Relevant ChEBI RDF in WP Endpoint

[DeniseSl22]

@egonw Create Jenkins job for:

1. Download full OWL file of ChEBI
2. Perform SPARQL query to obtain all ChEBI IDs in WP
3. Use ENanomapper Slimmer (?) to only retain ChEBI OWL which we have IDs for (and parent classes).
4. Convert remaining ChEBI OWL to .ttl with Robot.
5. Update the WP SPARQL endpoint with this ttl.

[egonw]

Implemented:

export ONTO=chebi
#rm -f *.owl
#rm -f *.owl.*
rm -f ${ONTO}.props*
rm -f ${ONTO}.iris*
wget https://raw.githubusercontent.com/enanomapper/ontologies/master/config/${ONTO}.props
wget -N `grep "owl=" ${ONTO}.props | cut -d'=' -f2`

echo "SELECT DISTINCT ?chebi WHERE { [] wp:bdbChEBI ?chebi }" > chebi.rq
curl -H "Accept: text/tab-separated-values" --data-urlencode query@chebi.rq -G http://sparql.wikipathways.org/sparql -o chebi.tsv
grep -v "\"chebi\"" chebi.tsv > chebi2.tsv
sed -i 's/"http:\/\/identifiers.org\/chebi\/CHEBI:/+U:http:\/\/purl.obolibrary.org\/obo\/CHEBI_/' chebi2.tsv
sed -i 's/\"//' chebi2.tsv
cp chebi2.tsv ${ONTO}.iris

wget -N https://github.com/enanomapper/slimmer/releases/download/v1.0.1/slimmer-1.0.1-jar-with-dependencies.jar
java -Dhttps.proxyHost=proxy.unimaas.nl -Dhttps.proxyPort=3128 -Dhttp.proxyHost=proxy.unimaas.nl -Dhttp.proxyPort=3128 -cp slimmer-1.0.1-jar-with-dependencies.jar com.github.enanomapper.Slimmer .

rapper -i rdfxml -o turtle chebi-slim.owl > chebi-slim.ttl

[egonw]

@marvinm2, can you update the SPARQL data loading procedure to load the chebi-slim.ttl into the SPARQL endpoint, plz?

[egonw]

@marvinm2, this was now done, right?

[marvinm2]

Yes, it's in the endpoint!