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# Example SPARQL endpoint for Python function
A SPARQL endpoint to serve machine learning models, or any other logic implemented in Python. Serve drug/disease predictions using the OpenPredict classifier.
Built with [RDFLib](https://github.com/RDFLib/rdflib) and [FastAPI](https://fastapi.tiangolo.com/), CORS enabled.
## Example queries 📬
### Get predictions
Concatenate the 2 given string, and also return the length as additional Length variable
```SPARQL
PREFIX myfunctions: <https://w3id.org/um/sparql-functions/>
SELECT ?concat ?concatLength WHERE {
BIND("First" AS ?first)
BIND(myfunctions:custom_concat(?first, "last") AS ?concat)
}
```
### Try a federated query
Use this federated query to retrieve predicted treatments for a drug or disease (OMIM or DRUGBANK) from any other SPARQL endpoint supporting federated queries (note that this query use our test SPARQL endpoints, it might not be always up)
**From another SPARQL endpoint:**
```SPARQL
PREFIX myfunctions: <https://w3id.org/um/sparql-functions/>
SELECT * WHERE
{
SERVICE <https://service.openpredict.137.120.31.102.nip.io/sparql> {
SELECT ?concat ?concatLength WHERE {
BIND("First" AS ?first)
BIND(myfunctions:custom_concat(?first, "last") AS ?concat)
}
}
}
```
**From the RDFLib SPARQL endpoint**
⚠️ RDFLib has a few limitation related to federated queries:
* Unfortunately, the `PREFIX` keyword can crash 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 the RDFLib endpoint https://service.translator.137.120.31.102.nip.io to resolve drug/disease labels retrieved from the Nanopublication network:
```SPARQL
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
}
}
```
### Insert data
Insert data in the in-memory rdflib graph:
```SPARQL
INSERT DATA {
<http://subject> <http://predicate> <http://object> .
}
```
## Install and run ✨️
1. Install dependencies
```bash
pip install -r requirements.txt
```
2. Run the server on http://localhost:8000
```bash
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`:
```bash
docker-compose up -d --build
```
Or build and run with docker:
```bash
docker build -t rdflib-endpoint .
```
Run on http://localhost:8080
```bash
docker run -p 8080:80 rdflib-endpoint
```
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