EuropePMCLinks

Repository for code to create the Europe PMC external links.

The idea is to create links from Europe PMC to WikiPathways for articles cited in our pathways. The links are provided to Europe PMC as a combination of two XML files, one with a profile (profile.xml) and the other a link set. This one can be generated from the RDF, which already takes care of detection of (some) faulty PubMed identifiers.

Generation

Step 1 is the listing of all PubMed identifiers and associated pathways from the Analysis and Reactome collections:

curl -H "Accept: text/csv" --data-urlencode query@query.rq -G https://sparql.wikipathways.org/sparql -o pmid2wpid.csv

Step 2 is the generation of the links XML (using Groovy and Java8), which requires passing the provider ID as allocated by EuropePMC:

groovy makeLinkXML.groovy <providerID> > links.xml

Step 3 is the validation of the links XML:

curl https://europepmc.org/docs/labslink.xsd -o labslink.xsd
xmllint --noout --schema labslink.xsd links.xml

Example output

<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<links>
  <link providerId="-1">
    <resource>
      <title>DAP12 interactions (Homo sapiens)</title>
      <url>https://www.wikipathways.org/instance/WP2694</url>
      <image>https://www.wikipathways.org//wpi/wpi.php?action=downloadFile&amp;type=png&amp;pwTitle=Pathway:WP2694</image>
    </resource>
    <record>
      <source>MED</source>
      <id>10021361</id>
    </record>
  </link>
</links>

Upload to EuropePMC

Finally, the links.xml and profile.xml files are uploaded to EuropePMC's FTP server. The credentials are available with the current uploader. The file is placed in a hidden folder.

ncftp -u <secretuser> -p <password> something.ebi.ac.uk
cd <hiddenFolder>