SPARQL endpoint for Translator services

A SPARQL endpoint to serve NCATS Translator services as SPARQL custom functions. Built with rdflib-endpoint

Access the SPARQL service endpoint at https://service.translator.137.120.31.102.nip.io/sparql

OpenAPI docs at https://service.translator.137.120.31.102.nip.io

Translator APIs integrated:

• https://nodenormalization-sri.renci.org/docs

Available functions 📬

Try the queries on YASGUI

Get label for entity

From a CURIE, or URI following this pattern: https://identifiers.org/NAMESPACE:ID

PREFIX umtranslator: <https://w3id.org/um/translator/>
SELECT ?entity ?label WHERE {
    BIND("MONDO:0005146" AS ?entity)
    BIND(umtranslator:get_label(?entity) AS ?label)
}

Get preferred ID

From a CURIE, or URI following this pattern: https://identifiers.org/NAMESPACE:ID

PREFIX umtranslator: <https://w3id.org/um/translator/>
SELECT ?entity ?pref_id WHERE {
    BIND("MONDO:0005146" AS ?entity)
    BIND(umtranslator:pref_id(?entity) AS ?pref_id)
}

Try a federated query

Use this federated query to retrieve labels from any other SPARQL endpoint supporting federated queries.

From another SPARQL endpoint

PREFIX umtranslator: <https://w3id.org/um/translator/>
SELECT * WHERE
{
  SERVICE <https://service.translator.137.120.31.102.nip.io/sparql> {
    SELECT ?entity ?label WHERE {
        BIND("MONDO:0005146" AS ?entity)
        BIND(umtranslator:get_label(?entity) AS ?label)
    }
  }
}

From the RDFLib SPARQL endpoint

⚠️ RDFLib has a few limitation related to federated queries:

• Unfortunately, the PREFIX keyword does not work with federated queries in RDFLib, so we need to write the full URIs

• The latest version of RDFLib (5.0.0 ) only recognize lowercase service. This will be fixed in the next versions.

Run this federated query on this RDFLib endpoint to resolve drug/disease labels retrieved from the Nanopublication network:

SELECT DISTINCT ?label ?subject ?object (<https://w3id.org/um/translator/get_label>(str(?subject)) AS ?subjectLabel) (<https://w3id.org/um/translator/get_label>(str(?object)) AS ?objectLabel)
WHERE {
  	service <http://virtuoso.np.dumontierlab.137.120.31.101.nip.io/sparql> {
        SELECT * WHERE {
            GRAPH ?np_assertion {
              ?association <http://www.w3.org/2000/01/rdf-schema#label> ?label ;
                <http://www.w3.org/1999/02/22-rdf-syntax-ns#subject> ?subject ;
                <http://www.w3.org/1999/02/22-rdf-syntax-ns#predicate> ?predicate ;
                <http://www.w3.org/1999/02/22-rdf-syntax-ns#object> ?object .
              optional {
                ?association <https://w3id.org/biolink/vocab/relation> ?relation .
              }
              optional {
                ?association <https://w3id.org/biolink/vocab/provided_by> ?provided_by .
              }
              optional {
                ?association <https://w3id.org/biolink/vocab/association_type> ?association_type .
              }
              ?subject <https://w3id.org/biolink/vocab/category> ?subject_category .
              ?object <https://w3id.org/biolink/vocab/category> ?object_category .
            }
            filter ( ?subject_category = <https://w3id.org/biolink/vocab/Drug> || ?subject_category = <https://w3id.org/biolink/vocab/ChemicalSubstance> )
            filter ( ?object_category = <https://w3id.org/biolink/vocab/Disease> )
            GRAPH ?np_head {
                ?np_uri <http://www.nanopub.org/nschema#hasAssertion> ?np_assertion .
            }
                ?np_uri <http://purl.org/dc/terms/creator> <https://orcid.org/0000-0002-7641-6446> .
            	filter NOT EXISTS { ?creator <http://purl.org/nanopub/x/retracts> ?np_uri }
        } LIMIT 5
  	}
}

Note: Adding this filter make the federated query crash in RDFLib (works with Fuseki functions):

            GRAPH <http://purl.org/nanopub/admin/graph> {
                ?np_uri <http://purl.org/nanopub/admin/hasValidSignatureForPublicKey> ?pubkey .
            }

Install and run ✨️

1. Install dependencies

pip install -r requirements.txt

2. Run the server on http://localhost:8000

uvicorn main:app --reload --app-dir app

Or run with docker 🐳

Checkout the Dockerfile to see how the image is built, and run it with the docker-compose.yml:

docker-compose up -d --build

Or build and run with docker:

docker build -t rdflib-endpoint .

Run on http://localhost:8080

docker run -p 8080:80 rdflib-endpoint

Or deploy on the DSRI

Build from the Dockerfile and deploy in a DSRI project with HTTPS enabled:

oc new-build --name translator-sparql --binary
oc start-build translator-sparql --from-dir=. --follow --wait
oc new-app translator-sparql
oc patch deployment/translator-sparql --patch '{"spec":{"template": {"spec":{"serviceAccountName": "anyuid"}}}}'
oc expose svc/translator-sparql
oc patch route/translator-sparql --patch '{"spec":{"tls": {"termination": "edge", "insecureEdgeTerminationPolicy": "Redirect"}}}'

Get the routes exposed in your project:

oc get route

Delete:

oc delete build translator-sparql