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...
• compare: Compare two sets of phenotypes using...
• entity: Retrieve an entity by ID
• histopheno: Retrieve the histopheno data for an entity...
• mappings
• multi-entity-associations: Paginate through associations for multiple...
• release: Retrieve metadata for a specific release
• releases: List all available releases of the Monarch...
• 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:{biolink:PairwiseGeneToGeneInteraction|biolink:GeneToExpressionSiteAssociation|biolink:VariantToGeneAssociation|biolink:MacromolecularMachineToBiologicalProcessAssociation|biolink:GeneToPhenotypicFeatureAssociation|biolink:MacromolecularMachineToMolecularActivityAssociation|biolink:MacromolecularMachineToCellularComponentAssociation|biolink:Association|biolink:GeneToGeneHomologyAssociation|biolink:GenotypeToPhenotypicFeatureAssociation|biolink:DiseaseToPhenotypicFeatureAssociation|biolink:GeneToPathwayAssociation|biolink:DiseaseOrPhenotypicFeatureToLocationAssociation|biolink:ChemicalToPathwayAssociation|biolink:GenotypeToDiseaseAssociation|biolink:CorrelatedGeneToDiseaseAssociation|biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation|biolink:VariantToDiseaseAssociation|biolink:CausalGeneToDiseaseAssociation|biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation}

Arguments:

• ENTITY: The entity to get associations for [required]
• CATEGORY:{biolink:PairwiseGeneToGeneInteraction|biolink:GeneToExpressionSiteAssociation|biolink:VariantToGeneAssociation|biolink:MacromolecularMachineToBiologicalProcessAssociation|biolink:GeneToPhenotypicFeatureAssociation|biolink:MacromolecularMachineToMolecularActivityAssociation|biolink:MacromolecularMachineToCellularComponentAssociation|biolink:Association|biolink:GeneToGeneHomologyAssociation|biolink:GenotypeToPhenotypicFeatureAssociation|biolink:DiseaseToPhenotypicFeatureAssociation|biolink:GeneToPathwayAssociation|biolink:DiseaseOrPhenotypicFeatureToLocationAssociation|biolink:ChemicalToPathwayAssociation|biolink:GenotypeToDiseaseAssociation|biolink:CorrelatedGeneToDiseaseAssociation|biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation|biolink:VariantToDiseaseAssociation|biolink:CausalGeneToDiseaseAssociation|biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation}: The association category to get associations for, ex. biolink:GeneToPhenotypicFeatureAssociation [required]

Options:

• -q, --query TEXT
• -t, --traverse-orthologs: Whether to traverse orthologs when getting associations
• -s, --sort 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 [biolink:PairwiseGeneToGeneInteraction|biolink:GeneToExpressionSiteAssociation|biolink:VariantToGeneAssociation|biolink:MacromolecularMachineToBiologicalProcessAssociation|biolink:GeneToPhenotypicFeatureAssociation|biolink:MacromolecularMachineToMolecularActivityAssociation|biolink:MacromolecularMachineToCellularComponentAssociation|biolink:Association|biolink:GeneToGeneHomologyAssociation|biolink:GenotypeToPhenotypicFeatureAssociation|biolink:DiseaseToPhenotypicFeatureAssociation|biolink:GeneToPathwayAssociation|biolink:DiseaseOrPhenotypicFeatureToLocationAssociation|biolink:ChemicalToPathwayAssociation|biolink:GenotypeToDiseaseAssociation|biolink:CorrelatedGeneToDiseaseAssociation|biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation|biolink:VariantToDiseaseAssociation|biolink:CausalGeneToDiseaseAssociation|biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation]: Category to get associations for
• -s, --subject TEXT: Subject ID to get associations for
• -p, --predicate [biolink:interacts_with|biolink:expressed_in|biolink:has_phenotype|biolink:is_sequence_variant_of|biolink:enables|biolink:actively_involved_in|biolink:orthologous_to|biolink:located_in|biolink:subclass_of|biolink:related_to|biolink:participates_in|biolink:acts_upstream_of_or_within|biolink:active_in|biolink:part_of|biolink:model_of|biolink:causes|biolink:acts_upstream_of|biolink:has_mode_of_inheritance|biolink:contributes_to|biolink:gene_associated_with_condition|biolink:treats_or_applied_or_studied_to_treat|biolink:colocalizes_with|biolink:acts_upstream_of_positive_effect|biolink:acts_upstream_of_or_within_positive_effect|biolink:acts_upstream_of_negative_effect|biolink:acts_upstream_of_or_within_negative_effect]: Predicate ID to get associations for
• -o, --object TEXT: Object ID to get associations for
• -e, --entity TEXT: Entity (subject or object) ID to get associations for
• -d, --direct: Whether to exclude associations with subject/object as ancestors
• -C, --compact: Whether to return a compact representation of the associations
• -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 compare

Compare two sets of phenotypes using semantic similarity via SemSimian

Usage:

$ monarch compare [OPTIONS] SUBJECTS OBJECTS

Arguments:

• SUBJECTS: Comma separated list of subjects to compare [required]
• OBJECTS: Comma separated list of objects to compare [required]

Options:

• -m, --metric [ancestor_information_content|jaccard_similarity|phenodigm_score]: The metric to use for comparison [default: ancestor_information_content]
• -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 mappings

Usage:

$ monarch mappings [OPTIONS]

Options:

• -e, --entity-id TEXT: entity ID to get mappings for
• -s, --subject-id TEXT: subject ID to get mappings for
• -p, --predicate-id [skos:exactMatch|skos:broadMatch]: predicate ID to get mappings for
• -o, --object-id TEXT: object ID to get mappings for
• -m, --mapping-justification TEXT: mapping justification to get mappings for
• --offset INTEGER: The offset of the first mapping to be retrieved [default: 0]
• -l, --limit INTEGER: The number of mappings to return [default: 20]
• -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 multi-entity-associations

Paginate through associations for multiple entities

Args: entity: A comma-separated list of entities counterpart_category: A comma-separated list of counterpart categories 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 multi-entity-associations [OPTIONS]

Options:

• -e, --entity TEXT: Comma-separated list of entities
• -c, --counterpart-category 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 release

Retrieve metadata for a specific release

Args: release_ver: The release version to get metadata for fmt: The format of the output (json, yaml, tsv, table) output: The path to the output file (stdout if not specified)

Usage:

$ monarch release [OPTIONS] [RELEASE_VER]

Arguments:

• [RELEASE_VER]: The release version to get metadata 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 releases

List all available releases of the Monarch Knowledge Graph

Usage:

$ monarch releases [OPTIONS]

Options:

• --dev: Get dev releases of the KG (default is False)
• -l, --limit INTEGER: The number of releases to return [default: 0]
• --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 in_taxon_label: The taxon label to filter by 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 [biolink:SequenceVariant|biolink:Gene|biolink:Genotype|biolink:PhenotypicFeature|biolink:BiologicalProcessOrActivity|biolink:Disease|biolink:GrossAnatomicalStructure|biolink:Cell|biolink:Pathway|biolink:NamedThing|biolink:AnatomicalEntity|biolink:CellularComponent|biolink:MolecularEntity|biolink:BiologicalProcess|biolink:MacromolecularComplex|biolink:MolecularActivity|biolink:Protein|biolink:CellularOrganism|biolink:Vertebrate|biolink:Virus|biolink:BehavioralFeature|biolink:ChemicalEntity|biolink:LifeStage|biolink:PathologicalProcess|biolink:Drug|biolink:SmallMolecule|biolink:OrganismTaxon|biolink:InformationContentEntity|biolink:NucleicAcidEntity|biolink:EvidenceType|biolink:RNAProduct|biolink:Transcript|biolink:Fungus|biolink:Plant|biolink:ProcessedMaterial|biolink:Activity|biolink:Agent|biolink:ConfidenceLevel|biolink:Dataset|biolink:EnvironmentalFeature|biolink:GeneticInheritance|biolink:Haplotype|biolink:Invertebrate|biolink:Mammal|biolink:PopulationOfIndividualOrganisms|biolink:ProteinFamily|biolink:Publication|biolink:AccessibleDnaRegion|biolink:Bacterium|biolink:BiologicalSex|biolink:CellLine|biolink:ChemicalExposure|biolink:ChemicalMixture|biolink:DatasetDistribution|biolink:DiagnosticAid|biolink:DrugExposure|biolink:EnvironmentalProcess|biolink:Event|biolink:Exon|biolink:Genome|biolink:GenotypicSex|biolink:Human|biolink:IndividualOrganism|biolink:MaterialSample|biolink:MicroRNA|biolink:OrganismalEntity|biolink:Patent|biolink:PhenotypicSex|biolink:Polypeptide|biolink:ProteinDomain|biolink:ReagentTargetedGene|biolink:RegulatoryRegion|biolink:SiRNA|biolink:Snv|biolink:Study|biolink:StudyVariable|biolink:TranscriptionFactorBindingSite|biolink:Treatment|biolink:WebPage|biolink:Zygosity]
• -t, --in-taxon-label 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...
• mappings
• multi-entity-associations: Paginate through associations for multiple...
• 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: 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]:[biolink:PairwiseGeneToGeneInteraction|biolink:GeneToExpressionSiteAssociation|biolink:VariantToGeneAssociation|biolink:MacromolecularMachineToBiologicalProcessAssociation|biolink:GeneToPhenotypicFeatureAssociation|biolink:MacromolecularMachineToMolecularActivityAssociation|biolink:MacromolecularMachineToCellularComponentAssociation|biolink:Association|biolink:GeneToGeneHomologyAssociation|biolink:GenotypeToPhenotypicFeatureAssociation|biolink:DiseaseToPhenotypicFeatureAssociation|biolink:GeneToPathwayAssociation|biolink:DiseaseOrPhenotypicFeatureToLocationAssociation|biolink:ChemicalToPathwayAssociation|biolink:GenotypeToDiseaseAssociation|biolink:CorrelatedGeneToDiseaseAssociation|biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation|biolink:VariantToDiseaseAssociation|biolink:CausalGeneToDiseaseAssociation|biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation]

Arguments:

• ENTITY: The entity to get associations for [required]
• [CATEGORY]:[biolink:PairwiseGeneToGeneInteraction|biolink:GeneToExpressionSiteAssociation|biolink:VariantToGeneAssociation|biolink:MacromolecularMachineToBiologicalProcessAssociation|biolink:GeneToPhenotypicFeatureAssociation|biolink:MacromolecularMachineToMolecularActivityAssociation|biolink:MacromolecularMachineToCellularComponentAssociation|biolink:Association|biolink:GeneToGeneHomologyAssociation|biolink:GenotypeToPhenotypicFeatureAssociation|biolink:DiseaseToPhenotypicFeatureAssociation|biolink:GeneToPathwayAssociation|biolink:DiseaseOrPhenotypicFeatureToLocationAssociation|biolink:ChemicalToPathwayAssociation|biolink:GenotypeToDiseaseAssociation|biolink:CorrelatedGeneToDiseaseAssociation|biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation|biolink:VariantToDiseaseAssociation|biolink:CausalGeneToDiseaseAssociation|biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation]: The association category to get associations for, ex. biolink:GeneToPhenotypicFeatureAssociation

Options:

• -t, --traverse-orthologs: Whether to traverse orthologs when getting associations
• -q, --query TEXT
• -s, --sort 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: The category of the association (multi-valued) subject: The subject of the association (multi-valued) predicate: The predicate of the association (multi-valued) object: The object of the association (multi-valued) entity: The entity (subject or object) of the association (multi-valued) limit: The number of associations to return (default 20) direct: Whether to exclude associations with subject/object as ancestors (default False) offset: The offset of the first association to be retrieved fmt: The format of the output (json, yaml, tsv, table) (default json) output: The path to the output file (stdout if not specified) (default None)

Usage:

$ monarch solr associations [OPTIONS]

Options:

• -c, --category [biolink:PairwiseGeneToGeneInteraction|biolink:GeneToExpressionSiteAssociation|biolink:VariantToGeneAssociation|biolink:MacromolecularMachineToBiologicalProcessAssociation|biolink:GeneToPhenotypicFeatureAssociation|biolink:MacromolecularMachineToMolecularActivityAssociation|biolink:MacromolecularMachineToCellularComponentAssociation|biolink:Association|biolink:GeneToGeneHomologyAssociation|biolink:GenotypeToPhenotypicFeatureAssociation|biolink:DiseaseToPhenotypicFeatureAssociation|biolink:GeneToPathwayAssociation|biolink:DiseaseOrPhenotypicFeatureToLocationAssociation|biolink:ChemicalToPathwayAssociation|biolink:GenotypeToDiseaseAssociation|biolink:CorrelatedGeneToDiseaseAssociation|biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation|biolink:VariantToDiseaseAssociation|biolink:CausalGeneToDiseaseAssociation|biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation]: Category to get associations for
• -s, --subject TEXT: Subject ID to get associations for
• -p, --predicate [biolink:interacts_with|biolink:expressed_in|biolink:has_phenotype|biolink:is_sequence_variant_of|biolink:enables|biolink:actively_involved_in|biolink:orthologous_to|biolink:located_in|biolink:subclass_of|biolink:related_to|biolink:participates_in|biolink:acts_upstream_of_or_within|biolink:active_in|biolink:part_of|biolink:model_of|biolink:causes|biolink:acts_upstream_of|biolink:has_mode_of_inheritance|biolink:contributes_to|biolink:gene_associated_with_condition|biolink:treats_or_applied_or_studied_to_treat|biolink:colocalizes_with|biolink:acts_upstream_of_positive_effect|biolink:acts_upstream_of_or_within_positive_effect|biolink:acts_upstream_of_negative_effect|biolink:acts_upstream_of_or_within_negative_effect]: Predicate ID to get associations for
• -o, --object TEXT: Object ID to get associations for
• -e, --entity TEXT: Entity (subject or object) ID to get associations for
• -d, --direct: Whether to exclude associations with subject/object as ancestors
• -C, --compact: Whether to return a compact representation of the associations
• -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:

• --version TEXT: [default: latest]
• --overwrite / --no-overwrite: [default: no-overwrite]
• --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: 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 mappings

Usage:

$ monarch solr mappings [OPTIONS]

Options:

• -e, --entity-id TEXT: entity ID to get mappings for
• -s, --subject-id TEXT: subject ID to get mappings for
• -p, --predicate-id [skos:exactMatch|skos:broadMatch]: predicate ID to get mappings for
• -o, --object-id TEXT: object ID to get mappings for
• -m, --mapping-justification TEXT: mapping justification to get mappings for
• --offset INTEGER: The offset of the first mapping to be retrieved [default: 0]
• -l, --limit INTEGER: The number of mappings to return [default: 20]
• -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 multi-entity-associations

Paginate through associations for multiple entities

Args: entity: A comma-separated list of entities counterpart_category: A comma-separated list of counterpart categories 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 solr multi-entity-associations [OPTIONS]

Options:

• -e, --entity TEXT: Entity ID to get associations for
• -c, --counterpart-category TEXT: Counterpart category to get associations for
• -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 search

Search for entities

Optional Args: q: The query string to search for category: The category of the entity in_taxon_label: The taxon label to filter on 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: [default: :]
• -c, --category [biolink:SequenceVariant|biolink:Gene|biolink:Genotype|biolink:PhenotypicFeature|biolink:BiologicalProcessOrActivity|biolink:Disease|biolink:GrossAnatomicalStructure|biolink:Cell|biolink:Pathway|biolink:NamedThing|biolink:AnatomicalEntity|biolink:CellularComponent|biolink:MolecularEntity|biolink:BiologicalProcess|biolink:MacromolecularComplex|biolink:MolecularActivity|biolink:Protein|biolink:CellularOrganism|biolink:Vertebrate|biolink:Virus|biolink:BehavioralFeature|biolink:ChemicalEntity|biolink:LifeStage|biolink:PathologicalProcess|biolink:Drug|biolink:SmallMolecule|biolink:OrganismTaxon|biolink:InformationContentEntity|biolink:NucleicAcidEntity|biolink:EvidenceType|biolink:RNAProduct|biolink:Transcript|biolink:Fungus|biolink:Plant|biolink:ProcessedMaterial|biolink:Activity|biolink:Agent|biolink:ConfidenceLevel|biolink:Dataset|biolink:EnvironmentalFeature|biolink:GeneticInheritance|biolink:Haplotype|biolink:Invertebrate|biolink:Mammal|biolink:PopulationOfIndividualOrganisms|biolink:ProteinFamily|biolink:Publication|biolink:AccessibleDnaRegion|biolink:Bacterium|biolink:BiologicalSex|biolink:CellLine|biolink:ChemicalExposure|biolink:ChemicalMixture|biolink:DatasetDistribution|biolink:DiagnosticAid|biolink:DrugExposure|biolink:EnvironmentalProcess|biolink:Event|biolink:Exon|biolink:Genome|biolink:GenotypicSex|biolink:Human|biolink:IndividualOrganism|biolink:MaterialSample|biolink:MicroRNA|biolink:OrganismalEntity|biolink:Patent|biolink:PhenotypicSex|biolink:Polypeptide|biolink:ProteinDomain|biolink:ReagentTargetedGene|biolink:RegulatoryRegion|biolink:SiRNA|biolink:Snv|biolink:Study|biolink:StudyVariable|biolink:TranscriptionFactorBindingSite|biolink:Treatment|biolink:WebPage|biolink:Zygosity]
• -t, --in-taxon-label 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 direct: Whether to exclude associations with subject/object as ancestors compact: Whether to return a compact representation of the associations 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 [biolink:PairwiseGeneToGeneInteraction|biolink:GeneToExpressionSiteAssociation|biolink:VariantToGeneAssociation|biolink:MacromolecularMachineToBiologicalProcessAssociation|biolink:GeneToPhenotypicFeatureAssociation|biolink:MacromolecularMachineToMolecularActivityAssociation|biolink:MacromolecularMachineToCellularComponentAssociation|biolink:Association|biolink:GeneToGeneHomologyAssociation|biolink:GenotypeToPhenotypicFeatureAssociation|biolink:DiseaseToPhenotypicFeatureAssociation|biolink:GeneToPathwayAssociation|biolink:DiseaseOrPhenotypicFeatureToLocationAssociation|biolink:ChemicalToPathwayAssociation|biolink:GenotypeToDiseaseAssociation|biolink:CorrelatedGeneToDiseaseAssociation|biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation|biolink:VariantToDiseaseAssociation|biolink:CausalGeneToDiseaseAssociation|biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation]: Category to get associations for
• -s, --subject TEXT: Subject ID to get associations for
• -p, --predicate [biolink:interacts_with|biolink:expressed_in|biolink:has_phenotype|biolink:is_sequence_variant_of|biolink:enables|biolink:actively_involved_in|biolink:orthologous_to|biolink:located_in|biolink:subclass_of|biolink:related_to|biolink:participates_in|biolink:acts_upstream_of_or_within|biolink:active_in|biolink:part_of|biolink:model_of|biolink:causes|biolink:acts_upstream_of|biolink:has_mode_of_inheritance|biolink:contributes_to|biolink:gene_associated_with_condition|biolink:treats_or_applied_or_studied_to_treat|biolink:colocalizes_with|biolink:acts_upstream_of_positive_effect|biolink:acts_upstream_of_or_within_positive_effect|biolink:acts_upstream_of_negative_effect|biolink:acts_upstream_of_or_within_negative_effect]: Predicate ID to get associations for
• -o, --object TEXT: Object ID to get associations for
• -e, --entity TEXT: Entity (subject or object) ID to get associations for
• -d, --direct: Whether to exclude associations with subject/object as ancestors
• -C, --compact: Whether to return a compact representation of the associations
• -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.