monarch

Usage:

$ monarch [OPTIONS] COMMAND [ARGS]...

Options:

• --version / --no-version
• --quiet / --no-quiet: [default: no-quiet]
• --debug / --no-debug: [default: no-debug]
• --install-completion: Install completion for the current shell.
• --show-completion: Show completion for the current shell, to copy it or customize the installation.
• --help: Show this message and exit.

Commands:

• association-counts: Retrieve association counts for an entity...
• association-table
• associations: Paginate through associations
• autocomplete: Return entity autcomplete matches for a...
• entity: Retrieve an entity by ID
• histopheno: Retrieve the histopheno data for an entity...
• schema: Print the linkml schema for the data model
• search: Search for entities
• solr
• sql
• test: Test the CLI

monarch association-counts

Retrieve association counts for an entity by ID

Args: entity: The entity to get association counts for fmt: The format of the output (json, yaml, tsv, table). Default JSON output: The path to the output file. Default stdout

Returns: A list of association counts for the given entity containing association type, label and count

Usage:

$ monarch association-counts [OPTIONS] [ENTITY]

Arguments:

• [ENTITY]: The entity to get association counts for

Options:

• -f, --format TEXT: The format of the output (json, yaml, tsv, table) [default: json]
• -o, --output TEXT: The path to the output file
• --help: Show this message and exit.

monarch association-table

Usage:

$ monarch association-table [OPTIONS] ENTITY CATEGORY

Arguments:

• ENTITY: The entity to get associations for [required]
• CATEGORY: The association category to get associations for, ex. biolink:GeneToPhenotypicFeatureAssociation [required]

Options:

• -q, --query TEXT
• -l, --limit INTEGER: [default: 5]
• --offset INTEGER: [default: 0]
• -f, --format TEXT: The format of the output (json, yaml, tsv, table) [default: json]
• -o, --output TEXT: The path to the output file
• --help: Show this message and exit.

monarch associations

Paginate through associations

Args: category: A comma-separated list of categories subject: A comma-separated list of subjects predicate: A comma-separated list of predicates object: A comma-separated list of objects entity: A comma-separated list of entities limit: The number of associations to return direct: Whether to exclude associations with subject/object as ancestors offset: The offset of the first association to be retrieved fmt: The format of the output (json, yaml, tsv, table) output: The path to the output file (stdout if not specified)

Usage:

$ monarch associations [OPTIONS]

Options:

• -c, --category TEXT: Comma-separated list of categories
• -s, --subject TEXT: Comma-separated list of subjects
• -p, --predicate TEXT: Comma-separated list of predicates
• -o, --object TEXT: Comma-separated list of objects
• -e, --entity TEXT: Comma-separated list of entities
• -d, --direct: Whether to exclude associations with subject/object as ancestors
• -l, --limit INTEGER: The number of associations to return [default: 20]
• --offset INTEGER: The offset of the first association to be retrieved [default: 0]
• -f, --format TEXT: The format of the output (json, yaml, tsv, table) [default: json]
• -o, --output TEXT: The path to the output file
• --help: Show this message and exit.

monarch autocomplete

Return entity autcomplete matches for a query string

Args: q: The query string to autocomplete against fmt: The format of the output (json, yaml, tsv, table) output: The path to the output file (stdout if not specified)

Usage:

$ monarch autocomplete [OPTIONS] [Q]

Arguments:

• [Q]: Query string to autocomplete against

Options:

• -f, --format TEXT: The format of the output (json, yaml, tsv, table) [default: json]
• -o, --output TEXT: The path to the output file
• --help: Show this message and exit.

monarch entity

Retrieve an entity by ID

Args: id: The identifier of the entity to be retrieved fmt: The format of the output (json, yaml, tsv, table) output: The path to the output file (stdout if not specified)

Usage:

$ monarch entity [OPTIONS] [ID]

Arguments:

• [ID]: The identifier of the entity to be retrieved

Options:

• -e, --extra: Include extra fields in the output (association_counts and node_hierarchy)
• -f, --format TEXT: The format of the output (json, yaml, tsv, table) [default: json]
• -o, --output TEXT: The path to the output file
• --help: Show this message and exit.

monarch histopheno

Retrieve the histopheno data for an entity by ID

Args: subject: The subject of the association

Optional Args: fmt (str): The format of the output (json, yaml, tsv, table). Default JSON output (str): The path to the output file. Default stdout

Usage:

$ monarch histopheno [OPTIONS] [SUBJECT]

Arguments:

• [SUBJECT]: The subject of the association

Options:

• -f, --format TEXT: The format of the output (json, yaml, tsv, table) [default: json]
• -o, --output TEXT: The path to the output file
• --help: Show this message and exit.

monarch schema

Print the linkml schema for the data model

Usage:

$ monarch schema [OPTIONS]

Options:

• --help: Show this message and exit.

monarch search

Search for entities

Args: q: The query string to search for category: The category of the entity taxon: The taxon of the entity limit: The number of entities to return offset: The offset of the first entity to be retrieved fmt: The format of the output (json, yaml, tsv, table) output: The path to the output file (stdout if not specified)

Usage:

$ monarch search [OPTIONS]

Options:

• -q, --query TEXT
• -c, --category TEXT
• -t, --in-taxon TEXT
• -ff, --facet-fields TEXT
• --facet-queries TEXT
• -l, --limit INTEGER: [default: 20]
• --offset INTEGER: [default: 0]
• -f, --format TEXT: The format of the output (json, yaml, tsv, table) [default: json]
• -o, --output TEXT: The path to the output file
• --help: Show this message and exit.

monarch solr

Usage:

$ monarch solr [OPTIONS] COMMAND [ARGS]...

Options:

• --quiet / --no-quiet: [default: no-quiet]
• --debug / --no-debug: [default: no-debug]
• --help: Show this message and exit.

Commands:

• association-counts: Retrieve the association counts for a...
• association-table
• associations: Paginate through associations
• autocomplete: Return entity autcomplete matches for a...
• download: Download the Monarch Solr KG.
• entity: Retrieve an entity by ID
• histopheno: Retrieve the histopheno associations for a...
• search: Search for entities
• start: Starts a local Solr container.
• status: Checks the status of the local Solr...
• stop: Stops the local Solr container.

monarch solr association-counts

Retrieve the association counts for a given entity

Args: entity (str): The entity to get association counts for

Optional Args: update (bool): Whether to re-download the Monarch KG. Default False fmt (str): The format of the output (json, yaml, tsv, table). Default JSON output (str): The path to the output file. Default stdout

Usage:

$ monarch solr association-counts [OPTIONS] [ENTITY]

Arguments:

• [ENTITY]: The entity to get association counts for

Options:

• -f, --format TEXT: The format of the output (json, yaml, tsv, table) [default: json]
• -o, --output TEXT: The path to the output file
• --help: Show this message and exit.

monarch solr association-table

Usage:

$ monarch solr association-table [OPTIONS] ENTITY CATEGORY

Arguments:

• ENTITY: The entity to get associations for [required]
• CATEGORY: The association category to get associations for, ex. biolink:GeneToPhenotypicFeatureAssociation [required]

Options:

• -q, --query TEXT
• -l, --limit INTEGER: [default: 5]
• --offset INTEGER: [default: 0]
• -f, --format TEXT: The format of the output (json, yaml, tsv, table) [default: json]
• -o, --output TEXT: The path to the output file
• --help: Show this message and exit.

monarch solr associations

Paginate through associations

Args: category: A comma-separated list of categories subject: A comma-separated list of subjects predicate: A comma-separated list of predicates object: A comma-separated list of objects entity: A comma-separated list of entities limit: The number of associations to return direct: Whether to exclude associations with subject/object as ancestors offset: The offset of the first association to be retrieved fmt: The format of the output (json, yaml, tsv, table) output: The path to the output file (stdout if not specified)

Usage:

$ monarch solr associations [OPTIONS]

Options:

• -c, --category TEXT: Comma-separated list of categories
• -s, --subject TEXT: Comma-separated list of subjects
• -p, --predicate TEXT: Comma-separated list of predicates
• -o, --object TEXT: Comma-separated list of objects
• -e, --entity TEXT: Comma-separated list of entities
• -d, --direct: Whether to exclude associations with subject/object as ancestors
• -l, --limit INTEGER: The number of associations to return [default: 20]
• --offset INTEGER: The offset of the first association to be retrieved [default: 0]
• -f, --format TEXT: The format of the output (json, yaml, tsv, table) [default: json]
• -o, --output TEXT: The path to the output file
• --help: Show this message and exit.

monarch solr autocomplete

Return entity autcomplete matches for a query string

Args: q: The query string to autocomplete against fmt: The format of the output (json, yaml, tsv, table) output: The path to the output file (stdout if not specified)

Usage:

$ monarch solr autocomplete [OPTIONS] [Q]

Arguments:

• [Q]: Query string to autocomplete against

Options:

• -f, --format TEXT: The format of the output (json, yaml, tsv, table) [default: json]
• -o, --output TEXT: The path to the output file
• --help: Show this message and exit.

monarch solr download

Download the Monarch Solr KG.

Usage:

$ monarch solr download [OPTIONS]

Options:

• --help: Show this message and exit.

monarch solr entity

Retrieve an entity by ID

Args: id (str): The identifier of the entity to be retrieved

Optional Args: fmt (str): The format of the output (json, yaml, tsv, table). Default JSON output (str): The path to the output file. Default stdout

Usage:

$ monarch solr entity [OPTIONS] [ID]

Arguments:

• [ID]: The identifier of the entity to be retrieved

Options:

• -e, --extra: Include extra fields in the output (association_counts and node_hierarchy)
• -f, --format TEXT: The format of the output (json, yaml, tsv, table) [default: json]
• -o, --output TEXT: The path to the output file
• --help: Show this message and exit.

monarch solr histopheno

Retrieve the histopheno associations for a given subject

Args: subject (str): The subject of the association

Optional Args: update (bool): Whether to re-download the Monarch KG. Default False fmt (str): The format of the output (json, yaml, tsv, table). Default JSON output (str): The path to the output file. Default stdout

Usage:

$ monarch solr histopheno [OPTIONS] [SUBJECT]

Arguments:

• [SUBJECT]: The subject of the association

Options:

• -f, --format TEXT: The format of the output (json, yaml, tsv, table) [default: JSON]
• -o, --output TEXT: The path to the output file
• --help: Show this message and exit.

monarch solr search

Search for entities

Optional Args: q: The query string to search for category: The category of the entity taxon: The taxon of the entity facet_fields: The fields to facet on facet_queries: The queries to facet on limit: The number of entities to return offset: The offset of the first entity to be retrieved fmt (str): The format of the output (json, yaml, tsv, table). Default JSON output (str): The path to the output file. Default stdout

Usage:

$ monarch solr search [OPTIONS]

Options:

• -q, --query TEXT
• -c, --category TEXT
• -t, --in-taxon TEXT
• -ff, --facet-fields TEXT
• --facet-queries TEXT
• -l, --limit INTEGER: [default: 20]
• --offset INTEGER: [default: 0]
• -f, --format TEXT: The format of the output (json, yaml, tsv, table) [default: json]
• -o, --output TEXT: The path to the output file
• --help: Show this message and exit.

monarch solr start

Starts a local Solr container.

Usage:

$ monarch solr start [OPTIONS]

Options:

• --update / --no-update: [default: no-update]
• --help: Show this message and exit.

monarch solr status

Checks the status of the local Solr container.

Usage:

$ monarch solr status [OPTIONS]

Options:

• --help: Show this message and exit.

monarch solr stop

Stops the local Solr container.

Usage:

$ monarch solr stop [OPTIONS]

Options:

• --help: Show this message and exit.

monarch sql

Usage:

$ monarch sql [OPTIONS] COMMAND [ARGS]...

Options:

• --quiet / --no-quiet: [default: no-quiet]
• --debug / --no-debug: [default: no-debug]
• --help: Show this message and exit.

Commands:

• associations: Paginate through associations
• entity: Retrieve an entity by ID

monarch sql associations

Paginate through associations

Args: category: A comma-separated list of categories subject: A comma-separated list of subjects predicate: A comma-separated list of predicates object: A comma-separated list of objects entity: A comma-separated list of entities limit: The number of associations to return offset: The offset of the first association to be retrieved fmt: The format of the output (json, yaml, tsv, table) output: The path to the output file (stdout if not specified)

Usage:

$ monarch sql associations [OPTIONS]

Options:

• -c, --category TEXT: Comma-separated list of categories
• -s, --subject TEXT: Comma-separated list of subjects
• -p, --predicate TEXT: Comma-separated list of predicates
• -o, --object TEXT: Comma-separated list of objects
• -e, --entity TEXT: Comma-separated list of entities
• -d, --direct: Whether to exclude associations with subject/object as ancestors
• -l, --limit INTEGER: The number of associations to return [default: 20]
• --offset INTEGER: The offset of the first association to be retrieved [default: 0]
• -f, --format TEXT: The format of the output (json, yaml, tsv, table) [default: json]
• -o, --output TEXT: The path to the output file
• --help: Show this message and exit.

monarch sql entity

Retrieve an entity by ID

Args: id (str): The identifier of the entity to be retrieved update (bool): = Whether to re-download the Monarch KG. Default False fmt (str): The format of the output (json, yaml, tsv, table). Default JSON output (str): The path to the output file. Default stdout

Usage:

$ monarch sql entity [OPTIONS] [ID]

Arguments:

• [ID]: The identifier of the entity to be retrieved

Options:

• -e, --extra: Include extra fields in the output (association_counts and node_hierarchy)
• -u, --update: Whether to re-download the Monarch KG
• -f, --format TEXT: The format of the output (json, yaml, tsv, table) [default: json]
• -o, --output TEXT: The path to the output file
• --help: Show this message and exit.

monarch test

Test the CLI

Usage:

$ monarch test [OPTIONS]

Options:

• --help: Show this message and exit.