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STARDOG.md

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EVSRESTAPI - STARDOG SETUP

Information on downloading and using stardog with EVSRESTAPI.

Running Stardog Locally

Initial setup (create a volume to store data/license)

  • Verify your $dir points to the correct path we set in the previous steps. If not, set it now:
    export set dir=c:/Users/carlsenbr/eclipse-workspace/data/

    docker pull stardog/stardog:latest
docker volume create --name stardog-home2 -d local

  • Using an existing stardog license (in $dir). Make sure your license file is called stardog-license-key.bin and is in the $dir directory on your local machine.

    docker run -it --entrypoint "/bin/bash" -v "$dir":/data -v stardog-home2:/var/opt/stardog stardog/stardog
[stardog@0b9fbb0b90ba bin]# cp /data/stardog-license-key.bin /var/opt/stardog
[stardog@0b9fbb0b90ba bin]# exit

  • Obtaining Stardog Licence - Request License from Stardog directly.

    • This isn't a guaranteed solution unfortunately and you could be denied.

  • Download the ThesaurusInferred.owl and save it in $dir

  • Loading NCIt ThesaurusInferred.owl (after license is setup). Make sure the local volume being mounted is the one that contains the ThesaurusInferred.owl file.

    docker run -it --entrypoint "/bin/bash" -p 5820:5820 -v "$dir":/data -v stardog-home2:/var/opt/stardog stardog/stardog
[stardog@0b9fbb0b90ba bin]# export STARDOG_SERVER_JAVA_ARGS="-Xmx4g -Xms3g -XX:MaxDirectMemorySize=4g"
[stardog@0b9fbb0b90ba bin]# /opt/stardog/bin/stardog-admin server start

# Check if the NCIT2 db already exists
[stardog@0b9fbb0b90ba bin]# /opt/stardog/bin/stardog-admin db list

# If not, create it
[stardog@0b9fbb0b90ba bin]# /opt/stardog/bin/stardog-admin db create -n NCIT2
[stardog@0b9fbb0b90ba bin]# /opt/stardog/bin/stardog data add --named-graph http://NCI_T NCIT2 /data/ThesaurusInferred.owl
[stardog@0b9fbb0b90ba bin]# /opt/stardog/bin/stardog-admin db optimize NCIT2

Running Stardog Locally (after data is loaded)

  dir=c:/Users/carlsenbr/eclipse-workspace/data/
  docker run -d --name=stardog_evs --rm -p 5820:5820 -v "$dir":/data -v stardog-home2:/var/opt/stardog -e STARDOG_SERVER_JAVA_ARGS="-Xmx4g -Xms3g -XX:MaxDirectMemorySize=4g" stardog/stardog

Log into a Running Stardog Container

  docker exec -it <container_id, e.g. 3c29d72babc2> /bin/bash
  • Running a sparql query (assumes stardog running on localhost and curl and jq are installed)

Start by configuring your environment

STARDOG_HOST=localhost
STARDOG_PORT=5820
STARDOG_USERNAME=admin
STARDOG_PASSWORD=admin
STARDOG_URL=http://${STARDOG_HOST}:${STARDOG_PORT}
STARDOG_DB=NCIT2

Next, put your query into a file. Make sure to include prefixes and the correct graph name.

cat > query.txt << EOF
PREFIX :<http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#> 
PREFIX base:<http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#>
PREFIX owl:<http://www.w3.org/2002/07/owl#>
PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>
PREFIX xsd:<http://www.w3.org/2001/XMLSchema#>
PREFIX dc:<http://purl.org/dc/elements/1.1/>
PREFIX oboInOwl:<http://www.geneontology.org/formats/oboInOwl#>
PREFIX xml:<http://www.w3.org/2001/XMLSchema#>
SELECT ?code
{ GRAPH <http://NCI_T_monthly> 
    { 
      ?x a owl:Class . 
      ?x :NHC0 ?code .
      ?x :P108 "Melanoma"
    }
}
ORDER BY ?conceptCode
EOF

Then, run the query.

q=`cat query.txt`
curl -v -g -u "${STARDOG_USERNAME}:$STARDOG_PASSWORD" "$STARDOG_URL/NCIT2/query" --data-urlencode "query=$q" -H "Accept: application/sparql-results+json" | jq