SPARQL queries for models and instance data #229

[cmungall]

See https://github.com/linkml/linkml/issues/46

BiolinkML SPARQL checks

These sparql checks can be used to query either biolinkML schemas or instance data for biolinkML schemas.

The schema should be in the form of a .ttl file (using gen-rdf).

For instance data, this should be merged with the schema.ttl

The script meta-sparql.sh provides a convenient wrapper that use robot to merge files and do queries.

Naming conventions

• queries over schemas are named schema-*.rq
• queries intended to check for warnings/errors are named *-check.rq

Examples (schemas)

To query for all elements in a schema:

./sparql/meta-sparql.sh -s examples/organization2.ttl -q sparql/element-list.rq

The metamodel can be queried:

./sparql/meta-sparql.sh -s meta.ttl -q sparql/element-list.rq

Examples (instance data)

Find all unyped instances

./sparql/meta-sparql.sh -i examples/organization2.ttl -s examples/organization2.ttl -q sparql/untyped-instance-violation.rq

TODO

• move validation into python code
• add tests
• add more constraint checking

[cmungall]

discussed with @hsolbrig - we will merge for now even if incomplete, we want to know how best to integrate this with tests