Ontology Commands¶

Manage controlled vocabulary (CV) ontology data used by QPX, including PSI-MS and PRIDE CV.

Overview¶

The ontology command group manages the controlled vocabulary (CV) ontology data that QPX uses to annotate and validate proteomics metadata. QPX ships with pre-built Parquet files for PSI-MS and PRIDE CV ontologies.

Available Commands¶

info - Show loaded ontology sources, versions, and cache status
search - Search for CV terms matching a query string
update - Force download the latest ontology data
build - Rebuild ontology Parquet files from OBO sources (maintainer)

info¶

Show loaded ontology sources, versions, and cache status.

Parameters¶

Parameter	Type	Required	Default	Description
`--source`	TEXT	No	-	Ontology source (e.g. psi_ms, pride_cv). Show all if omitted.

Usage Examples¶

Show ontology source status:

# Show all ontology sources
qpxc ontology info

# Show a specific source
qpxc ontology info --source psi_ms

search¶

Search for CV terms matching a query string.

Parameters¶

Parameter	Type	Required	Default	Description
`--source`	TEXT	No	`psi_ms`	Ontology source to search.
`--top-k`	INTEGER	No	10	Max results.
`QUERY`	TEXT	Yes	-	Positional argument

Usage Examples¶

Search for CV terms:

# Search PSI-MS ontology (default)
qpxc ontology search "mass spectrometry"

# Search PRIDE CV with more results
qpxc ontology search "instrument" --source pride_cv --top-k 20

update¶

Force download the latest ontology data from the repository.

Parameters¶

Parameter	Type	Required	Default	Description
`--source`	TEXT	No	all	Update specific source (default: all).

Usage Examples¶

Update ontology data:

# Update all ontology sources
qpxc ontology update

# Update a specific source
qpxc ontology update --source psi_ms

build¶

Rebuild ontology Parquet files from OBO sources. This is a maintainer command for regenerating the bundled ontology data.

Parameters¶

Parameter	Type	Required	Default	Description
`--source`	TEXT	No	-	Ontology source to build (e.g. psi_ms).
`--all-sources`	FLAG	No	-	Build all configured sources.

Usage Examples¶

Rebuild ontology Parquet files:

# Build a specific ontology source
qpxc ontology build --source psi_ms

# Build all configured sources
qpxc ontology build --all-sources