Merge pull request #7 from Minitour/feature/sparql-query

Add sparql_query tool for SPARQL querying over OWL files

Author: Minitour

Cargo.lock

@@ -23,6 +23,7 @@ rust-mcp-sdk = { version = "0.8", default-features = false, features = [
 ] }
 horned-owl = "1.4"
 whelk = { git = "https://github.com/INCATools/whelk-rs" }
+oxigraph = { version = "0.5", default-features = false }
 curie = "0.1"
 tokio = { version = "1", features = ["full"] }
 serde = { version = "1", features = ["derive"] }

Cargo.toml

@@ -12,7 +12,7 @@ Built as a drop-in replacement for [ai4curation/owl-mcp](https://github.com/ai4c
 
 ## Features
 
-- **11 MCP tools** — add, remove, search, and inspect axioms; manage prefixes, labels, and ontology IRIs; scan for modeling pitfalls; evaluate ontology quality
+- **12 MCP tools** — add, remove, search, and inspect axioms; manage prefixes, labels, and ontology IRIs; scan for modeling pitfalls; evaluate ontology quality; run SPARQL queries
 - **CLI mode** — every tool is also available as a direct CLI subcommand (`owl-mcp find-axioms ...`)
 - **2 transport modes** — `stdio` (default, for Cursor/Claude Desktop) and `http` (Streamable HTTP + SSE)
 - **Live file watching** — automatically reloads ontology files modified externally
@@ -71,6 +71,8 @@ owl-mcp find-axioms --file ontology.owl --pattern "Dog" --limit 50
 owl-mcp get-all-axioms --file ontology.owl --include-labels
 owl-mcp test-pitfalls --file ontology.owl
 owl-mcp test-quality --file ontology.owl
+owl-mcp sparql --file ontology.owl --query "SELECT ?c WHERE { ?c a owl:Class }"
+owl-mcp sparql --file schema.owl --file data.owl --query "ASK { ?i a :Plan }"
 ```
 
 Run `owl-mcp --help` for a full list of commands, or `owl-mcp <command> --help` for details on a specific command.
@@ -144,6 +146,14 @@ All tools operate on OWL files by absolute path. The manager lazily loads files
 
 `test_quality` uses the [whelk](https://github.com/INCATools/whelk-rs) OWL EL reasoner to compute inferred class hierarchy and returns a JSON report containing 19 raw and scaled metrics (ANOnto, AROnto, CBOOnto, CROnto, DITOnto, INROnto, LCOMOnto, NACOnto, NOCOnto, NOMOnto, RFCOnto, RROnto, TMOnto, WMCOnto, and variants), 22 subcharacteristics, 7 quality characteristics (Structural, Functional Adequacy, Maintainability, Operability, Reliability, Transferability, Compatibility), and an overall OQuaRE score on a 1–5 scale.
 
+### Querying
+
+| Tool | Description |
+|---|---|
+| `sparql_query` | Run a SPARQL query over one or more OWL files |
+
+`sparql_query` takes `owl_file_paths` (one or more absolute paths) and a `query` string. Each file is serialized to RDF and loaded together into an in-memory [oxigraph](https://github.com/oxigraph/oxigraph) store, so passing several paths merges a schema with its ABox or imports before the query runs. `SELECT` and `ASK` return the standard [SPARQL 1.1 JSON results](https://www.w3.org/TR/sparql11-results-json/) format; `CONSTRUCT` and `DESCRIBE` return a list of N-Triples. Queries run over asserted triples (no reasoning is applied).
+
 ## Development
 
 ```bash

README.md

@@ -138,6 +138,16 @@ pub enum CliCommand {
         #[arg(long)]
         pitfalls: Option<String>,
     },
+
+    /// Run a SPARQL query over one or more OWL files (merged into one RDF graph)
+    Sparql {
+        /// Absolute path to an OWL file. Repeat --file to merge several (e.g. schema + ABox).
+        #[arg(long = "file", required = true)]
+        files: Vec<String>,
+        /// SPARQL query string (SELECT, ASK, CONSTRUCT, or DESCRIBE)
+        #[arg(long)]
+        query: String,
+    },
 }
 
 fn print_result(result: CallToolResult) {
@@ -285,6 +295,16 @@ pub async fn dispatch(cmd: CliCommand, manager: Manager) {
             )
             .await
         }
+        CliCommand::Sparql { files, query } => {
+            tools::SparqlQuery::run_tool(
+                tools::SparqlQuery {
+                    owl_file_paths: files,
+                    query,
+                },
+                &manager,
+            )
+            .await
+        }
     };
 
     match result {

src/cli.rs

@@ -61,6 +61,7 @@ impl ServerHandler for OwlMcpHandler {
             OwlTools::SetOntologyIri(p) => SetOntologyIri::run_tool(p, mgr).await,
             OwlTools::TestQuality(p) => TestQuality::run_tool(p, mgr).await,
             OwlTools::TestPitfalls(p) => TestPitfalls::run_tool(p, mgr).await,
+            OwlTools::SparqlQuery(p) => SparqlQuery::run_tool(p, mgr).await,
         }
     }
 

src/handler.rs

@@ -3,6 +3,7 @@ mod handler;
 mod ontology;
 mod pitfalls;
 mod quality;
+mod sparql;
 mod tools;
 
 use std::sync::Arc;