odk-robot

name

odk-robot

description

Run ROBOT for ontology QC, merge, reason, convert, template, or query. Use whenever the user needs to verify an ontology, validate OWL profile, merge OWL files, run a reasoner, convert OWL/OBO, build terms from CSV+template, or run SPARQL/DL over an ontology—e.g. "run robot verify", "merge these OWL files", "convert to OBO", "template from this CSV". This is the only skill for ROBOT; do not use odk-run for robot.

ODK Robot Skill

Use this skill when the user needs to run ROBOT for: verify (rule-based QC), validate OWL 2 profile, merge ontologies, reason (classification/inference), convert format (OWL ↔ OBO etc.), template (generate terms from CSV + template), or query (SPARQL or DL). Use the odk_robot tool (activate with setup_tools(skills: ["odk-robot"]), then call_tool(name: "odk_robot", data: {...}))—do not run robot via shell or odk_run. This is the only way to run ROBOT in this project.

Paths: The ODK Docker wrapper mounts a project directory at /work. Paths in robot_args are relative to that mounted root.

• Workspace ontology (no project_dir): Omit or leave project_dir empty. The current working directory is mounted; paths are relative to it (e.g. ontology/edit.owl).
• Cloned project under projects/<slug>/: Pass project_dir = the clone root (e.g. projects/owner-repo). Paths in robot_args are then relative to the clone root (e.g. ontology/edit.owl or the edit file path in the project). Always use the built-in odk_robot tool with project_dir for clones—do not run node scripts/odk-docker-run.js manually from the shell.

When to Use This Skill (by outcome)

• User wants QC / rule checks on an OWL file → use verify.
• User wants to check OWL 2 profile (e.g. DL) → use validate-profile.
• User wants a single merged OWL file from several inputs → use merge.
• User wants reasoning (classification, consistency, inferred axioms) → use reason.
• User wants format conversion (e.g. OWL to OBO, RDF/XML to functional) → use convert.
• User wants to generate or update terms from a ROBOT template and CSV → use template.
• User wants to run a SPARQL or DL query and get results → use query.
• User wants other ROBOT subcommands (annotate, extract, filter, report, etc.) → use odk_robot with the appropriate robot_args.

What Each ROBOT Subcommand Does and How to Use It

verify

What it does: Runs rule-based checks on an ontology (e.g. required annotations, logical consistency). Produces a report of violations or success.

How it works: robot verify --input <path> [--output report.txt] [other options]. Paths relative to project root.

Example (verify and write report):

robot verify --input edit.owl --output report.txt

odk_robot call: robot_args = verify --input edit.owl --output report.txt

Example (verify only, no output file):

robot verify --input upper-level/bfo.owl

---

validate-profile

What it does: Checks whether the ontology conforms to an OWL 2 profile (e.g. OWL 2 DL). Outputs profile validation result.

How it works: robot validate-profile --input <path> [--profile DL]. Paths relative to project root.

Example:

robot validate-profile --input edit.owl --profile DL

odk_robot call: robot_args = validate-profile --input edit.owl --profile DL

---

merge

What it does: Merges two or more OWL files into one ontology. Output is a single OWL file.

How it works: robot merge --inputs <file1> <file2> ... --output <out.owl>. Paths relative to project root.

Example:

robot merge --inputs upper-level/bfo.owl upper-level/sulo.owl edit.owl --output merged.owl

odk_robot call: robot_args = merge --inputs upper-level/bfo.owl upper-level/sulo.owl edit.owl --output merged.owl

---

reason

What it does: Runs a reasoner (e.g. ELK, HermiT) to classify the ontology and optionally output inferred axioms. Produces a reasoned ontology and/or consistency result.

How it works: robot reason --input <path> [--reasoner elk|hermit] --output reasoned.owl [--annotate-inferred-axioms true]. Paths relative to project root.

Example (reason with ELK, output inferred axioms):

robot reason --input edit.owl --reasoner elk --output reasoned.owl --annotate-inferred-axioms true

odk_robot call: robot_args = reason --input edit.owl --reasoner elk --output reasoned.owl --annotate-inferred-axioms true

---

convert

What it does: Converts between ontology formats (e.g. RDF/XML, OWL functional, OBO). Output is a file in the requested format.

How it works: robot convert --input <path> --output <path> [--format obo|owl|ofn|owlxml|rdfxml|turtle]. Paths relative to project root.

Example (OWL to OBO):

robot convert --input edit.owl --output edit.obo --format obo

odk_robot call: robot_args = convert --input edit.owl --output edit.obo --format obo

Example (OWL to OWL functional):

robot convert --input edit.owl --output edit.owl --format ofn

---

template

What it does: Builds or updates ontology terms from a ROBOT template (CSV + template YAML). Output is an ontology or mergeable file with generated axioms.

How it works: robot template --template <template.yaml> --input <data.csv> [--output output.owl]. Paths relative to project root.

Example:

robot template --template templates/terms.yaml --input terms.csv --output terms.owl

odk_robot call: robot_args = template --template templates/terms.yaml --input terms.csv --output terms.owl

---

query

What it does: Runs a SPARQL or DL query over an ontology and writes results (e.g. to CSV). Output is the query result file.

How it works: robot query --input <ontology> --query <query.rq|query.sparql> <results.csv>. Paths relative to project root.

Example (SPARQL):

robot query --input edit.owl --query query.rq results.csv

odk_robot call: robot_args = query --input edit.owl --query query.rq results.csv

---

Other subcommands

annotate, extract, filter, report, remove, rename, repair, collapse, expand, diff, explain, materialize, measure, mirror, reduce, relax, unmerge, etc. Use odk_robot with robot_args set to the full robot command (e.g. extract --input edit.owl --term-file terms.txt --output subset.owl). See ROBOT documentation for each subcommand.

Example (extract subset):

robot extract --input edit.owl --term-file terms.txt --output subset.owl

odk_robot call: robot_args = extract --input edit.owl --term-file terms.txt --output subset.owl

---

When Not to Use This Skill

• owltools, dosdp-tools, riot, sparql, runoak, sssom, etc. → use odk-run and odk_run.
• Seeding a new ODK repo → use odk-seed and odk_seed.
• ODK Make targets (test, prepare_release, refresh-imports, update_repo, odkversion) → use odk-make and odk_make.

Tool and Arguments

Argument	Type	Required	Description
robot_args	string	yes	The full ROBOT subcommand and options. Paths relative to the mounted project root (e.g. ontology/edit.owl).
project_dir	string	no	Optional. When working on a cloned or project dir under projects/<slug>/, set to that root (e.g. projects/pizza, projects/owner-repo) so the correct project is mounted. Relative paths resolved from repo root. Omit or leave empty for the workspace ontology.

Examples (calling the tool)

• Verify (workspace): odk_robot with robot_args: verify --input ontology/edit.owl --output report.txt
• Validate profile (clone): odk_robot with robot_args: validate-profile --input ontology/edit.owl --profile DL, project_dir: projects/owner-repo
• Reason: odk_robot with robot_args: reason --input ontology/edit.owl --reasoner elk --output reasoned.owl
• Merge: odk_robot with robot_args: merge --inputs ontology/a.owl ontology/b.owl --output merged.owl
• Convert: odk_robot with robot_args: convert --input ontology/edit.owl --output edit.obo --format obo
• Template: odk_robot with robot_args: template --template templates/terms.yaml --input terms.csv --output terms.owl
• Query: odk_robot with robot_args: query --input ontology/edit.owl --query query.rq results.csv
• Version: odk_robot with robot_args: --version

Tool Requirement

This skill requires: odk_robot

After learning this skill, call setup_tools(skills: ["odk-robot"]) to activate the tool, then use call_tool(name: "odk_robot", data: {"robot_args": "..."}) to invoke it.