Code for the new WikiPathways website to convert datanodes.tsv into WikiPathways RDF triples

createBridgeDbMappings.groovy

@Grab(group='org.bridgedb', module='org.bridgedb.bio', version='3.1.1')

import java.util.ArrayList
import java.util.List
import java.util.Map
import java.util.HashMap

import java.nio.file.Path
import java.nio.file.Files

import static groovy.io.FileType.FILES

import org.bridgedb.Xref
import org.bridgedb.DataSource
import org.bridgedb.bio.DataSourceTxt

DataSourceTxt.init()

// extract the BridgDb ID mappings

Map<String,List> mappings = new HashMap<>();

def dir = new File("pathways");
def files = [];
dir.traverse(type: FILES, maxDepth: 2) {
  if (it.name.endsWith("-datanodes.tsv")) {
    files.add(it)
  }
};

files.each { file ->
  file.eachLine { line ->
    mappedIDs = new ArrayList<String>()
    fields = line.split('\t')
    if (fields.size() > 4) {
      mainID = fields[2]
      for (col in 4..(fields.size()-1)) {
        field = fields[col]
        if (field != null && field.length() > 0) {
          mappedIDs.addAll(fields[col].split(';'))
        }
      }
      mappings.put(mainID, mappedIDs)
    }
  }
}

// export Turtle

def String asIdentifiersOrg(String compactId) {
  xref = Xref.fromBioregistryIdentifier(compactId)
  if (xref != null && "Opt".equals(xref.getDataSource().getSystemCode()))
    xref = new Xref(xref.getId(), DataSource.getExistingBySystemCode("En"))
  if (xref == null) return null
  return xref.getMiriamURN().replace("urn:miriam:", "https://identifiers.org/").replace(":", "/")
}

mappings.each { id ->
  //println "== ${id.key}"
  iri = asIdentifiersOrg(id.key)
  if (iri != null) {
    id.value.each { mappedId ->
      mappedIri = asIdentifiersOrg(mappedId)
      if (mappedIri != null) {
        if (mappedId.startsWith("ensembl:")) { println "<${iri} wp:bdbEnsembl <${mappedIri}> ." }
        else if (mappedId.startsWith("wikidata:")) { println "<${iri} wp:bdbWikidata <${mappedIri}> ." }
        else if (mappedId.startsWith("wikidata:")) { println "<${iri} wp:bdbUniprot <${mappedIri}> ." }
      }
    }
  } else {
    // println "NULL xref for ${id}"
  }
}