Information for Libraries

Introduction

Libraries that do not implement their local link resolver as an Outside Tool may manage their LinkOut holdings using a local link resolver (LinkOut Local). LinkOut Local allows one library icon to appear on all PubMed citations for which a library can provide online full text or print holdings records. Clicking on the icon directs users to your local link resolver.

Libraries that implement LinkOut Local do not manage their holdings information through the Library Submission Utility; they upload holdings information directly to LinkOut in the form of XML files.

To implement LinkOut Local, you will need to upload two LinkOut files to NCBI, a resource file and an identity file. The resource file contains a list of your library’s holdings and is usually generated by your link resolver. The identity file contains information about your library. The resource file should be updated at least once a year to keep the holdings data current in the LinkOut database.

NOTE: Libraries should be able to produce files compliant to the LinkOut format. Libraries should contact their link resolver vendors for assistance. The LinkOut team does not provide technical assistance in this area.

Evaluating Your Link Resolver

Before submitting a registration request, your library should test your link resolver. The link resolver should provide one of the following items in your library’s holdings:

• Online full text: The link should lead directly to the article-level for the online full text, not the table of contents or the journal homepage.

• Library holdings via the local OPAC: The link should lead directly to the OPAC Holdings display or to the corresponding bibliographic record with holdings/location information displayed. The link should not lead to a general catalog or search form.

Preparing LinkOut Files

To implement LinkOut Local send two files, a resource file and an identity file, to NCBI, either directly or through a third-party service that you authorize. You will need to prepare an identity file and a resource file (journal holdings) before submitting your registration information.

• The identity file contains the information about your library that NCBI needs to list your library in LinkOut.

• The resource file contains the list of your library holdings that LinkOut will use to apply your icons to PubMed citations.

About PubMed & OpenURL-based Services

OpenURL is a syntax for packaging metadata and identifiers describing information objects and for pointing to a user-specific appropriate copy of the object. The syntax has been accepted as a NISO standard.

PubMed supports OpenURL-based services through LinkOut and through Outside Tool. With LinkOut, links to an OpenURL-based service are attached to the set of PubMed records for which a library can provide links to online full text or print holdings. Outside Tool allows libraries to place a link to their OpenURL-based service on all PubMed records.

For more information about PubMed and OpenURL, see the LinkOut, Outside Tool, and OpenURL FAQ.

Implementing OpenURL-based Services in PubMed

OpenURL-based services can be registered with NCBI to provide a link from the Abstract and Citation displays of PubMed records. This link points back to a service offered by the institution for their local users.

Your library’s OpenURL-based service can be implemented through LinkOut Local or may be registered as an Outside Tool.

When an OpenURL-based service is implemented through LinkOut Local, the account has all the advantages of a LinkOut account, including the ability to limit a search to library holdings, display library holdings as a filter tab in the search result, and apply different icons to print and online holdings.

Outside Tool does not allow users to limit a search to library holdings or to display library holdings as a filter tab in the search result; these functions are only available to libraries that submit LinkOut holdings. Outside Tool does not differentiate between online holdings, print holdings, or items that will have to be ordered from another institution.

The differences between LinkOut and Outside Tool are summarized in Table 1.

Evaluating Your OpenURL-based Service

Most services that can provide a link to online full text and/or a local print holdings record can be implemented through LinkOut Local.

To implement an OpenURL-based service through Outside Tool, we require the service to provide functional links to the following qualified resources from each PubMed record. This requirement allows us to best serve our user community, by avoiding "blind" links that do not provide useful and specific information for the individual PubMed record.

Qualified resources are:

• Full-text: The link should lead directly to the article level for the online full text, not the table of contents or the journal homepage.

• Library holdings via the local OPAC: The link should lead directly to the OPAC Holdings display or to the corresponding bibliographic record with holdings/location information displayed. The link should not lead to a general catalog or search page.

• Local document delivery service: The link should produce a form with citation information already entered for the user. Due to the scope of PubMed, it is unlikely that any single library will be able to provide print or electronic holdings for every citation in PubMed. A link to a local ILL service must be available to provide users a means to obtain the full text for citations the library does not hold in print or electronically.

To determine whether your OpenURL-based service meets the qualifications for implementation as an Outside Tool, construct a URL to your service and retrieve the PubMed records listed below.

To construct the URL to your OpenURL-based service, combine the base URL of your service with a PMID:

Please test all of the following PMIDs to verify that your service is working correctly. Your service MUST provide one qualified resource for each PMID tested.

PMIDs for testing

All resources must be in place before the registration request is submitted. If your local service cannot provide one qualified resource for each PMID tested, it cannot be implemented as an Outside Tool. In this case, please see LinkOut Local for instructions on registering your service through LinkOut.

If your service can provide one qualified resource for each sample PMID, it may be implemented in PubMed as an Outside Tool. Proceed with the registration process described in Outside Tool: Register Your Service.

Viewing and Using Library Links

Library links submitted through LinkOut can be viewed in PubMed in two ways, as icons in PubMed’s AbstractPlus, Abstract and Citation displays, or as links in the LinkOut Display (to learn more about the LinkOut Display, see Viewing LinkOut Resources in Entrez Records: The LinkOut Display in this manual.) Outside Tool links can be viewed as an icon in PubMed’s AbstractPlus, Abstract and Citation displays.

To view links as icons, they must be activated by entering PubMed through a special URL or by selecting the library as a Filter in My NCBI. To learn how to activate icons, see Activating Library Icons in PubMed.

When links are displayed as icons in the AbstractPlus, Abstract and Citation displays, users click your library icon to access the online full text or print holdings information (see Access to LinkOut Resources for LinkOut’s access policy). If the library has implemented an OpenURL-based service in PubMed, the link will lead to that service.

If your library has links to both print holdings and online full text, users will see two icons, one for full-text and one for print holdings.

For example, in the image below, online and print icons for the University of South Carolina School of Medicine (USC-SOM) Library are shown in the AbstractPlus display. USC-SOM has both online and print holdings for J Fam Pract. Each icon will link to the respective collection.

Activating Library Icons in PubMed

Library icons may be activated in PubMed in the following ways:

• 1

  Through a special URL to access PubMed

• 2

  Using a shared My NCBI account

• 3

  Through a special URL to access Clinical Queries, Single Citation Matcher, Advanced Search, the Entrez Cross-Database Search (Gquery) or the Health Services Research Queries

• 4

  By signing in to My NCBI

Unless the user chooses to sign in to My NCBI, icons are activated using a special URL. If you are using a special URL to localize PubMed for your users, you should create a button or link to this URL from your library website. Replace your current PubMed links (in your catalog, on subject pages, etc) with this URL. You should also send out a general announcement so that other departments, faculty, etc. can update their websites and personal computers. More information about using special URLs is available in the About Cookies and Special URLs section of this manual.

How Will Localizing PubMed Help My Users?

A medical resident comes into the library to find information for his Grand Rounds presentation in 4 hours. He performs a quick PubMed search, and retrieves 428 citations. In the search result, the library’s icon marks articles which are immediately available, online or in print. Next to the complete set of results, a tab tells him that 53 articles are available from the library. He clicks the tab to focus on what can be accessed quickly. After selecting several articles under the library tab, the resident returns to the complete set of results and finds several more articles that are not available at the library for further study. He requests them from the library's document delivery service directly through PubMed.

Too good to be true? Not at all. LinkOut, Outside Tool and Document Delivery Service (DDS) allow libraries to connect users to local resources (“localize”) in PubMed by providing easier, more focused, means of linking to a wide variety of related web-accessible resources and additional services, such as OpenURL-based link resolvers and local document delivery services.

The ability to localize online resources for a user population is a feature increasingly valued by both researchers and librarians. For users, localization features provide seamless access to available resources. For libraries, localization features allow spotlighting of and direction to resources that are readily available or of high interest to their users.

A variety of special URLs and My NCBI Filters are available for use in localizing PubMed. Special URLs allow users to activate a library’s local profile in PubMed. The MyNCBI feature allows easy branding and identification of a library’s holdings in a PubMed search result by grouping library holdings as a result tab in PubMed searches. Citations with links to other materials of interest can be grouped as result tabs as well.

A few examples of how localization might be used:

About Cookies and Special URLs

Many of the features used to create a localized PubMed environment use “special URLs”. When a user enters PubMed through a special URL, a cookie is placed in the workstation that instructs PubMed to set the preferences indicated by the URL. To use special URLs, the workstation must be able to accept cookies.

Cookies will expire after 8 hours of inactivity. At this time, the PubMed options will be reset to the default settings. To reactivate your preferences, the user must enter PubMed through the special URL again. You can set LinkOut preferences that will not time out on a workstation by signing the workstation into My NCBI and selecting Keep me signed in unless I sign off.

If you are using a special URL to localize PubMed for your users, you should create a button or link to this URL from your library website. Replace your current PubMed links (in your catalog, on subject pages, etc) with this URL. You should also send out a general announcement so that other departments, faculty, etc. can update their websites and personal computers.

Sharing My NCBI Account Settings

My NCBI accounts can be configured so that Filter selections (including icons), Document Delivery, Outside Tool, and highlighting selections can be shared by multiple users.

To share account settings:

• 1

  Register for a My NCBI account that will be used to share settings with patrons. Libraries should use their LinkOut User Name as the My NCBI account User Name.

• 2

  Sign in to the account and click Preferences to select the services you want for your library’s My NCBI account. Under PubMed Preferences:

  • a

    To select Filters and LinkOut icons, click PubMed Filters and Icons. On the resulting page search for your library and click the check boxes next to “Add as a result tab” and “Add as a link icon.” If you wish to change the library Display Name on the filter tab, you can do so by updating your Library Information in the Submission Utility.

  • b

    To select an Outside Tool, click Outside Tool. On the next page, select the radio button next to the desired library and click “Save”

  • c

    To set a Document Delivery preference, click Document Delivery. On the next page, select the radio button next to the desired library and click “Save”

  • d

    To select highlighting preferences, click Preferences on the Table of Contents. Under “Common Preferences,” click “Highlighting” and select the radio button next to the desired color and click “Save”

• 3

  To select which services to share click Preferences on the Table of Contents and click the Shared Settings link. On the resulting page, click the check boxes for the settings you would like to share. Only the settings for a service where the Share Selection box is checked will be shared. For example as shown in the image below, if you check to share the Filter selections only, the Outside Tool, Document Delivery and Highlighting settings will not be shared.

• 4

  After selecting the features you want to share, use the following special URL to activate the settings:

The myncbishare= parameter can also be appended to www.pubmed.gov.

Create a link to this URL on your library's website and provide it to your patrons to bookmark in their browsers.

The settings activated by the URL parameter myncbishare=username will work in conjunction with the URL parameter holding=, which activates LinkOut icons. To share your My NBCI settings and apply your library icon to citations with free full-text links, use both myncbishare= and holding=NameAbbr_fft. These parameters can be combined using “&”, as shown below:

Outside Tool and Document Delivery Service settings in a shared My NCBI account, if any, will override those set by using the parameters otool= or tool=.

Settings activated using a shared My NCBI account URL will time out after 8 hours of inactivity.

NOTE: A user accessing PubMed through this URL is not signed into My NCBI - the My NCBI box in the upper right will not display, "Welcome username". If the user decides to sign into My NCBI with a personal account, the settings for the personal account will override the library's settings. However, if a user who has accessed PubMed via a shared account URL decides to register for a personal account, the shared settings will be copied to this new account. The user may then edit the My NCBI settings for the personal account as desired.

It is important that library staff store the username and password and the answer to the security question for their shared account in a safe but accessible place; NCBI is not able to provide this information. Keep in mind also that libraries can establish multiple My NCBI accounts, so shared settings may be created for different user groups.

Locating Library Holdings in PubMed

Filter tabs, available through My NCBI, allow users to group library holdings in the search result. You may want to use filter tabs to highlight new library resources or to spotlight other resources that are of interest to your patrons. Libraries can activate filter tabs for their users by sharing My NCBI account settings.

To learn how to display your library holdings as a filter tab, see Using Filters to Display Entrez Records with Links to Specific Resources or view the Library LinkOut Filters Quick Tour (Macromedia Flash™ Player required). To display filters without signing into My NCBI, set up a shared My NCBI account for your patrons.

Alternatively, you can limit a single search to your library holdings by including loprovNameAbbr[sb] in the search. (Replace NameAbbr with the library’s LinkOut User Name). This can be used in any search.

Applying Your LinkOut Icon to Citations with Free Full-Text Links: _fft

To have your library’s LinkOut icon appear on all citations with free full-text links, append holding=NameAbbr_ftt to the PubMed URL and enter PubMed through the resulting URL:

The holding= parameter can also be appended to www.pubmed.gov.

When _fft is appended to the library’s LinkOut User Name in this special URL, library icons will be automatically applied to all citations with links to free full text. _fft can only be used with holding=.

Many LinkOut libraries have added free full-text journals to which they do not subscribe to their library holdings in the Submission Utility, so that their library icon will display on citations with free full-text links. We recommend that libraries include only journals to which they subscribe in their holdings and use _fft to apply library icons to free full-text citations.

Using this special URL will not override library holdings defined in the Submission Utility. If you have designated a fee-based provider for a publication that is freely available elsewhere, your settings will be maintained. For example, if you selected OVID as a provider for a journal that is available elsewhere for free, your library icon will continue to link to OVID, rather than the free site.

This special URL does not add free full-text journals to your library holdings. Your library icon will appear on citations with free full-text links, but the related journals will not appear in your holdings in the Submission Utility, the Libraries list, or the LinkOut Display.

Omitting Default Icons from PubMed Citations:_fft_ndi

Some users have found it confusing to see both the default icon and the library icon, especially when they cannot access the full-text article through the default icon because their library does not have a subscription to the journal. To alleviate this confusion, default icons can be omitted when library icons are applied to citations with free full-text links.

Omitting default icons will remove all default icons from PubMed abstracts, including those that link to free full text. Library icons will appear on citations that are in your library holdings and citations with free full-text links. If your library chooses to omit default icons, library holdings must be kept up to date or users will lose access to online publications.

To omit default icons from the PubMed display and have your library’s LinkOut icon appear on all citations with free full-text links, append holding=NameAbbr_fft_ndi to the PubMed URL:

The holding= parameter can also be appended to www.pubmed.gov.

The ability to omit default icons exists as an enhancement to the ability to automatically apply library icons to citations with free full-text links and cannot be used separately.

Setting the Display Format for a Single Citation

By default, the author names or icons to the left of each citation link to the AbstractPlus format. To change the link to display a different format use the following special URL:

“dr=Display_Format” can also be used with the following special queries:

Setting Document Delivery Service Preferences in PubMed

To set your Document Delivery Service preference through a direct link to PubMed, use the following special URL:

To set your Document Delivery Service preference through a through a direct link to Clinical Queries, Single Citation Matcher, Entrez Cross-Database Search (Gquery) or the Health Services Research use one of the following URLs:

Document Delivery Service preferences can also be set using a shared My NCBI account or by signing in to My NCBI. Instructions for selecting a DDS in My NCBI are available in the Document Delivery section of My NCBI Help.

Clearing Settings Using a Special URL

To clear LinkOut settings activated using a special URL and return to the default PubMed display, access PubMed using the following URLs:

In the above URLs, there are two underscores ( _ ) preceding reset.

Note: The above URLs will only clear icons that have been activated using the specific parameter (holding=, otool=, myncbishare=) in a special URL.