Introduction

The external links service is a mechanism for people to publish links from articles in Europe PMC to related information or tools. Simply put, you provide us with the information we need to generate the links in a straightforward data description, and we publish them on the Europe PMC website.

The motivation for the external links service stems from the need for the data mining community to showcase results within a live production service. In return, we hope that fostering the long tail of innovation in this way will lead to the identification of useful applications by the users of Europe PMC.

Use of the external links service is not limited to data miners. It is a mechanism that could be used to link databases, datasets, full text articles or coursework too. If it is in scope for Europe PMC and can be linked to sets of articles, then it is possible to participate.

Ground rules

• Links should have destinations that are relevant to, and extend Europe PMC content.
• Link destinations should be public and accessible without restrictions (no subscriptions, log-in screens).
• Links to marketing or sales content are not appropriate (spam).
• Image URLs supplied with links should convey useful information (no product or company logos).
• All links we publish will be considered public domain and will be published both on the website and shared in the web services.
• We strongly encourage any algorithms/code used to generate link sets are sharable/open source.
• We reserve the right to take down links, if, for example, the content is not in scope, or is no longer reasonably maintained.

Getting started

Please email us at labslink@europepmc.org, briefly describing the links you wish to share. We will assign you with the information you need to generate the files and upload your links.

Once you have generated files according to the instructions below, you will be able to upload data to a private directory on the external links service FTP site.

We have tried to make it easy, so that even if you do not have strong technical skills then it should be possible to contribute, and have developed some tools to help with file generation that are described below.

Data requirements

Once you have contacted us at the email address above, we will assign you a providerID that you will need to use in the following submitted files:

We require two components for each set of links:

1. A profile file that describes the link set you are submitting.
2. A file containing the links.

Each set of links needs to have a profile and providerID. An individual person can have more than one profile and therefore more than one providerID. The profile and providerID relate to the set of links being supplied, not the contact person.

Example of a profile file

<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<providers>
  <provider>
    <id>4580</id>
    <resourceName>Biodiversity Browser</resourceName>
    <description>Species names mined from text and linked to Wikipedia</description>
    <email>jbloggs@biodivres.org</email>
  </provider>
</providers>
			

Example of a links file

<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<links>
  <link providerId="4580">
    <resource>
      <title>Scleractinia (stoney corals)</title>
      <url>http://en.wikipedia.org/wiki/Scleractinia</url>
    </resource>
    <record>
      <source>MED</source>
      <id>23457605</id>
    </record>
  </link>
  <link providerId="4580">
    <resource>
      <title>Millepora alcicornis (sea ginger)</title>
      <url>http://en.wikipedia.org/wiki/Millepora_alcicornis</url>
      <image>https://upload.wikimedia.org/wikipedia/commons/thumb/9/9c/Millepora_alcicornis_%28Branching_Fire_Coral%29.jpg/240px-Millepora_alcicornis_%28Branching_Fire_Coral%29.jpg</image>
    </resource>
    <record>
      <source>PMC</source>
      <id>PMC3407933</id>
    </record>
  </link>
  <link providerId="4580">
    <resource>
      <title>Tubastrea</title>
      <url>http://en.wikipedia.org/wiki/Tubastrea</url>
    </resource>
    <record>
      <source>MED</source>
      <id>17134995</id>
    </record>
  </link>
</links>
			

Materials and tools for file generation

• Schema: labslink.xsd.
• Technical documentation: labslink_schema_documentation.pdf.
• Using Excel to generate external links data: labslink_excel_instructions.pdf.
• Demonstration Perl program to generate LabsLink files: labslink_tab_convert.zip.
• If you are familiar with LinkOut from the NCBI, then we may be able to convert those files for use in Europe PMC. Please send us examples of the LinkOut files you use, and we will let you know if we can convert them.

What happens once I have uploaded my files to the FTP site?

Monitoring scripts will check directories for files with new date stamps. These files will be checked for validity and loaded into the external links service database, after which they will be processed for publication on the Europe PMC website.

It is important to note that whatever is in the directory is what will appear on the Europe PMC website. It is up to you to maintain the data in this directory, for example, deleting links you no longer wish to display, or uploading updates based on new content. The current file size limit is 2 MB per file (compressed, this represents about 100,000 links; uncompressed, about 5,000 links).

Publication view

Once your links files have been processed, you will be able to view links from a PMID or PMCID. There will be an 'External Links' tab on pages displaying articles under which links will be displayed. For the data used in this example, the display would look like this

Finding articles that have external links

A search term can be used to retrieve all the articles linked to a provider, for example: HAS_LABSLINKS:y