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Information for Libraries

Created: ; Last Update: September 17, 2012.

LinkOut provides direct links from PubMed and other NCBI databases to a wide range of information and services beyond the NCBI systems. LinkOut aims to facilitate access to relevant online resources to extend, clarify, and supplement information found in NCBI databases. LinkOut resources include full-text publications, biological databases, consumer health information, research tools, and more (see examples of LinkOut resources).

Through LinkOut, links specially assigned to specific citations and database records provide direct access to relevant external resources.

“Information for Libraries” contains the information you need to set up and support LinkOut for your library and users.

For answers to Frequently Asked Questions, see the FAQ for LinkOut Libraries.

For additional information about the various types of links found in NCBI databases, please see Databases in Entrez Help.

How LinkOut Works for Libraries

LinkOut allows participating libraries to link directly from PubMed citations to their library’s online full-text subscriptions and local print holdings records or to an OpenURL-based service (link resolver) implemented by the institution. Through LinkOut, links are specially assigned to specific PubMed citations. Resources that have been linked to PubMed citations through LinkOut can be accessed directly with no additional searching required.

There are three types of library links available:

1.

link to online full text for a citation from the library’s full-text provider

2.

link to a library print holdings record

3.

link to the library’s link resolver or other local service

To add library links to PubMed citations available electronically or in print from the library, libraries must submit holdings information to NCBI. LinkOut looks at the library’s holdings information and applies the appropriate link to PubMed citations included in the library’s holdings.

When a user clicks a link for online full text or a local service, the user leaves PubMed and is redirected to the full-text provider’s site or the local service. When a user clicks a link for a print holdings record, they are shown a print holdings record generated by LinkOut.

Links to online full text are created using linking information submitted by full-text providers, including publishers, aggregators, and agents working on behalf of publishers. For libraries to link to full text from a particular provider, that provider must submit linking information to NCBI. To see a list of full-text providers that participate in LinkOut and the journals for which they submit links, see the list of LinkOut journals.

LinkOut does not perform any user verification. Once a user clicks on a link for online full text or a local link resolver, access depends on pre-existing licensing agreements between the library and the full-text provider(s).

Before Registering

You should:

  • Discuss with your library staff the NCBI Library LinkOut program
  • Review the section How LinkOut works for Libraries section of this manual and the LinkOut FAQs.
  • See the comparison table for LinkOut via the Submission Utility, LinkOut Local and Outside Tool which may help decide which service to implement for your library
Table 1: Comparing the features of LinkOut, LinkOut Local and Outside Tool

Table

Table 1: Comparing the features of LinkOut, LinkOut Local and Outside Tool.

If you have questions:

Managing Library Holdings in the Submission Utility

Send an email message to vog.hin.mln.ibcn@ger-bil to register for an account. Enter “LinkOut Registration Request” in the subject line of the email.

Please use the format:

Subject: LinkOut Registration Request
Library Name:
Organization Name:
Contact Person:
Email Address:
Phone Number:
Address:
LIBID: Optional. (Please include if your library is a member of NLM’s DOCLINE.)

Within a week, you will receive a User Name and Password that will allow you access to the Library Submission Utility.

In the Library Submission Utility, libraries can edit:

Managing Library Holdings using a Local Link Resolver (LinkOut Local)

Section Contents

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.

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.

Identity File

The identity file contains the information about your library that NCBI needs to list your library in LinkOut. This file must be named “providerinfo.xml”.

NOTE: This file should be composed in a text editor, such as Notepad, not in a word processing program, such as MS Word. Word processing programs add unnecessary formatting information to the file.

The following is an example providerinfo.xml file for University Library, with ProviderId “9999” and NameAbbr “unilib”:

<?xml version="1.0"?>
<!DOCTYPE Provider PUBLIC "-//NLM//DTD LinkOut 1.0//EN"
"http://www.ncbi.nlm.nih.gov/projects/linkout/doc/LinkOut.dtd">
<Provider>
<!---ProviderId is assigned by NCBI-->
<ProviderId>9999</ProviderId>
   <Name>University Library</Name>
   <NameAbbr>unilib</NameAbbr>
   <SubjectType>libraries</SubjectType>
   <Url>http://www.librarywebsite.edu</Url>
</Provider>

See LinkOut Technical Information: Identity File or the LinkOut DTD for complete file specifications and description of elements.

Resource File

The resource file contains the list of your library holdings that LinkOut will use to apply your icons to PubMed citations. The resource file is usually generated by your link resolver. See LinkOut Technical Information: Resource File or the LinkOut DTD for complete file specifications and description of elements.

NOTE: This file should contain only journals included in PubMed. A list of PubMed journals is available. Only one <Query> line should appear per journal (ISSN).

The resource file should have the following format:

<?xml version="1.0" ?>
<!DOCTYPE LinkSet PUBLIC "-//NLM//DTD LinkOut 1.0//EN"
"http://www.ncbi.nlm.nih.gov/projects/linkout/doc/LinkOut.dtd">
<LinkSet>
   <Link>
     <LinkId>openurl_local</LinkId>
     <ProviderId>9999</ProviderId>
     <IconUrl>http://www.mylibrary.org/icon.gif</IconUrl>
     <ObjectSelector>
        <Database>PubMed</Database>
        <ObjectList>
           <Query>"1234-5678" [is] AND 1994:2010 [dp]</Query>
           <!---Additional queries-->
           <Query>"9999-9999" [is] AND 1990:2010 [dp]</Query>
        </ObjectList>
     </ObjectSelector>
     <ObjectUrl>
        <Base>http://baseURL/OpenURL_local</Base>
        <Rule>?sid=Entrez:PubMed&amp;id=pmid:&lo.id;</Rule>
        <UrlName>Link to Resolver/Service Name</UrlName>
     </ObjectUrl>
   </Link>
</LinkSet>

Validate your LinkOut files using the File Validation Utility available here: http://www.ncbi.nlm.nih.gov/projects/linkout/doc/validate.shtml.

Once your files are validated proceed to register for a LinkOut Local account.

Registering for LinkOut Local

Libraries that implement LinkOut Local upload holdings information directly to LinkOut in the form of XML files. Libraries that seek to implement LinkOut Local should have technical expertise in XML, and should be able to produce files compliant to the LinkOut format independently. See the LinkOut Local section of this manual for file preparation.

After the files have been validated, send an email to vog.hin.mln.ibcn@tuoknil-bil. Attach your identity and resource files to the email. If your library participates in LinkOut or Outside Tool, please also include your LinkOut/Outside Tool User Name.

In the body of the message, include the following information. Please use this format:

Subject: Request to Implement LinkOut Local
Library Name:
Contact Person:
Email Address:
Phone Number:
Address:
LinkOut/Outside Tool User Name:
Link resolver vendor:
LIBID: Optional. Please include if your library participates in NLM SERHOLD.

NCBI staff will email the contact person regarding the request in a month.

Note: Since only a limited number of LinkOut Local requests are handled each week, the implementation process can be a lengthy one.

PubMed and OpenURL-based Services

Section Contents

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 display 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 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 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

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.

In order to best serve all users and expedite processing, libraries requesting Outside Tool must provide a unique base URL that identifies their link resolver. Outside Tool requests that list a base URL already registered with NCBI will not be assigned a new Outside Tool account. Instead, the existing Tool registered with NCBI with the same base URL should be used.

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:

Example
Base URL: http://baseURL/OpenURL_local
Tail: ?sid=Entrez:PubMed&id=pmid:
PMID: 12345678
Resulting URL: http://baseURL/OpenURL_local?sid=Entrez:PubMed&id=pmid:12345678

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

18984876
20042755
14316043
15390390
12337850
12076440
12259237

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.

Localizing PubMed for Your Users

In addition to displaying library icons in PubMed, there are a variety of ways to “localize” the PubMed display, allowing users to link directly from PubMed to library services and other resources. This section provides information on:

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 filters as well.

A few examples of how localization might be used:

- A small hospital library uses a special URL to display library holdings and automatically apply their library icon to all PubMed citations with links to free full-text, clearly marking all articles available to their users.

- A departmental library at a large institution uses a filter to group departmental holdings and a special URL to display a link to the institution-wide link resolver on PubMed citations. Users recognize which articles are immediately available and can locate or order others.

- A hospital library selects two additional filters besides their library holdings: one filter highlights citations with links to National Guideline Clearinghouse material, of particular interest to their clinicians, and another filter displays the holdings of their affiliated medical school.

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 view a brief animated tutorial, see My NCBI Share Settings.

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 NCBI Site 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 under the columns “Filter” and “Link icon.” If you wish to change the library Display Name on the filter link, 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 the link Highlighting under Common Preferences. Select the radio button next to the desired color and click “Save”

3.

To select which services to share click the links NCBI Site Preferences and click the Shared Settings link under Common Preferences. 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.

Image lib.G3.jpg

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

PubMed: http://www.ncbi.nlm.nih.gov/pubmed?myncbishare=MyNCBIusername
Single Citation Matcher: http://www.ncbi.nlm.nih.gov/pubmed/citmatch?myncbishare=MyNCBIusername
Clinical Queries: http://www.ncbi.nlm.nih.gov/pubmed/clinical?myncbishare=MyNCBIusername
Advanced Search: http://www.ncbi.nlm.nih.gov/pubmed/advanced?myncbishare=MyNCBIusername
GQuery: http://www.ncbi.nlm.nih.gov/gquery?myncbishare= MyNCBIusername

Replace username with the shared My NCBI account User Name.

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:

http://www.ncbi.nlm.nih.gov/pubmed?myncbishare=MyNCBIUserName&holding=NameAbbr_fft
Replace MyNCBIUserName with the shared My NCBI account name and NameAbbr with the library’s LinkOut User Name.

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.

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

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

To learn how to display your library holdings as a filter, see Using Filters to Display NCBI Database Records with Links to Specific Resources. 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.

Example: Search PubMed for citations with MESH term “AIDS” included in the LinkOut Demo Library collection (User Name: psrmlib)
AIDS[mh] AND loprovpsrmlib[sb]

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:

http://www.ncbi.nlm.nih.gov/pubmed?holding=NameAbbr_fft
Replace NameAbbr with your library’s LinkOut User Name.

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=.

Example: Automatically apply LinkOut icons for the PSRML Demonstration Library, User Name psrmlib, to all citations with free full-text links
http://www​.ncbi.nlm.nih​.gov/pubmed?holding=psrmlib_fft
To see the icons, try the following:
1. Enter PubMed through the URL above.
2. Search for free full text [sb].
3. Select Abstract from the Display pull-down menu.
4. The PSRML Library icons will display on all citations.

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.

Caution! The decision to omit default icons from PubMed search results should be made with special care! Please discuss this decision with library staff before omitting default icons. Omitting default icons may deprive users of access to materials. Additionally, users may inadvertently deprive others of access by sharing the URL you provide to them.

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:

http://www.ncbi.nlm.nih.gov/pubmed?holding=NameAbbr_fft_ndi
Replace NameAbbr with your library’s LinkOut User Name.

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

Example: Display icons for the PSRML Demonstration Library, User Name psrmlib, apply PSRML icons to all citations with free full-text links, and omit default icons
http://www​.ncbi.nlm.nih​.gov/pubmed?holding=psrmlib_fft_ndi
To see the icons, try the following:
1. Enter PubMed through the URL above.
2. Search for free full text [sb].
3. Select Abstract from the display settings menu
4. The PSRML Library icons will display on all citations.

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 Document Delivery Service Preferences in PubMed

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

http://www.ncbi.nlm.nih.gov/pubmed?tool=DDS
Replace DDS with the Document Delivery Service user name assigned by NCBI.

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

Single Citation Matcher: http://www.ncbi.nlm.nih.gov/pubmed/citmatch?tool=DDS
Advanced Search: http://www.ncbi.nlm.nih.gov/pubmed/advanced?tool=DDS
Clinical Queries: http://www.ncbi.nlm.nih.gov/pubmed/clinical?tool=DDS
GQuery: http://www.ncbi.nlm.nih.gov/gquery?tool=DDS
HSR Queries http://www.nlm.nih.gov/nichsr/hedges/search.html?tool=DDS

Replace DDS with the Document Delivery Service user name assigned by NCBI.

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:

To clear the LinkOut icon:
http://www.ncbi.nlm.nih.gov/pubmed?holding=__reset
To clear the Outside Tool icon:
http://www.ncbi.nlm.nih.gov/pubmed?otool=__reset
To clear the myncbishare setting:
http://www.ncbi.nlm.nih.gov/pubmed?myncbishare=__reset
To clear the document delivery setting:
http://www.ncbi.nlm.nih.gov/pubmed?tool=__reset

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.

PubReader format: click here to try

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