Saved Data. Select all items you wish to remove. Click on the red X icon. Select Remove Items from the popup window. A confirmation note will appear stating the number of citations was successfully removed. Editing My Bibliography Settings When viewing My Bibliography items, you can Edit My Bibliography Settings to share your Bibliography settings (just like Sharing Collections) and by adding delegates. My Bibliography is defaulted to be private. To Share your Bibliography: 1 Make sure you are signed in to My NCBI.

24 Page 24 2 Click on My Bibliography or Other Citations. This takes you to the citation list for the bibliography. 3 On this screen, use the link, Edit My Bibliography Settings to go to the screen where you can change the sharing settings. Note: 4 Select the radio button for Public Bibliography Sharing. A Direct URL and HTML code will be provided for you to now easily send to others to view your Bibliography items. 5 Click Save. The URL, or the link created by the HTML, displays the citations currently in the collection maintained by the user of the My NCBI account. Updating the collection does not require a change to the URL If a collection is changed back to Private, the URL is no longer valid. Click Save after making changes

25 Page 25 Delegates are other persons who will be granted access by you, the user, to view and manage your Bibliography. The delegate will then be able to add and remove citations to the Bibliography and perform other functions. Note that the option to Add a Delegate only appears when a Bibliography has been created in My NCBI. To enable other persons to be delegates: 1 Make sure you are signed in to My NCBI. 2 Click on My Bibliography. 3 Click Edit My Bibliography Settings. 4 Click Add a Delegate. 5 Enter your delegate s address. 6 Click Add Delegate.

26 Page 26 Recent Activity 7 Your delegate will receive an in which the delegate must then confirm by clicking on a link in the . The Recent Activity section under Saved Data in MyNCBI is a listing of users searches and records viewed for the last 6 months. All searches and records in Recent Activity are hyperlinked so that users can easily view them again or keep a record of all past queries. Recent Activity will only save results for registered MyNCBI users when they are signed in. Section Contents Turning Recent Activity On and Off Clearing Recent Activity Sorting Recent Activity Deleting Items in Recent Activity Creating Saved Searches in Recent Activity Moving Recent Activity to Collections Turning Recent Activity On and Off The Recent Activity option is automatically defaulted to be On. Users can opt to turn off the Recent Activity option by clicking on the drop down menu icon,, and scrolling down to the option Turn Recent Activity Off. You can also turn Recent Activity off directly from Entrez databases. You will notice that in the databases, a Recent Activity box is present to the right of the screen. Click Turn Off.

27 Page 27 Clearing Recent Activity When users opt to turn off Recent Activity, a pink strip stating that Recent Activity is off will display each time you visit your Recent Activity in MyNCBI. If at a later time users would like to turn the Recent Activity option back on, click on the link Turn Recent Activity On or you can also click on the drop down menu icon,, and scroll down to Turn Recent Activity On. To clear all Recent Activity records, click on the drop down menu icon, option Clear Recent Activity.. Select the

28 Page 28 Sorting Recent Activity You can also clear Recent Activity from an Entrez database by clicking Clear in the Recent Activity box. Once you agree to Clear Recent Activity, the action cannot be undone. A popup message will confirm if you want to clear all items for Recent Activity. Click Clear Recent Activity if you are sure you want to erase all records. To sort Recent Activity, be sure you are in the Recent Activity section of MyNCBI. There are two ways to Sort items: by Date/Time and by Entrez database. To sort your Recent Activity by Date/Time, Click on the icon with the number 15,. The most recent searches will be listed first.

29 Page 29 To sort your Recent Activity by Application, or Entrez database, click on the green, blue, and yellow colored icon,. Deleting Items in Recent Activity You may either select all items in your Recent Activity to be deleted or individually click each item. After you have selected items to be deleted, click on the red X icon,. A message will notify you that the amount of items you have deleted have been removed. Creating Saved Searches in Recent Activity If you want to save a search from a past query, you can now go to your Recent Activity without having to run the search again in a database. Go to Recent Activity, select an item that you would now like to save, and click on the icon with the paper and arrow,. Enter a name for your new saved search. Click Save. The search is successful if the message appears under the Actions toolbar Search saved successfully. You can then also opt to edit your saved search. Moving Recent Activity to Collections Using Preferences Only past Records may be moved to a Collection in your MyNCBI. Select an item you wish to incorporate into one of your Collections. Go to the Actions toolbar and click on the folder icon,. Select the Collection where you wish to move the item. Click Move. The My NCBI Preferences can be found in the blue sidebar of the My NCBI page (to see the My NCBI blue sidebar, click on My NCBI located at the top right of any database page). My NCBI Preferences currently allows you to change the display of the links menu, update your address for automatic search updates, activate search term highlighting, save shared settings, turn off the Auto Suggest feature and Search Details ad for PubMed, and customize your search results display for PubMed. Section Contents Changing the Display of the Links Menu Changing Your Address Highlighting Search Terms in PubMed Searches Save Shared Settings

30 Page 30 Changing Abstract Supplemental Data Display for PubMed Turning Off Auto Suggest for PubMed Customizing Search Results Display for PubMed Changing the Display of the Links Menu Users can change the display of the Links menu on any results page. To learn about Links, see the Entrez Help Document. To change the display format of the Links menu, click on Links Display located in the Preferences section of My NCBI. Select your preferences and save. The available formats are: Changing Your Address Plain Links: Displays links as separate selections. Pop-up Window: Opens a separate small window with link selections. To change your address for receiving updates: Note: 1 Click Preferences on the My NCBI sidebar. 2 Click on Address. 3 Enter an address. 4 Click Save. A confirmation message will be sent to the address to activate automatic updates For the Send to option, you may enter a different address that will not affect your My NCBI updates Highlighting Search Terms in PubMed Searches You can choose to have your search terms highlighted in retrieved database records. By default this option is off, but you can pick one of the ten colors available in the Highlighting section of My NCBI Preferences to have your search terms highlighted. Highlighting is only active when you are signed into My NCBI. Terms other than the one(s) you have used in your query are also highlighted at times. For example, if you search PubMed using the term cancer, you will also find citations with the term neoplasm highlighted. That is because Entrez has a dictionary of synonymous terms, such as cancer and neoplasm that are equally considered when you search a database using one of them. In some cases, you will retrieve PubMed citations that have no highlighting in its abstract, which means that neither the search term nor a synonymous word was found in the abstract of the article. However, terms that appear as MeSH (Medical Subject Headings) terms or Substances on a record will be highlighted in the supplemental information section of the citation. For example, a search in PubMed with the term ABCD4 retrieves, among others, the following record that does not have the term ABCD4 (or any synonymous term) in its abstract: The four murine peroxisomal ABC-transporter genes differ in constitutive, inducible and developmental expression.

31 Page 31 Just scroll to the bottom of the page and expand the Publication Types, MeSH Terms, Substances list (see image below), and you will see that the term ABCD4 (full term ABCD4 protein, mouse ) appears in the record. Note: Save Shared Settings MeSH is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. Click here for more information on MeSH terms. Located in the Common Preferences section, the Shared Settings option allows users to set Document Delivery settings, Filter settings, Highlight settings, and Outside Tool settings all at once instead of having to set these options separately. This is an option that institutions can utilize in order to have all of their users access the Entrez databases with the same settings from one URL. Shared Settings eliminates the need for each individual having to sign up for an account, or to minimize users from signing in and out from their accounts.

32 Page 32 To create shared settings: 1 Go to the Preferences section in MyNCBI. 2 Click on the Shared Settings link. 3 Select which settings to share by clicking the appropriate box. 4 Save. 5 You can then create a URL, myncbishare=username, where the username is the shared MyNCBI account name. This URL can be used to create a link or button for PubMed on a library s Web site, and also sent to patrons to bookmark in their browsers. More information about My NCBI Shared Accounts: Settings activated using a My NCBI shared account URL will timeout after eight hours of inactivity A user accessing PubMed using shared settings is not signed in to My NCBI so the My NCBI box will not display Welcome username If a user signs in to My NCBI the setting for their personal account will take precedent over the shared account settings Changing Abstract Supplemental Data Display for PubMed The Abstract Supplemental Data display lists MeSH terms, Publication Types and other supplemental information when clicking on the plus button (+).

33 Page 33 To change the Abstract format to display the supplemental information by default: 1 Sign into My NCBI 2 Click on Preferences on the My NCBI sidebar 3 Click Abstract supplemental data 4 Check Open 5 Save

34 Page 34 Turning Off the Auto Suggest feature for PubMed New to PubMed, the Auto Suggest feature is defaulted to be on whenever users start typing in search terms. When users start typing letters into the Search box within the PubMed database, the Auto Suggest will suggest some of the most popular PubMed searches. You can click on any of the suggested terms. To turn off the Auto Suggest feature scroll to the bottom of the Auto Suggest menu when you start to type in a term. There is a Turn Off option. To turn the Auto Suggest feature back on, go to your MyNCBI page. Go to the Preferences page. Click on the Auto Suggest link within your PubMed Preferences. Then click the radio button for On. Click Save.

35 Page 35 Note: The Auto Suggest feature will be turned back on after eight hours of inactivity. Customizing Seach Results Display for PubMed The PubMed default settings for displaying search results are: Summary display format, 20 citations per page, and sorted by recently added citations listed first. To customize your search results display, log into My NCBI and click PubMed Preferences and then Result Display Settings. In the resulting page select, either the Abstract or the Summary format, the number of citations to be displayed per page and a sort option among the following: Recently Added, Pub Date (Publication Date), First Author, Last Author, Journal, or Title. After your results display selections are saved in My NCBI and while logged into My NCBI, go to PubMed to see your display selections applied to your search results. In the image below the customized display selections appear next to the Display Settings drop-down menu.

36 Page 36 Notes: Working with Filters The Filter Display You must be signed into My NCBI for your display selections to be applied to your PubMed search results Section Contents The Filter Display Setting Up Your Filters Setting Up Custom Filters Search results are grouped into subsets by filters. For example, in the PubMed database, filters can be used to group results into reviews, or clinical trials, among other choices. In My NCBI, you can select your preferred filter to be active every time you run a search. In the figure below, two filters have been activated: Review and Free Full Text. Filtered results with their respective counts are displayed as links, in a section located to the right of the web page, which contains the complete list of records retrieved in each search. In the example below, a search in PubMed

37 Page 37 with the term human genetic deficiences has generated 2,337 citations, of which 945 are grouped in the Review result tab; 566 are in Free Full Text. Up to five filters are allowed for all databases, except for PubMed where the maximum number of filters allowed is 15. Setting Up Filters To set up your filter selection, click on Search Filters in the sidebar of the My NCBI screen. Choose the database in which you want to set your filter preferences. Under the blue tab My Filters, click your preferences for filters. Then click the blue tab Frequently Requested Filters which lists most commonly requested filters.

38 Page 38 In Browse Filters, you can browse a list of filters that is divided in three categories: LinkOut, Links, and Properties. LinkOut and Properties are divided into subcategories that might include additional subcategories. Records that have links to resources provided by outside organizations can be grouped using LinkOut (more on LinkOut). Records that have links to other Entrez databases can be grouped using Links. For example, you can select Links to OMIM to create a result tab that groups all records retrieved in a search that have links to OMIM. The result tab is active every time you search any Entrez database (see image below). Properties groups records according to specific criteria such as languages, gender, age groups, publication date, publication types or Clinical Queries. Simply click on the Properties Subcategories you are interested in then on each appropriate checkbox and the filter is automatically generated. In the case of LinkOut and Properties, you can choose to have either a single filter added to your search results or an entire category or subcategory. Libraries using LinkOut can set up a filter for their holdings, see Library LinkOut Filters. If you know the name of the filter you are interested in, you can search for filter names and descriptions using the Search for Filters tab. To see your active filters and icon settings, check My Filters. You can also create Custom Filters. Some databases have a default set of result tabs that are active whether you have a My NCBI account or not. Default filters can be replaced by your filter selection, which can also be accessed and changed from all Entrez results pages. When on a results page, look for Filter you results and use the link Manage Filters to access the filter selection page My Filters. (see the image above). Setting Up Custom Filters It is now possible to customize your own filters for any of the Entrez databases. To create a custom filter: 1 In MyNCBI, click Search Filters (from the Table of Contents sidebar).

39 Page 39 Filter type Address of first author 2 Click on a database link. 3 Click on the Custom Filters tab. Click on the link create a new one. 4 Enter the Name for this Custom Filter and the Search terms that you wish to use for this Filter. You can then Run Filter to see the number of citations retrieved by the filter search. 5 If you are satisfied with the Custom Filter, click Save. The window will then display your customized filters. Make sure to click the checkbox next to your newly created Custom Filter in order to activate it. After you select your newly created Filter, a green text box will confirm that the Filter has been added. Examples of custom filters: Library holdings or anything available free Articles identified by a funding agency Items from particular journals Any term Any combination of terms Free text searching Notes: Filter search mayo [ad] AND clinic [ad] "loprovnlmlib"[filter] OR free full text [sb] "loprovnlmlib"[filter] OR free full text [sb] Birth Defects Res A Clin Mol Teratol [ta] OR Birth Defects Res B Dev Reprod Toxicol [ta] OR Birth Defects Res C Embryo Today [ta] OR Clin Dysmorphol [ta] OR Congenit Anom Kyoto [ta] delivery of health care [mh] clinical trial [pt] AND aged [mh] health disparities When you click on a filter link a plus symbol will appear next to the filter link. Click the plus symbol to append the filter to your search. Custom Filters cannot be appended to a search There is a limit of five filters (including custom filters) that can be selected and listed under My Filters. For PubMed up to 15 filters can be selected. Make sure you are signed into My NCBI to have your Filters activatec while searching the Entrez databases Using My NCBI to Set Up LinkOut LinkOut Section Contents LinkOut Outside Tool Document Delivery LinkOut is a feature that links individual records retrieved in a search to a variety of external resources, such as full-text publications, biological databases, consumer health information, library holdings and research tools. The available links are supplied by outside providers interested in linking their resources to NCBI databases. Not every database record has links to external resources. To set up LinkOut, start by selecting Search Filters (from the Table of Contents sidebar) in the same way you would set up any filter, as explained in the previous section. Select the database

40 Page 40 in which you want LinkOut to be displayed. You can either browse or search the list of available external resources. To search the list, enter the name of a provider in the search box. Then click Search. The name of the provider, if available, will be displayed in the Results Section. You can click on the (website) of the provider for more information. As explained earlier, there are three types of available filters; LinkOut is one of them. Under the name of the provider in the Results Section are two possible selections. Although these two possibilities are shown regardless of the database you have selected, the Add as a link icon is only available to users of PubMed. In any other databases, LinkOut can only be displayed as a result tab. The link icon display might be available in other Entrez databases in the future. The image below shows LinkOut displayed as link icons, available in PubMed only. You may also access links to full text by clicking on the LinkOut links beneath the citation. Libraries that use LinkOut to link their subscriptions to PubMed can access the full text of a citation by clicking a library icon/logo or by clicking the link LinkOut Holdings under the LinkOut more resources links list.

41 Page 41 Outside Tool You can also use My NCBI to browse a list of available external resources and providers. To do this, start by selecting Saved Filters in My NCBI, as explained previously. Select the database in which you want LinkOut to be displayed. Click on Browse Filters and select LinkOut. Choose a subcategory of LinkOut and proceed as described in the beginning of this section. Remember that the icon display is available only to users of PubMed. You can also choose to have LinkOut icons included in your automatic updates of searches done in PubMed (to learn about automatic updates, see Setting Up Automatic Updates). To do this, select Abstract as the display format for your s when setting up your search alert. If available, all LinkOut icons that you have selected in My NCBI will be included in your alerts, together with your PubMed search updates. For full documentation help on LinkOut, visit rid=helplinkout.chapter.public. Outside Tool allows libraries to add a link from PubMed citations to a link resolver available at their institution. These links are displayed as icons in PubMed s Abstract display (see image below). When you click on the icon, you are directed to the available services for that citation offered by the sponsoring library. These services might include access to electronic full text or information on local print holdings. To turn on an Outside Tool, click on Preferences on the My NCBI sidebar and then click Outside Tool. Select an institution from the available list and click Save; the selected icon will display in PubMed s Abstract format. Keep in mind that most Outside Tools are fully accessible only to individuals affiliated with the sponsoring institution. For more information on Outside Tool, visit rid=helplinkout.section.related.outside_tool. Document Delivery Service Document Delivery Service (DDS) is a feature of PubMed that allows you to order articles described in PubMed citations from an institution of your choice. By default, orders are sent

42 Page 42 Tutorials to Loansome Doc, the document delivery service of the National Library of Medicine. To change the DDS for your orders, click Preferences in the My NCBI sidebar and then choose a service from the list of institutions found the Document Delivery link. After you have made your selection, your orders will be sent to the selected institution. Please note that Document Delivery Service providers may restrict the service to affiliated users or may charge for document delivery. To order documents, click the checkbox next to the article(s) you want to order. When you are ready to order, select Order from the Send to pull-down menu, as shown below. You will be directed to the Document Delivery Service form. You can mark several citations to be included in a single order. Alternatively, before ordering all your selections, you can save them temporarily in the Clipboard. To send your selections to the Clipboard, proceed as usual but select Clipboard from the Send to pull-down menu, instead of Order. When you have decided what articles you want to order, click the Clipboard link. To remove unwanted articles from the Clipboard, click the Remove from Clipboard link next to the citation. When you are ready to order, select Order from the Send to pull-down menu. You will be directed to the Document Delivery Service form. Complete the requested information. Your DDS selection is active only while signed into My NCBI. When you sign out, the DDS default choice is restored. Document delivery services sponsored by some institutions might be available only to users of that institution. Some institutions may also charge a fee for their services. Several tutorials are available on how to use My NCBI with PubMed.