An integrated ontology for Phenomics
An ontology for accessing and comparing knowledge concerning phenotypes across species and genetic backgrounds.
[{"category": "Individual", "contact_details": [{"contact_type": "email", "value": "jhc@lbl.gov"}, {"contact_type": "github", "value": "caufieldjh"}], "label": "J. Harry Caufield"}]
[{"category": "Product", "compression": "gzip", "description": "OWL version of phenio", "format": "owl", "id": "phenio.model", "license": {"id": "https://opensource.org/license/bsd-3-clause", "label": "BSD3"}, "name": "phenio", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "phenio"}], "product_file_size": 124412326, "product_url": "https://github.com/monarch-initiative/phenio/releases/latest/download/phenio.owl.gz", "repository": "https://github.com/monarch-initiative/phenio"}, {"category": "GraphProduct", "compatibility": [{"standard": "biolink", "version": "4.2.5"}], "compression": "targz", "description": "PHENIO as a KGX graph", "format": "kgx", "id": "phenio.graph", "license": {"id": "https://opensource.org/license/bsd-3-clause", "label": "BSD3"}, "name": "KG-Phenio", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "phenio"}], "product_file_size": 71579307, "product_url": "https://github.com/Knowledge-Graph-Hub/kg-phenio/releases/latest/download/kg-phenio.tar.gz", "repository": "https://github.com/Knowledge-Graph-Hub/kg-phenio"}, {"category": "GraphProduct", "description": "KGX Distribution of KG-Monarch", "edge_count": 15211571, "format": "kgx", "id": "kg-monarch.graph", "name": "KGX Distribution of KG-Monarch", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "biolink:Case", "biolink:Cell", "biolink:CellularComponent", "biolink:ChemicalEntity", "biolink:Disease", "biolink:Gene", "biolink:Genotype", "biolink:LifeStage", "biolink:MolecularActivity", "biolink:MolecularEntity", "biolink:NamedThing", "biolink:OrganismTaxon", "biolink:Pathway", "biolink:PhenotypicFeature", "biolink:Protein", "biolink:SequenceVariant"], "node_count": 1462594, "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "alliance"}, {"relation_type": "prov:hadPrimarySource", "source": "bgee"}, {"relation_type": "prov:hadPrimarySource", "source": "biogrid"}, {"relation_type": "prov:hadPrimarySource", "source": "clingen"}, {"relation_type": "prov:hadPrimarySource", "source": "clinvar"}, {"relation_type": "prov:hadPrimarySource", "source": "ctd"}, {"relation_type": "prov:hadPrimarySource", "source": "dictybase"}, {"relation_type": "prov:hadPrimarySource", "source": "go"}, {"relation_type": "prov:hadPrimarySource", "source": "hp"}, {"relation_type": "prov:hadPrimarySource", "source": "kg-monarch"}, {"relation_type": "prov:hadPrimarySource", "source": "maxo"}, {"relation_type": "prov:hadPrimarySource", "source": "panther"}, {"relation_type": "prov:hadPrimarySource", "source": "phenio"}, {"relation_type": "prov:hadPrimarySource", "source": "pombase"}, {"relation_type": "prov:hadPrimarySource", "source": "reactome"}, {"relation_type": "prov:hadPrimarySource", "source": "string"}, {"relation_type": "prov:hadPrimarySource", "source": "xenbase"}, {"relation_type": "prov:hadPrimarySource", "source": "zfin"}], "predicates": ["biolink:actively_involved_in", "biolink:acts_upstream_of", "biolink:acts_upstream_of_negative_effect", "biolink:acts_upstream_of_or_within", "biolink:acts_upstream_of_or_within_negative_effect", "biolink:acts_upstream_of_or_within_positive_effect", "biolink:acts_upstream_of_positive_effect", "biolink:affects", "biolink:applied_to_treat", "biolink:associated_with_increased_likelihood_of", "biolink:capable_of", "biolink:caused_by", "biolink:causes", "biolink:coexists_with", "biolink:colocalizes_with", "biolink:contributes_to", "biolink:correlated_with", "biolink:derives_from", "biolink:develops_from", "biolink:directly_physically_interacts_with", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:expresses", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_adverse_event", "biolink:has_disease", "biolink:has_gene", "biolink:has_input", "biolink:has_mode_of_inheritance", "biolink:has_output", "biolink:has_part", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:homologous_to", "biolink:in_taxon", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_input_of", "biolink:is_output_of", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:location_of", "biolink:model_of", "biolink:occurs_in", "biolink:orthologous_to", "biolink:overlaps", "biolink:part_of", "biolink:participates_in", "biolink:preceded_by", "biolink:precedes", "biolink:produced_by", "biolink:produces", "biolink:regulates", "biolink:related_to", "biolink:same_as", "biolink:subclass_of", "biolink:temporally_related_to", "biolink:treats", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 230877741, "product_url": "http://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.tar.gz"}, {"category": "GraphProduct", "description": "KGX JSON-Lines Distribution of KG-Monarch", "edge_count": 15211571, "format": "kgx-jsonl", "id": "kg-monarch.graph.jsonl", "name": "KGX JSON-L Distribution of KG-Monarch", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "biolink:Case", "biolink:Cell", "biolink:CellularComponent", "biolink:ChemicalEntity", "biolink:Disease", "biolink:Gene", "biolink:Genotype", "biolink:LifeStage", "biolink:MolecularActivity", "biolink:MolecularEntity", "biolink:NamedThing", "biolink:OrganismTaxon", "biolink:Pathway", "biolink:PhenotypicFeature", "biolink:Protein", "biolink:SequenceVariant"], "node_count": 1462594, "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "alliance"}, {"relation_type": "prov:hadPrimarySource", "source": "bgee"}, {"relation_type": "prov:hadPrimarySource", "source": "biogrid"}, {"relation_type": "prov:hadPrimarySource", "source": "clingen"}, {"relation_type": "prov:hadPrimarySource", "source": "clinvar"}, {"relation_type": "prov:hadPrimarySource", "source": "ctd"}, {"relation_type": "prov:hadPrimarySource", "source": "dictybase"}, {"relation_type": "prov:hadPrimarySource", "source": "go"}, {"relation_type": "prov:hadPrimarySource", "source": "hp"}, {"relation_type": "prov:hadPrimarySource", "source": "kg-monarch"}, {"relation_type": "prov:hadPrimarySource", "source": "maxo"}, {"relation_type": "prov:hadPrimarySource", "source": "panther"}, {"relation_type": "prov:hadPrimarySource", "source": "phenio"}, {"relation_type": "prov:hadPrimarySource", "source": "pombase"}, {"relation_type": "prov:hadPrimarySource", "source": "reactome"}, {"relation_type": "prov:hadPrimarySource", "source": "string"}, {"relation_type": "prov:hadPrimarySource", "source": "xenbase"}, {"relation_type": "prov:hadPrimarySource", "source": "zfin"}], "predicates": ["biolink:actively_involved_in", "biolink:acts_upstream_of", "biolink:acts_upstream_of_negative_effect", "biolink:acts_upstream_of_or_within", "biolink:acts_upstream_of_or_within_negative_effect", "biolink:acts_upstream_of_or_within_positive_effect", "biolink:acts_upstream_of_positive_effect", "biolink:affects", "biolink:applied_to_treat", "biolink:associated_with_increased_likelihood_of", "biolink:capable_of", "biolink:caused_by", "biolink:causes", "biolink:coexists_with", "biolink:colocalizes_with", "biolink:contributes_to", "biolink:correlated_with", "biolink:derives_from", "biolink:develops_from", "biolink:directly_physically_interacts_with", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:expresses", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_adverse_event", "biolink:has_disease", "biolink:has_gene", "biolink:has_input", "biolink:has_mode_of_inheritance", "biolink:has_output", "biolink:has_part", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:homologous_to", "biolink:in_taxon", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_input_of", "biolink:is_output_of", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:location_of", "biolink:model_of", "biolink:occurs_in", "biolink:orthologous_to", "biolink:overlaps", "biolink:part_of", "biolink:participates_in", "biolink:preceded_by", "biolink:precedes", "biolink:produced_by", "biolink:produces", "biolink:regulates", "biolink:related_to", "biolink:same_as", "biolink:subclass_of", "biolink:temporally_related_to", "biolink:treats", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 315667976, "product_url": "https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.jsonl.tar.gz"}, {"category": "GraphProduct", "description": "RDF Distribution of KG-Monarch", "edge_count": 15211571, "format": "rdfxml", "id": "kg-monarch.graph.rdf", "name": "RDF Distribution of KG-Monarch", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "biolink:Case", "biolink:Cell", "biolink:CellularComponent", "biolink:ChemicalEntity", "biolink:Disease", "biolink:Gene", "biolink:Genotype", "biolink:LifeStage", "biolink:MolecularActivity", "biolink:MolecularEntity", "biolink:NamedThing", "biolink:OrganismTaxon", "biolink:Pathway", "biolink:PhenotypicFeature", "biolink:Protein", "biolink:SequenceVariant"], "node_count": 1462594, "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "alliance"}, {"relation_type": "prov:hadPrimarySource", "source": "bgee"}, {"relation_type": "prov:hadPrimarySource", "source": "biogrid"}, {"relation_type": "prov:hadPrimarySource", "source": "clingen"}, {"relation_type": "prov:hadPrimarySource", "source": "clinvar"}, {"relation_type": "prov:hadPrimarySource", "source": "ctd"}, {"relation_type": "prov:hadPrimarySource", "source": "dictybase"}, {"relation_type": "prov:hadPrimarySource", "source": "go"}, {"relation_type": "prov:hadPrimarySource", "source": "hp"}, {"relation_type": "prov:hadPrimarySource", "source": "kg-monarch"}, {"relation_type": "prov:hadPrimarySource", "source": "maxo"}, {"relation_type": "prov:hadPrimarySource", "source": "panther"}, {"relation_type": "prov:hadPrimarySource", "source": "phenio"}, {"relation_type": "prov:hadPrimarySource", "source": "pombase"}, {"relation_type": "prov:hadPrimarySource", "source": "reactome"}, {"relation_type": "prov:hadPrimarySource", "source": "string"}, {"relation_type": "prov:hadPrimarySource", "source": "xenbase"}, {"relation_type": "prov:hadPrimarySource", "source": "zfin"}], "predicates": ["biolink:actively_involved_in", "biolink:acts_upstream_of", "biolink:acts_upstream_of_negative_effect", "biolink:acts_upstream_of_or_within", "biolink:acts_upstream_of_or_within_negative_effect", "biolink:acts_upstream_of_or_within_positive_effect", "biolink:acts_upstream_of_positive_effect", "biolink:affects", "biolink:applied_to_treat", "biolink:associated_with_increased_likelihood_of", "biolink:capable_of", "biolink:caused_by", "biolink:causes", "biolink:coexists_with", "biolink:colocalizes_with", "biolink:contributes_to", "biolink:correlated_with", "biolink:derives_from", "biolink:develops_from", "biolink:directly_physically_interacts_with", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:expresses", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_adverse_event", "biolink:has_disease", "biolink:has_gene", "biolink:has_input", "biolink:has_mode_of_inheritance", "biolink:has_output", "biolink:has_part", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:homologous_to", "biolink:in_taxon", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_input_of", "biolink:is_output_of", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:location_of", "biolink:model_of", "biolink:occurs_in", "biolink:orthologous_to", "biolink:overlaps", "biolink:part_of", "biolink:participates_in", "biolink:preceded_by", "biolink:precedes", "biolink:produced_by", "biolink:produces", "biolink:regulates", "biolink:related_to", "biolink:same_as", "biolink:subclass_of", "biolink:temporally_related_to", "biolink:treats", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 879238775, "product_url": "https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.nt.gz"}, {"category": "GraphProduct", "description": "Neo4j Dump of KG-Monarch", "dump_format": "neo4j", "edge_count": 15211571, "format": "neo4j", "id": "kg-monarch.graph.neo4j", "name": "Neo4j Dump of KG-Monarch", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "biolink:Case", "biolink:Cell", "biolink:CellularComponent", "biolink:ChemicalEntity", "biolink:Disease", "biolink:Gene", "biolink:Genotype", "biolink:LifeStage", "biolink:MolecularActivity", "biolink:MolecularEntity", "biolink:NamedThing", "biolink:OrganismTaxon", "biolink:Pathway", "biolink:PhenotypicFeature", "biolink:Protein", "biolink:SequenceVariant"], "node_count": 1462594, "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "alliance"}, {"relation_type": "prov:hadPrimarySource", "source": "bgee"}, {"relation_type": "prov:hadPrimarySource", "source": "biogrid"}, {"relation_type": "prov:hadPrimarySource", "source": "clingen"}, {"relation_type": "prov:hadPrimarySource", "source": "clinvar"}, {"relation_type": "prov:hadPrimarySource", "source": "ctd"}, {"relation_type": "prov:hadPrimarySource", "source": "dictybase"}, {"relation_type": "prov:hadPrimarySource", "source": "go"}, {"relation_type": "prov:hadPrimarySource", "source": "hp"}, {"relation_type": "prov:hadPrimarySource", "source": "kg-monarch"}, {"relation_type": "prov:hadPrimarySource", "source": "maxo"}, {"relation_type": "prov:hadPrimarySource", "source": "panther"}, {"relation_type": "prov:hadPrimarySource", "source": "phenio"}, {"relation_type": "prov:hadPrimarySource", "source": "pombase"}, {"relation_type": "prov:hadPrimarySource", "source": "reactome"}, {"relation_type": "prov:hadPrimarySource", "source": "string"}, {"relation_type": "prov:hadPrimarySource", "source": "xenbase"}, {"relation_type": "prov:hadPrimarySource", "source": "zfin"}], "predicates": ["biolink:actively_involved_in", "biolink:acts_upstream_of", "biolink:acts_upstream_of_negative_effect", "biolink:acts_upstream_of_or_within", "biolink:acts_upstream_of_or_within_negative_effect", "biolink:acts_upstream_of_or_within_positive_effect", "biolink:acts_upstream_of_positive_effect", "biolink:affects", "biolink:applied_to_treat", "biolink:associated_with_increased_likelihood_of", "biolink:capable_of", "biolink:caused_by", "biolink:causes", "biolink:coexists_with", "biolink:colocalizes_with", "biolink:contributes_to", "biolink:correlated_with", "biolink:derives_from", "biolink:develops_from", "biolink:directly_physically_interacts_with", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:expresses", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_adverse_event", "biolink:has_disease", "biolink:has_gene", "biolink:has_input", "biolink:has_mode_of_inheritance", "biolink:has_output", "biolink:has_part", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:homologous_to", "biolink:in_taxon", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_input_of", "biolink:is_output_of", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:location_of", "biolink:model_of", "biolink:occurs_in", "biolink:orthologous_to", "biolink:overlaps", "biolink:part_of", "biolink:participates_in", "biolink:preceded_by", "biolink:precedes", "biolink:produced_by", "biolink:produces", "biolink:regulates", "biolink:related_to", "biolink:same_as", "biolink:subclass_of", "biolink:temporally_related_to", "biolink:treats", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 1438250397, "product_url": "https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.neo4j.dump", "warnings": []}, {"category": "GraphProduct", "description": "DuckDB database of KG-Monarch", "edge_count": 15211571, "format": "mixed", "id": "kg-monarch.graph.duckdb", "name": "DuckDB database of KG-Monarch", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "biolink:Case", "biolink:Cell", "biolink:CellularComponent", "biolink:ChemicalEntity", "biolink:Disease", "biolink:Gene", "biolink:Genotype", "biolink:LifeStage", "biolink:MolecularActivity", "biolink:MolecularEntity", "biolink:NamedThing", "biolink:OrganismTaxon", "biolink:Pathway", "biolink:PhenotypicFeature", "biolink:Protein", "biolink:SequenceVariant"], "node_count": 1462594, "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "alliance"}, {"relation_type": "prov:hadPrimarySource", "source": "bgee"}, {"relation_type": "prov:hadPrimarySource", "source": "biogrid"}, {"relation_type": "prov:hadPrimarySource", "source": "clingen"}, {"relation_type": "prov:hadPrimarySource", "source": "clinvar"}, {"relation_type": "prov:hadPrimarySource", "source": "ctd"}, {"relation_type": "prov:hadPrimarySource", "source": "dictybase"}, {"relation_type": "prov:hadPrimarySource", "source": "go"}, {"relation_type": "prov:hadPrimarySource", "source": "hp"}, {"relation_type": "prov:hadPrimarySource", "source": "kg-monarch"}, {"relation_type": "prov:hadPrimarySource", "source": "maxo"}, {"relation_type": "prov:hadPrimarySource", "source": "panther"}, {"relation_type": "prov:hadPrimarySource", "source": "phenio"}, {"relation_type": "prov:hadPrimarySource", "source": "pombase"}, {"relation_type": "prov:hadPrimarySource", "source": "reactome"}, {"relation_type": "prov:hadPrimarySource", "source": "string"}, {"relation_type": "prov:hadPrimarySource", "source": "xenbase"}, {"relation_type": "prov:hadPrimarySource", "source": "zfin"}], "predicates": ["biolink:actively_involved_in", "biolink:acts_upstream_of", "biolink:acts_upstream_of_negative_effect", "biolink:acts_upstream_of_or_within", "biolink:acts_upstream_of_or_within_negative_effect", "biolink:acts_upstream_of_or_within_positive_effect", "biolink:acts_upstream_of_positive_effect", "biolink:affects", "biolink:applied_to_treat", "biolink:associated_with_increased_likelihood_of", "biolink:capable_of", "biolink:caused_by", "biolink:causes", "biolink:coexists_with", "biolink:colocalizes_with", "biolink:contributes_to", "biolink:correlated_with", "biolink:derives_from", "biolink:develops_from", "biolink:directly_physically_interacts_with", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:expresses", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_adverse_event", "biolink:has_disease", "biolink:has_gene", "biolink:has_input", "biolink:has_mode_of_inheritance", "biolink:has_output", "biolink:has_part", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:homologous_to", "biolink:in_taxon", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_input_of", "biolink:is_output_of", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:location_of", "biolink:model_of", "biolink:occurs_in", "biolink:orthologous_to", "biolink:overlaps", "biolink:part_of", "biolink:participates_in", "biolink:preceded_by", "biolink:precedes", "biolink:produced_by", "biolink:produces", "biolink:regulates", "biolink:related_to", "biolink:same_as", "biolink:subclass_of", "biolink:temporally_related_to", "biolink:treats", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 6827814912, "product_url": "https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.duckdb"}, {"category": "GraphProduct", "compression": "targz", "description": "KGX JSON-Lines Distribution of KG-Monarch (Edges)", "edge_count": 15211571, "format": "kgx-jsonl", "id": "kg-monarch.graph.jsonl.edges", "name": "KGX JSON-L Distribution of KG-Monarch Edges", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "biolink:Case", "biolink:Cell", "biolink:CellularComponent", "biolink:ChemicalEntity", "biolink:Disease", "biolink:Gene", "biolink:Genotype", "biolink:LifeStage", "biolink:MolecularActivity", "biolink:MolecularEntity", "biolink:NamedThing", "biolink:OrganismTaxon", "biolink:Pathway", "biolink:PhenotypicFeature", "biolink:Protein", "biolink:SequenceVariant"], "node_count": 1462594, "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "alliance"}, {"relation_type": "prov:hadPrimarySource", "source": "bgee"}, {"relation_type": "prov:hadPrimarySource", "source": "biogrid"}, {"relation_type": "prov:hadPrimarySource", "source": "clingen"}, {"relation_type": "prov:hadPrimarySource", "source": "clinvar"}, {"relation_type": "prov:hadPrimarySource", "source": "ctd"}, {"relation_type": "prov:hadPrimarySource", "source": "dictybase"}, {"relation_type": "prov:hadPrimarySource", "source": "go"}, {"relation_type": "prov:hadPrimarySource", "source": "hp"}, {"relation_type": "prov:hadPrimarySource", "source": "kg-monarch"}, {"relation_type": "prov:hadPrimarySource", "source": "maxo"}, {"relation_type": "prov:hadPrimarySource", "source": "panther"}, {"relation_type": "prov:hadPrimarySource", "source": "phenio"}, {"relation_type": "prov:hadPrimarySource", "source": "pombase"}, {"relation_type": "prov:hadPrimarySource", "source": "reactome"}, {"relation_type": "prov:hadPrimarySource", "source": "string"}, {"relation_type": "prov:hadPrimarySource", "source": "xenbase"}, {"relation_type": "prov:hadPrimarySource", "source": "zfin"}], "predicates": ["biolink:actively_involved_in", "biolink:acts_upstream_of", "biolink:acts_upstream_of_negative_effect", "biolink:acts_upstream_of_or_within", "biolink:acts_upstream_of_or_within_negative_effect", "biolink:acts_upstream_of_or_within_positive_effect", "biolink:acts_upstream_of_positive_effect", "biolink:affects", "biolink:applied_to_treat", "biolink:associated_with_increased_likelihood_of", "biolink:capable_of", "biolink:caused_by", "biolink:causes", "biolink:coexists_with", "biolink:colocalizes_with", "biolink:contributes_to", "biolink:correlated_with", "biolink:derives_from", "biolink:develops_from", "biolink:directly_physically_interacts_with", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:expresses", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_adverse_event", "biolink:has_disease", "biolink:has_gene", "biolink:has_input", "biolink:has_mode_of_inheritance", "biolink:has_output", "biolink:has_part", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:homologous_to", "biolink:in_taxon", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_input_of", "biolink:is_output_of", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:location_of", "biolink:model_of", "biolink:occurs_in", "biolink:orthologous_to", "biolink:overlaps", "biolink:part_of", "biolink:participates_in", "biolink:preceded_by", "biolink:precedes", "biolink:produced_by", "biolink:produces", "biolink:regulates", "biolink:related_to", "biolink:same_as", "biolink:subclass_of", "biolink:temporally_related_to", "biolink:treats", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 487854288, "product_url": "https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.jsonl.tar.gz"}, {"category": "GraphProduct", "compression": "targz", "description": "KGX JSON-Lines Distribution of KG-Monarch (Nodes)", "edge_count": 15211571, "format": "kgx-jsonl", "id": "kg-monarch.graph.jsonl.nodes", "name": "KGX JSON-L Distribution of KG-Monarch Nodes", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "biolink:Case", "biolink:Cell", "biolink:CellularComponent", "biolink:ChemicalEntity", "biolink:Disease", "biolink:Gene", "biolink:Genotype", "biolink:LifeStage", "biolink:MolecularActivity", "biolink:MolecularEntity", "biolink:NamedThing", "biolink:OrganismTaxon", "biolink:Pathway", "biolink:PhenotypicFeature", "biolink:Protein", "biolink:SequenceVariant"], "node_count": 1462594, "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "alliance"}, {"relation_type": "prov:hadPrimarySource", "source": "bgee"}, {"relation_type": "prov:hadPrimarySource", "source": "biogrid"}, {"relation_type": "prov:hadPrimarySource", "source": "clingen"}, {"relation_type": "prov:hadPrimarySource", "source": "clinvar"}, {"relation_type": "prov:hadPrimarySource", "source": "ctd"}, {"relation_type": "prov:hadPrimarySource", "source": "dictybase"}, {"relation_type": "prov:hadPrimarySource", "source": "go"}, {"relation_type": "prov:hadPrimarySource", "source": "hp"}, {"relation_type": "prov:hadPrimarySource", "source": "kg-monarch"}, {"relation_type": "prov:hadPrimarySource", "source": "maxo"}, {"relation_type": "prov:hadPrimarySource", "source": "panther"}, {"relation_type": "prov:hadPrimarySource", "source": "phenio"}, {"relation_type": "prov:hadPrimarySource", "source": "pombase"}, {"relation_type": "prov:hadPrimarySource", "source": "reactome"}, {"relation_type": "prov:hadPrimarySource", "source": "string"}, {"relation_type": "prov:hadPrimarySource", "source": "xenbase"}, {"relation_type": "prov:hadPrimarySource", "source": "zfin"}], "predicates": ["biolink:actively_involved_in", "biolink:acts_upstream_of", "biolink:acts_upstream_of_negative_effect", "biolink:acts_upstream_of_or_within", "biolink:acts_upstream_of_or_within_negative_effect", "biolink:acts_upstream_of_or_within_positive_effect", "biolink:acts_upstream_of_positive_effect", "biolink:affects", "biolink:applied_to_treat", "biolink:associated_with_increased_likelihood_of", "biolink:capable_of", "biolink:caused_by", "biolink:causes", "biolink:coexists_with", "biolink:colocalizes_with", "biolink:contributes_to", "biolink:correlated_with", "biolink:derives_from", "biolink:develops_from", "biolink:directly_physically_interacts_with", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:expresses", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_adverse_event", "biolink:has_disease", "biolink:has_gene", "biolink:has_input", "biolink:has_mode_of_inheritance", "biolink:has_output", "biolink:has_part", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:homologous_to", "biolink:in_taxon", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_input_of", "biolink:is_output_of", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:location_of", "biolink:model_of", "biolink:occurs_in", "biolink:orthologous_to", "biolink:overlaps", "biolink:part_of", "biolink:participates_in", "biolink:preceded_by", "biolink:precedes", "biolink:produced_by", "biolink:produces", "biolink:regulates", "biolink:related_to", "biolink:same_as", "biolink:subclass_of", "biolink:temporally_related_to", "biolink:treats", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 487854288, "product_url": "https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.jsonl.tar.gz"}, {"category": "GraphProduct", "description": "Neo4j Dump of KG-Monarch Edges", "edge_count": 15211571, "format": "neo4j", "id": "kg-monarch.graph.neo4j.edges", "name": "Neo4j Dump of KG-Monarch Edges", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "biolink:Case", "biolink:Cell", "biolink:CellularComponent", "biolink:ChemicalEntity", "biolink:Disease", "biolink:Gene", "biolink:Genotype", "biolink:LifeStage", "biolink:MolecularActivity", "biolink:MolecularEntity", "biolink:NamedThing", "biolink:OrganismTaxon", "biolink:Pathway", "biolink:PhenotypicFeature", "biolink:Protein", "biolink:SequenceVariant"], "node_count": 1462594, "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "alliance"}, {"relation_type": "prov:hadPrimarySource", "source": "bgee"}, {"relation_type": "prov:hadPrimarySource", "source": "biogrid"}, {"relation_type": "prov:hadPrimarySource", "source": "clingen"}, {"relation_type": "prov:hadPrimarySource", "source": "clinvar"}, {"relation_type": "prov:hadPrimarySource", "source": "ctd"}, {"relation_type": "prov:hadPrimarySource", "source": "dictybase"}, {"relation_type": "prov:hadPrimarySource", "source": "go"}, {"relation_type": "prov:hadPrimarySource", "source": "hp"}, {"relation_type": "prov:hadPrimarySource", "source": "kg-monarch"}, {"relation_type": "prov:hadPrimarySource", "source": "maxo"}, {"relation_type": "prov:hadPrimarySource", "source": "panther"}, {"relation_type": "prov:hadPrimarySource", "source": "phenio"}, {"relation_type": "prov:hadPrimarySource", "source": "pombase"}, {"relation_type": "prov:hadPrimarySource", "source": "reactome"}, {"relation_type": "prov:hadPrimarySource", "source": "string"}, {"relation_type": "prov:hadPrimarySource", "source": "xenbase"}, {"relation_type": "prov:hadPrimarySource", "source": "zfin"}], "predicates": ["biolink:actively_involved_in", "biolink:acts_upstream_of", "biolink:acts_upstream_of_negative_effect", "biolink:acts_upstream_of_or_within", "biolink:acts_upstream_of_or_within_negative_effect", "biolink:acts_upstream_of_or_within_positive_effect", "biolink:acts_upstream_of_positive_effect", "biolink:affects", "biolink:applied_to_treat", "biolink:associated_with_increased_likelihood_of", "biolink:capable_of", "biolink:caused_by", "biolink:causes", "biolink:coexists_with", "biolink:colocalizes_with", "biolink:contributes_to", "biolink:correlated_with", "biolink:derives_from", "biolink:develops_from", "biolink:directly_physically_interacts_with", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:expresses", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_adverse_event", "biolink:has_disease", "biolink:has_gene", "biolink:has_input", "biolink:has_mode_of_inheritance", "biolink:has_output", "biolink:has_part", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:homologous_to", "biolink:in_taxon", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_input_of", "biolink:is_output_of", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:location_of", "biolink:model_of", "biolink:occurs_in", "biolink:orthologous_to", "biolink:overlaps", "biolink:part_of", "biolink:participates_in", "biolink:preceded_by", "biolink:precedes", "biolink:produced_by", "biolink:produces", "biolink:regulates", "biolink:related_to", "biolink:same_as", "biolink:subclass_of", "biolink:temporally_related_to", "biolink:treats", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 4386388748, "product_url": "https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg_edges.neo4j.csv"}, {"category": "GraphProduct", "description": "Neo4j Dump of KG-Monarch Nodes", "edge_count": 15211571, "format": "neo4j", "id": "kg-monarch.graph.neo4j.nodes", "name": "Neo4j Dump of KG-Monarch Nodes", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "biolink:Case", "biolink:Cell", "biolink:CellularComponent", "biolink:ChemicalEntity", "biolink:Disease", "biolink:Gene", "biolink:Genotype", "biolink:LifeStage", "biolink:MolecularActivity", "biolink:MolecularEntity", "biolink:NamedThing", "biolink:OrganismTaxon", "biolink:Pathway", "biolink:PhenotypicFeature", "biolink:Protein", "biolink:SequenceVariant"], "node_count": 1462594, "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "alliance"}, {"relation_type": "prov:hadPrimarySource", "source": "bgee"}, {"relation_type": "prov:hadPrimarySource", "source": "biogrid"}, {"relation_type": "prov:hadPrimarySource", "source": "clingen"}, {"relation_type": "prov:hadPrimarySource", "source": "clinvar"}, {"relation_type": "prov:hadPrimarySource", "source": "ctd"}, {"relation_type": "prov:hadPrimarySource", "source": "dictybase"}, {"relation_type": "prov:hadPrimarySource", "source": "go"}, {"relation_type": "prov:hadPrimarySource", "source": "hp"}, {"relation_type": "prov:hadPrimarySource", "source": "kg-monarch"}, {"relation_type": "prov:hadPrimarySource", "source": "maxo"}, {"relation_type": "prov:hadPrimarySource", "source": "panther"}, {"relation_type": "prov:hadPrimarySource", "source": "phenio"}, {"relation_type": "prov:hadPrimarySource", "source": "pombase"}, {"relation_type": "prov:hadPrimarySource", "source": "reactome"}, {"relation_type": "prov:hadPrimarySource", "source": "string"}, {"relation_type": "prov:hadPrimarySource", "source": "xenbase"}, {"relation_type": "prov:hadPrimarySource", "source": "zfin"}], "predicates": ["biolink:actively_involved_in", "biolink:acts_upstream_of", "biolink:acts_upstream_of_negative_effect", "biolink:acts_upstream_of_or_within", "biolink:acts_upstream_of_or_within_negative_effect", "biolink:acts_upstream_of_or_within_positive_effect", "biolink:acts_upstream_of_positive_effect", "biolink:affects", "biolink:applied_to_treat", "biolink:associated_with_increased_likelihood_of", "biolink:capable_of", "biolink:caused_by", "biolink:causes", "biolink:coexists_with", "biolink:colocalizes_with", "biolink:contributes_to", "biolink:correlated_with", "biolink:derives_from", "biolink:develops_from", "biolink:directly_physically_interacts_with", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:expresses", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_adverse_event", "biolink:has_disease", "biolink:has_gene", "biolink:has_input", "biolink:has_mode_of_inheritance", "biolink:has_output", "biolink:has_part", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:homologous_to", "biolink:in_taxon", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_input_of", "biolink:is_output_of", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:location_of", "biolink:model_of", "biolink:occurs_in", "biolink:orthologous_to", "biolink:overlaps", "biolink:part_of", "biolink:participates_in", "biolink:preceded_by", "biolink:precedes", "biolink:produced_by", "biolink:produces", "biolink:regulates", "biolink:related_to", "biolink:same_as", "biolink:subclass_of", "biolink:temporally_related_to", "biolink:treats", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 349573789, "product_url": "https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg_nodes.neo4j.csv"}, {"category": "Product", "description": "Phenio SQLite database in SemSQL format for ontology queries", "format": "sqlite", "id": "kg-monarch.phenio.semsql", "name": "Phenio SQLite (SemSQL)", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "kg-monarch"}, {"relation_type": "prov:hadPrimarySource", "source": "phenio"}], "product_file_size": 3425435914, "product_url": "https://data.monarchinitiative.org/monarch-kg/latest/phenio.db.gz"}, {"category": "GraphProduct", "compression": "targz", "description": "KGX Distribution of KG-Alzheimers", "format": "kgx", "id": "kg-alzheimers.graph", "name": "KGX Distribution of KG-Alzheimers", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "kg-alzheimers"}, {"relation_type": "prov:hadPrimarySource", "source": "monarchinitiative"}, {"relation_type": "prov:hadPrimarySource", "source": "phenio"}, {"relation_type": "prov:hadPrimarySource", "source": "mondo"}, {"relation_type": "prov:hadPrimarySource", "source": "hp"}, {"relation_type": "prov:hadPrimarySource", "source": "alliance"}, {"relation_type": "prov:hadPrimarySource", "source": "bgee"}, {"relation_type": "prov:hadPrimarySource", "source": "biogrid"}, {"relation_type": "prov:hadPrimarySource", "source": "ctd"}, {"relation_type": "prov:hadPrimarySource", "source": "dictybase"}, {"relation_type": "prov:hadPrimarySource", "source": "flybase"}, {"relation_type": "prov:hadPrimarySource", "source": "hgnc"}, {"relation_type": "prov:hadPrimarySource", "source": "mgi"}, {"relation_type": "prov:hadPrimarySource", "source": "ncbigene"}, {"relation_type": "prov:hadPrimarySource", "source": "panther"}, {"relation_type": "prov:hadPrimarySource", "source": "pombase"}, {"relation_type": "prov:hadPrimarySource", "source": "reactome"}, {"relation_type": "prov:hadPrimarySource", "source": "rgd"}, {"relation_type": "prov:hadPrimarySource", "source": "sgd"}, {"relation_type": "prov:hadPrimarySource", "source": "string"}, {"relation_type": "prov:hadPrimarySource", "source": "xenbase"}, {"relation_type": "prov:hadPrimarySource", "source": "zfin"}, {"relation_type": "prov:hadPrimarySource", "source": "chebi"}, {"relation_type": "prov:hadPrimarySource", "source": "mesh"}], "product_file_size": 210868256, "product_url": "https://kg-hub.berkeleybop.io/kg-alzheimers/current/kg-alzheimers.tar.gz", "warnings": ["File was not able to be retrieved when checked on 2026-07-01; no live download location was found (GitHub releases, kghub.io/current, and Zenodo all return 404 or have no published artifact)."]}, {"category": "GraphProduct", "description": "KGX distribution of the SRI-Reference KG", "format": "kgx", "id": "sri-reference-kg.graph", "name": "SRI-Reference KG (KGX distribution)", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "sri-reference-kg"}, {"relation_type": "prov:hadPrimarySource", "source": "alliance"}, {"relation_type": "prov:hadPrimarySource", "source": "bgee"}, {"relation_type": "prov:hadPrimarySource", "source": "biogrid"}, {"relation_type": "prov:hadPrimarySource", "source": "clingen"}, {"relation_type": "prov:hadPrimarySource", "source": "clinvar"}, {"relation_type": "prov:hadPrimarySource", "source": "ctd"}, {"relation_type": "prov:hadPrimarySource", "source": "dictybase"}, {"relation_type": "prov:hadPrimarySource", "source": "flybase"}, {"relation_type": "prov:hadPrimarySource", "source": "goa"}, {"relation_type": "prov:hadPrimarySource", "source": "hgnc"}, {"relation_type": "prov:hadPrimarySource", "source": "mgi"}, {"relation_type": "prov:hadPrimarySource", "source": "ncbigene"}, {"relation_type": "prov:hadPrimarySource", "source": "omim"}, {"relation_type": "prov:hadPrimarySource", "source": "orphanet"}, {"relation_type": "prov:hadPrimarySource", "source": "panther"}, {"relation_type": "prov:hadPrimarySource", "source": "pombase"}, {"relation_type": "prov:hadPrimarySource", "source": "reactome"}, {"relation_type": "prov:hadPrimarySource", "source": "rgd"}, {"relation_type": "prov:hadPrimarySource", "source": "sgd"}, {"relation_type": "prov:hadPrimarySource", "source": "string"}, {"relation_type": "prov:hadPrimarySource", "source": "wormbase"}, {"relation_type": "prov:hadPrimarySource", "source": "xenbase"}, {"relation_type": "prov:hadPrimarySource", "source": "zfin"}, {"relation_type": "prov:hadPrimarySource", "source": "phenio"}, {"relation_type": "prov:hadPrimarySource", "source": "bfo"}, {"relation_type": "prov:hadPrimarySource", "source": "bspo"}, {"relation_type": "prov:hadPrimarySource", "source": "chebi"}, {"relation_type": "prov:hadPrimarySource", "source": "cl"}, {"relation_type": "prov:hadPrimarySource", "source": "ddanat"}, {"relation_type": "prov:hadPrimarySource", "source": "ddpheno"}, {"relation_type": "prov:hadPrimarySource", "source": "doid"}, {"relation_type": "prov:hadPrimarySource", "source": "dpo"}, {"relation_type": "prov:hadPrimarySource", "source": "eco"}, {"relation_type": "prov:hadPrimarySource", "source": "emapa"}, {"relation_type": "prov:hadPrimarySource", "source": "fbbt"}, {"relation_type": "prov:hadPrimarySource", "source": "fbdv"}, {"relation_type": "prov:hadPrimarySource", "source": "foodon"}, {"relation_type": "prov:hadPrimarySource", "source": "fypo"}, {"relation_type": "prov:hadPrimarySource", "source": "go"}, {"relation_type": "prov:hadPrimarySource", "source": "hp"}, {"relation_type": "prov:hadPrimarySource", "source": "hsapdv"}, {"relation_type": "prov:hadPrimarySource", "source": "maxo"}, {"relation_type": "prov:hadPrimarySource", "source": "mondo"}, {"relation_type": "prov:hadPrimarySource", "source": "mp"}, {"relation_type": "prov:hadPrimarySource", "source": "mpath"}, {"relation_type": "prov:hadPrimarySource", "source": "nbo"}, {"relation_type": "prov:hadPrimarySource", "source": "ncbitaxon"}, {"relation_type": "prov:hadPrimarySource", "source": "ncit"}, {"relation_type": "prov:hadPrimarySource", "source": "oba"}, {"relation_type": "prov:hadPrimarySource", "source": "ordo"}, {"relation_type": "prov:hadPrimarySource", "source": "pato"}, {"relation_type": "prov:hadPrimarySource", "source": "pr"}, {"relation_type": "prov:hadPrimarySource", "source": "ro"}, {"relation_type": "prov:hadPrimarySource", "source": "so"}, {"relation_type": "prov:hadPrimarySource", "source": "uberon"}, {"relation_type": "prov:hadPrimarySource", "source": "upheno"}, {"relation_type": "prov:hadPrimarySource", "source": "wbbt"}, {"relation_type": "prov:hadPrimarySource", "source": "wbls"}, {"relation_type": "prov:hadPrimarySource", "source": "wbphenotype"}, {"relation_type": "prov:hadPrimarySource", "source": "xao"}, {"relation_type": "prov:hadPrimarySource", "source": "xpo"}, {"relation_type": "prov:hadPrimarySource", "source": "zfa"}, {"relation_type": "prov:hadPrimarySource", "source": "zfs"}, {"relation_type": "prov:hadPrimarySource", "source": "zp"}, {"relation_type": "prov:hadPrimarySource", "source": "icd10cm"}, {"relation_type": "prov:hadPrimarySource", "source": "icd11"}, {"relation_type": "prov:hadPrimarySource", "source": "decipher"}, {"relation_type": "prov:hadPrimarySource", "source": "mmrrc"}, {"relation_type": "prov:hadPrimarySource", "source": "cureid"}, {"relation_type": "prov:hadPrimarySource", "source": "phenopacket-store"}], "product_file_size": 230046094, "product_url": "https://data.monarchinitiative.org/monarch-kg-dev/latest/monarch-kg.tar.gz"}]
{"activity_status": "active", "category": "Resource", "contacts": [{"category": "Individual", "contact_details": [{"contact_type": "email", "value": "jhc@lbl.gov"}, {"contact_type": "github", "value": "caufieldjh"}], "label": "J. Harry Caufield"}], "creation_date": "2025-03-09T00:00:00Z", "description": "An ontology for accessing and comparing knowledge concerning phenotypes across species and genetic backgrounds.", "domains": ["phenotype"], "homepage_url": "https://monarch-initiative.github.io/phenio/", "id": "phenio", "infores_id": "phenio", "last_modified_date": "2026-06-27T00:00:00Z", "layout": "resource_detail", "license": {"id": "https://opensource.org/license/bsd-3-clause", "label": "BSD3"}, "name": "An integrated ontology for Phenomics", "products": [{"category": "Product", "compression": "gzip", "description": "OWL version of phenio", "format": "owl", "id": "phenio.model", "license": {"id": "https://opensource.org/license/bsd-3-clause", "label": "BSD3"}, "name": "phenio", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "phenio"}], "product_file_size": 124412326, "product_url": "https://github.com/monarch-initiative/phenio/releases/latest/download/phenio.owl.gz", "repository": "https://github.com/monarch-initiative/phenio"}, {"category": "GraphProduct", "compatibility": [{"standard": "biolink", "version": "4.2.5"}], "compression": "targz", "description": "PHENIO as a KGX graph", "format": "kgx", "id": "phenio.graph", "license": {"id": "https://opensource.org/license/bsd-3-clause", "label": "BSD3"}, "name": "KG-Phenio", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "phenio"}], "product_file_size": 71579307, "product_url": "https://github.com/Knowledge-Graph-Hub/kg-phenio/releases/latest/download/kg-phenio.tar.gz", "repository": "https://github.com/Knowledge-Graph-Hub/kg-phenio"}, {"category": "GraphProduct", "description": "KGX Distribution of KG-Monarch", "edge_count": 15211571, "format": "kgx", "id": "kg-monarch.graph", "name": "KGX Distribution of KG-Monarch", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "biolink:Case", "biolink:Cell", "biolink:CellularComponent", "biolink:ChemicalEntity", "biolink:Disease", "biolink:Gene", "biolink:Genotype", "biolink:LifeStage", "biolink:MolecularActivity", "biolink:MolecularEntity", "biolink:NamedThing", "biolink:OrganismTaxon", "biolink:Pathway", "biolink:PhenotypicFeature", "biolink:Protein", "biolink:SequenceVariant"], "node_count": 1462594, "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "alliance"}, {"relation_type": "prov:hadPrimarySource", "source": "bgee"}, {"relation_type": "prov:hadPrimarySource", "source": "biogrid"}, {"relation_type": "prov:hadPrimarySource", "source": "clingen"}, {"relation_type": "prov:hadPrimarySource", "source": "clinvar"}, {"relation_type": "prov:hadPrimarySource", "source": "ctd"}, {"relation_type": "prov:hadPrimarySource", "source": "dictybase"}, {"relation_type": "prov:hadPrimarySource", "source": "go"}, {"relation_type": "prov:hadPrimarySource", "source": "hp"}, {"relation_type": "prov:hadPrimarySource", "source": "kg-monarch"}, {"relation_type": "prov:hadPrimarySource", "source": "maxo"}, {"relation_type": "prov:hadPrimarySource", "source": "panther"}, {"relation_type": "prov:hadPrimarySource", "source": "phenio"}, {"relation_type": "prov:hadPrimarySource", "source": "pombase"}, {"relation_type": "prov:hadPrimarySource", "source": "reactome"}, {"relation_type": "prov:hadPrimarySource", "source": "string"}, {"relation_type": "prov:hadPrimarySource", "source": "xenbase"}, {"relation_type": "prov:hadPrimarySource", "source": "zfin"}], "predicates": ["biolink:actively_involved_in", "biolink:acts_upstream_of", "biolink:acts_upstream_of_negative_effect", "biolink:acts_upstream_of_or_within", "biolink:acts_upstream_of_or_within_negative_effect", "biolink:acts_upstream_of_or_within_positive_effect", "biolink:acts_upstream_of_positive_effect", "biolink:affects", "biolink:applied_to_treat", "biolink:associated_with_increased_likelihood_of", "biolink:capable_of", "biolink:caused_by", "biolink:causes", "biolink:coexists_with", "biolink:colocalizes_with", "biolink:contributes_to", "biolink:correlated_with", "biolink:derives_from", "biolink:develops_from", "biolink:directly_physically_interacts_with", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:expresses", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_adverse_event", "biolink:has_disease", "biolink:has_gene", "biolink:has_input", "biolink:has_mode_of_inheritance", "biolink:has_output", "biolink:has_part", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:homologous_to", "biolink:in_taxon", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_input_of", "biolink:is_output_of", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:location_of", "biolink:model_of", "biolink:occurs_in", "biolink:orthologous_to", "biolink:overlaps", "biolink:part_of", "biolink:participates_in", "biolink:preceded_by", "biolink:precedes", "biolink:produced_by", "biolink:produces", "biolink:regulates", "biolink:related_to", "biolink:same_as", "biolink:subclass_of", "biolink:temporally_related_to", "biolink:treats", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 230877741, "product_url": "http://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.tar.gz"}, {"category": "GraphProduct", "description": "KGX JSON-Lines Distribution of KG-Monarch", "edge_count": 15211571, "format": "kgx-jsonl", "id": "kg-monarch.graph.jsonl", "name": "KGX JSON-L Distribution of KG-Monarch", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "biolink:Case", "biolink:Cell", "biolink:CellularComponent", "biolink:ChemicalEntity", "biolink:Disease", "biolink:Gene", "biolink:Genotype", "biolink:LifeStage", "biolink:MolecularActivity", "biolink:MolecularEntity", "biolink:NamedThing", "biolink:OrganismTaxon", "biolink:Pathway", "biolink:PhenotypicFeature", "biolink:Protein", "biolink:SequenceVariant"], "node_count": 1462594, "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "alliance"}, {"relation_type": "prov:hadPrimarySource", "source": "bgee"}, {"relation_type": "prov:hadPrimarySource", "source": "biogrid"}, {"relation_type": "prov:hadPrimarySource", "source": "clingen"}, {"relation_type": "prov:hadPrimarySource", "source": "clinvar"}, {"relation_type": "prov:hadPrimarySource", "source": "ctd"}, {"relation_type": "prov:hadPrimarySource", "source": "dictybase"}, {"relation_type": "prov:hadPrimarySource", "source": "go"}, {"relation_type": "prov:hadPrimarySource", "source": "hp"}, {"relation_type": "prov:hadPrimarySource", "source": "kg-monarch"}, {"relation_type": "prov:hadPrimarySource", "source": "maxo"}, {"relation_type": "prov:hadPrimarySource", "source": "panther"}, {"relation_type": "prov:hadPrimarySource", "source": "phenio"}, {"relation_type": "prov:hadPrimarySource", "source": "pombase"}, {"relation_type": "prov:hadPrimarySource", "source": "reactome"}, {"relation_type": "prov:hadPrimarySource", "source": "string"}, {"relation_type": "prov:hadPrimarySource", "source": "xenbase"}, {"relation_type": "prov:hadPrimarySource", "source": "zfin"}], "predicates": ["biolink:actively_involved_in", "biolink:acts_upstream_of", "biolink:acts_upstream_of_negative_effect", "biolink:acts_upstream_of_or_within", "biolink:acts_upstream_of_or_within_negative_effect", "biolink:acts_upstream_of_or_within_positive_effect", "biolink:acts_upstream_of_positive_effect", "biolink:affects", "biolink:applied_to_treat", "biolink:associated_with_increased_likelihood_of", "biolink:capable_of", "biolink:caused_by", "biolink:causes", "biolink:coexists_with", "biolink:colocalizes_with", "biolink:contributes_to", "biolink:correlated_with", "biolink:derives_from", "biolink:develops_from", "biolink:directly_physically_interacts_with", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:expresses", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_adverse_event", "biolink:has_disease", "biolink:has_gene", "biolink:has_input", "biolink:has_mode_of_inheritance", "biolink:has_output", "biolink:has_part", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:homologous_to", "biolink:in_taxon", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_input_of", "biolink:is_output_of", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:location_of", "biolink:model_of", "biolink:occurs_in", "biolink:orthologous_to", "biolink:overlaps", "biolink:part_of", "biolink:participates_in", "biolink:preceded_by", "biolink:precedes", "biolink:produced_by", "biolink:produces", "biolink:regulates", "biolink:related_to", "biolink:same_as", "biolink:subclass_of", "biolink:temporally_related_to", "biolink:treats", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 315667976, "product_url": "https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.jsonl.tar.gz"}, {"category": "GraphProduct", "description": "RDF Distribution of KG-Monarch", "edge_count": 15211571, "format": "rdfxml", "id": "kg-monarch.graph.rdf", "name": "RDF Distribution of KG-Monarch", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "biolink:Case", "biolink:Cell", "biolink:CellularComponent", "biolink:ChemicalEntity", "biolink:Disease", "biolink:Gene", "biolink:Genotype", "biolink:LifeStage", "biolink:MolecularActivity", "biolink:MolecularEntity", "biolink:NamedThing", "biolink:OrganismTaxon", "biolink:Pathway", "biolink:PhenotypicFeature", "biolink:Protein", "biolink:SequenceVariant"], "node_count": 1462594, "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "alliance"}, {"relation_type": "prov:hadPrimarySource", "source": "bgee"}, {"relation_type": "prov:hadPrimarySource", "source": "biogrid"}, {"relation_type": "prov:hadPrimarySource", "source": "clingen"}, {"relation_type": "prov:hadPrimarySource", "source": "clinvar"}, {"relation_type": "prov:hadPrimarySource", "source": "ctd"}, {"relation_type": "prov:hadPrimarySource", "source": "dictybase"}, {"relation_type": "prov:hadPrimarySource", "source": "go"}, {"relation_type": "prov:hadPrimarySource", "source": "hp"}, {"relation_type": "prov:hadPrimarySource", "source": "kg-monarch"}, {"relation_type": "prov:hadPrimarySource", "source": "maxo"}, {"relation_type": "prov:hadPrimarySource", "source": "panther"}, {"relation_type": "prov:hadPrimarySource", "source": "phenio"}, {"relation_type": "prov:hadPrimarySource", "source": "pombase"}, {"relation_type": "prov:hadPrimarySource", "source": "reactome"}, {"relation_type": "prov:hadPrimarySource", "source": "string"}, {"relation_type": "prov:hadPrimarySource", "source": "xenbase"}, {"relation_type": "prov:hadPrimarySource", "source": "zfin"}], "predicates": ["biolink:actively_involved_in", "biolink:acts_upstream_of", "biolink:acts_upstream_of_negative_effect", "biolink:acts_upstream_of_or_within", "biolink:acts_upstream_of_or_within_negative_effect", "biolink:acts_upstream_of_or_within_positive_effect", "biolink:acts_upstream_of_positive_effect", "biolink:affects", "biolink:applied_to_treat", "biolink:associated_with_increased_likelihood_of", "biolink:capable_of", "biolink:caused_by", "biolink:causes", "biolink:coexists_with", "biolink:colocalizes_with", "biolink:contributes_to", "biolink:correlated_with", "biolink:derives_from", "biolink:develops_from", "biolink:directly_physically_interacts_with", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:expresses", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_adverse_event", "biolink:has_disease", "biolink:has_gene", "biolink:has_input", "biolink:has_mode_of_inheritance", "biolink:has_output", "biolink:has_part", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:homologous_to", "biolink:in_taxon", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_input_of", "biolink:is_output_of", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:location_of", "biolink:model_of", "biolink:occurs_in", "biolink:orthologous_to", "biolink:overlaps", "biolink:part_of", "biolink:participates_in", "biolink:preceded_by", "biolink:precedes", "biolink:produced_by", "biolink:produces", "biolink:regulates", "biolink:related_to", "biolink:same_as", "biolink:subclass_of", "biolink:temporally_related_to", "biolink:treats", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 879238775, "product_url": "https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.nt.gz"}, {"category": "GraphProduct", "description": "Neo4j Dump of KG-Monarch", "dump_format": "neo4j", "edge_count": 15211571, "format": "neo4j", "id": "kg-monarch.graph.neo4j", "name": "Neo4j Dump of KG-Monarch", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "biolink:Case", "biolink:Cell", "biolink:CellularComponent", "biolink:ChemicalEntity", "biolink:Disease", "biolink:Gene", "biolink:Genotype", "biolink:LifeStage", "biolink:MolecularActivity", "biolink:MolecularEntity", "biolink:NamedThing", "biolink:OrganismTaxon", "biolink:Pathway", "biolink:PhenotypicFeature", "biolink:Protein", "biolink:SequenceVariant"], "node_count": 1462594, "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "alliance"}, {"relation_type": "prov:hadPrimarySource", "source": "bgee"}, {"relation_type": "prov:hadPrimarySource", "source": "biogrid"}, {"relation_type": "prov:hadPrimarySource", "source": "clingen"}, {"relation_type": "prov:hadPrimarySource", "source": "clinvar"}, {"relation_type": "prov:hadPrimarySource", "source": "ctd"}, {"relation_type": "prov:hadPrimarySource", "source": "dictybase"}, {"relation_type": "prov:hadPrimarySource", "source": "go"}, {"relation_type": "prov:hadPrimarySource", "source": "hp"}, {"relation_type": "prov:hadPrimarySource", "source": "kg-monarch"}, {"relation_type": "prov:hadPrimarySource", "source": "maxo"}, {"relation_type": "prov:hadPrimarySource", "source": "panther"}, {"relation_type": "prov:hadPrimarySource", "source": "phenio"}, {"relation_type": "prov:hadPrimarySource", "source": "pombase"}, {"relation_type": "prov:hadPrimarySource", "source": "reactome"}, {"relation_type": "prov:hadPrimarySource", "source": "string"}, {"relation_type": "prov:hadPrimarySource", "source": "xenbase"}, {"relation_type": "prov:hadPrimarySource", "source": "zfin"}], "predicates": ["biolink:actively_involved_in", "biolink:acts_upstream_of", "biolink:acts_upstream_of_negative_effect", "biolink:acts_upstream_of_or_within", "biolink:acts_upstream_of_or_within_negative_effect", "biolink:acts_upstream_of_or_within_positive_effect", "biolink:acts_upstream_of_positive_effect", "biolink:affects", "biolink:applied_to_treat", "biolink:associated_with_increased_likelihood_of", "biolink:capable_of", "biolink:caused_by", "biolink:causes", "biolink:coexists_with", "biolink:colocalizes_with", "biolink:contributes_to", "biolink:correlated_with", "biolink:derives_from", "biolink:develops_from", "biolink:directly_physically_interacts_with", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:expresses", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_adverse_event", "biolink:has_disease", "biolink:has_gene", "biolink:has_input", "biolink:has_mode_of_inheritance", "biolink:has_output", "biolink:has_part", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:homologous_to", "biolink:in_taxon", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_input_of", "biolink:is_output_of", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:location_of", "biolink:model_of", "biolink:occurs_in", "biolink:orthologous_to", "biolink:overlaps", "biolink:part_of", "biolink:participates_in", "biolink:preceded_by", "biolink:precedes", "biolink:produced_by", "biolink:produces", "biolink:regulates", "biolink:related_to", "biolink:same_as", "biolink:subclass_of", "biolink:temporally_related_to", "biolink:treats", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 1438250397, "product_url": "https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.neo4j.dump", "warnings": []}, {"category": "GraphProduct", "description": "DuckDB database of KG-Monarch", "edge_count": 15211571, "format": "mixed", "id": "kg-monarch.graph.duckdb", "name": "DuckDB database of KG-Monarch", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "biolink:Case", "biolink:Cell", "biolink:CellularComponent", "biolink:ChemicalEntity", "biolink:Disease", "biolink:Gene", "biolink:Genotype", "biolink:LifeStage", "biolink:MolecularActivity", "biolink:MolecularEntity", "biolink:NamedThing", "biolink:OrganismTaxon", "biolink:Pathway", "biolink:PhenotypicFeature", "biolink:Protein", "biolink:SequenceVariant"], "node_count": 1462594, "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "alliance"}, {"relation_type": "prov:hadPrimarySource", "source": "bgee"}, {"relation_type": "prov:hadPrimarySource", "source": "biogrid"}, {"relation_type": "prov:hadPrimarySource", "source": "clingen"}, {"relation_type": "prov:hadPrimarySource", "source": "clinvar"}, {"relation_type": "prov:hadPrimarySource", "source": "ctd"}, {"relation_type": "prov:hadPrimarySource", "source": "dictybase"}, {"relation_type": "prov:hadPrimarySource", "source": "go"}, {"relation_type": "prov:hadPrimarySource", "source": "hp"}, {"relation_type": "prov:hadPrimarySource", "source": "kg-monarch"}, {"relation_type": "prov:hadPrimarySource", "source": "maxo"}, {"relation_type": "prov:hadPrimarySource", "source": "panther"}, {"relation_type": "prov:hadPrimarySource", "source": "phenio"}, {"relation_type": "prov:hadPrimarySource", "source": "pombase"}, {"relation_type": "prov:hadPrimarySource", "source": "reactome"}, {"relation_type": "prov:hadPrimarySource", "source": "string"}, {"relation_type": "prov:hadPrimarySource", "source": "xenbase"}, {"relation_type": "prov:hadPrimarySource", "source": "zfin"}], "predicates": ["biolink:actively_involved_in", "biolink:acts_upstream_of", "biolink:acts_upstream_of_negative_effect", "biolink:acts_upstream_of_or_within", "biolink:acts_upstream_of_or_within_negative_effect", "biolink:acts_upstream_of_or_within_positive_effect", "biolink:acts_upstream_of_positive_effect", "biolink:affects", "biolink:applied_to_treat", "biolink:associated_with_increased_likelihood_of", "biolink:capable_of", "biolink:caused_by", "biolink:causes", "biolink:coexists_with", "biolink:colocalizes_with", "biolink:contributes_to", "biolink:correlated_with", "biolink:derives_from", "biolink:develops_from", "biolink:directly_physically_interacts_with", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:expresses", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_adverse_event", "biolink:has_disease", "biolink:has_gene", "biolink:has_input", "biolink:has_mode_of_inheritance", "biolink:has_output", "biolink:has_part", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:homologous_to", "biolink:in_taxon", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_input_of", "biolink:is_output_of", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:location_of", "biolink:model_of", "biolink:occurs_in", "biolink:orthologous_to", "biolink:overlaps", "biolink:part_of", "biolink:participates_in", "biolink:preceded_by", "biolink:precedes", "biolink:produced_by", "biolink:produces", "biolink:regulates", "biolink:related_to", "biolink:same_as", "biolink:subclass_of", "biolink:temporally_related_to", "biolink:treats", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 6827814912, "product_url": "https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.duckdb"}, {"category": "GraphProduct", "compression": "targz", "description": "KGX JSON-Lines Distribution of KG-Monarch (Edges)", "edge_count": 15211571, "format": "kgx-jsonl", "id": "kg-monarch.graph.jsonl.edges", "name": "KGX JSON-L Distribution of KG-Monarch Edges", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "biolink:Case", "biolink:Cell", "biolink:CellularComponent", "biolink:ChemicalEntity", "biolink:Disease", "biolink:Gene", "biolink:Genotype", "biolink:LifeStage", "biolink:MolecularActivity", "biolink:MolecularEntity", "biolink:NamedThing", "biolink:OrganismTaxon", "biolink:Pathway", "biolink:PhenotypicFeature", "biolink:Protein", "biolink:SequenceVariant"], "node_count": 1462594, "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "alliance"}, {"relation_type": "prov:hadPrimarySource", "source": "bgee"}, {"relation_type": "prov:hadPrimarySource", "source": "biogrid"}, {"relation_type": "prov:hadPrimarySource", "source": "clingen"}, {"relation_type": "prov:hadPrimarySource", "source": "clinvar"}, {"relation_type": "prov:hadPrimarySource", "source": "ctd"}, {"relation_type": "prov:hadPrimarySource", "source": "dictybase"}, {"relation_type": "prov:hadPrimarySource", "source": "go"}, {"relation_type": "prov:hadPrimarySource", "source": "hp"}, {"relation_type": "prov:hadPrimarySource", "source": "kg-monarch"}, {"relation_type": "prov:hadPrimarySource", "source": "maxo"}, {"relation_type": "prov:hadPrimarySource", "source": "panther"}, {"relation_type": "prov:hadPrimarySource", "source": "phenio"}, {"relation_type": "prov:hadPrimarySource", "source": "pombase"}, {"relation_type": "prov:hadPrimarySource", "source": "reactome"}, {"relation_type": "prov:hadPrimarySource", "source": "string"}, {"relation_type": "prov:hadPrimarySource", "source": "xenbase"}, {"relation_type": "prov:hadPrimarySource", "source": "zfin"}], "predicates": ["biolink:actively_involved_in", "biolink:acts_upstream_of", "biolink:acts_upstream_of_negative_effect", "biolink:acts_upstream_of_or_within", "biolink:acts_upstream_of_or_within_negative_effect", "biolink:acts_upstream_of_or_within_positive_effect", "biolink:acts_upstream_of_positive_effect", "biolink:affects", "biolink:applied_to_treat", "biolink:associated_with_increased_likelihood_of", "biolink:capable_of", "biolink:caused_by", "biolink:causes", "biolink:coexists_with", "biolink:colocalizes_with", "biolink:contributes_to", "biolink:correlated_with", "biolink:derives_from", "biolink:develops_from", "biolink:directly_physically_interacts_with", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:expresses", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_adverse_event", "biolink:has_disease", "biolink:has_gene", "biolink:has_input", "biolink:has_mode_of_inheritance", "biolink:has_output", "biolink:has_part", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:homologous_to", "biolink:in_taxon", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_input_of", "biolink:is_output_of", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:location_of", "biolink:model_of", "biolink:occurs_in", "biolink:orthologous_to", "biolink:overlaps", "biolink:part_of", "biolink:participates_in", "biolink:preceded_by", "biolink:precedes", "biolink:produced_by", "biolink:produces", "biolink:regulates", "biolink:related_to", "biolink:same_as", "biolink:subclass_of", "biolink:temporally_related_to", "biolink:treats", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 487854288, "product_url": "https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.jsonl.tar.gz"}, {"category": "GraphProduct", "compression": "targz", "description": "KGX JSON-Lines Distribution of KG-Monarch (Nodes)", "edge_count": 15211571, "format": "kgx-jsonl", "id": "kg-monarch.graph.jsonl.nodes", "name": "KGX JSON-L Distribution of KG-Monarch Nodes", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "biolink:Case", "biolink:Cell", "biolink:CellularComponent", "biolink:ChemicalEntity", "biolink:Disease", "biolink:Gene", "biolink:Genotype", "biolink:LifeStage", "biolink:MolecularActivity", "biolink:MolecularEntity", "biolink:NamedThing", "biolink:OrganismTaxon", "biolink:Pathway", "biolink:PhenotypicFeature", "biolink:Protein", "biolink:SequenceVariant"], "node_count": 1462594, "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "alliance"}, {"relation_type": "prov:hadPrimarySource", "source": "bgee"}, {"relation_type": "prov:hadPrimarySource", "source": "biogrid"}, {"relation_type": "prov:hadPrimarySource", "source": "clingen"}, {"relation_type": "prov:hadPrimarySource", "source": "clinvar"}, {"relation_type": "prov:hadPrimarySource", "source": "ctd"}, {"relation_type": "prov:hadPrimarySource", "source": "dictybase"}, {"relation_type": "prov:hadPrimarySource", "source": "go"}, {"relation_type": "prov:hadPrimarySource", "source": "hp"}, {"relation_type": "prov:hadPrimarySource", "source": "kg-monarch"}, {"relation_type": "prov:hadPrimarySource", "source": "maxo"}, {"relation_type": "prov:hadPrimarySource", "source": "panther"}, {"relation_type": "prov:hadPrimarySource", "source": "phenio"}, {"relation_type": "prov:hadPrimarySource", "source": "pombase"}, {"relation_type": "prov:hadPrimarySource", "source": "reactome"}, {"relation_type": "prov:hadPrimarySource", "source": "string"}, {"relation_type": "prov:hadPrimarySource", "source": "xenbase"}, {"relation_type": "prov:hadPrimarySource", "source": "zfin"}], "predicates": ["biolink:actively_involved_in", "biolink:acts_upstream_of", "biolink:acts_upstream_of_negative_effect", "biolink:acts_upstream_of_or_within", "biolink:acts_upstream_of_or_within_negative_effect", "biolink:acts_upstream_of_or_within_positive_effect", "biolink:acts_upstream_of_positive_effect", "biolink:affects", "biolink:applied_to_treat", "biolink:associated_with_increased_likelihood_of", "biolink:capable_of", "biolink:caused_by", "biolink:causes", "biolink:coexists_with", "biolink:colocalizes_with", "biolink:contributes_to", "biolink:correlated_with", "biolink:derives_from", "biolink:develops_from", "biolink:directly_physically_interacts_with", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:expresses", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_adverse_event", "biolink:has_disease", "biolink:has_gene", "biolink:has_input", "biolink:has_mode_of_inheritance", "biolink:has_output", "biolink:has_part", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:homologous_to", "biolink:in_taxon", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_input_of", "biolink:is_output_of", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:location_of", "biolink:model_of", "biolink:occurs_in", "biolink:orthologous_to", "biolink:overlaps", "biolink:part_of", "biolink:participates_in", "biolink:preceded_by", "biolink:precedes", "biolink:produced_by", "biolink:produces", "biolink:regulates", "biolink:related_to", "biolink:same_as", "biolink:subclass_of", "biolink:temporally_related_to", "biolink:treats", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 487854288, "product_url": "https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.jsonl.tar.gz"}, {"category": "GraphProduct", "description": "Neo4j Dump of KG-Monarch Edges", "edge_count": 15211571, "format": "neo4j", "id": "kg-monarch.graph.neo4j.edges", "name": "Neo4j Dump of KG-Monarch Edges", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "biolink:Case", "biolink:Cell", "biolink:CellularComponent", "biolink:ChemicalEntity", "biolink:Disease", "biolink:Gene", "biolink:Genotype", "biolink:LifeStage", "biolink:MolecularActivity", "biolink:MolecularEntity", "biolink:NamedThing", "biolink:OrganismTaxon", "biolink:Pathway", "biolink:PhenotypicFeature", "biolink:Protein", "biolink:SequenceVariant"], "node_count": 1462594, "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "alliance"}, {"relation_type": "prov:hadPrimarySource", "source": "bgee"}, {"relation_type": "prov:hadPrimarySource", "source": "biogrid"}, {"relation_type": "prov:hadPrimarySource", "source": "clingen"}, {"relation_type": "prov:hadPrimarySource", "source": "clinvar"}, {"relation_type": "prov:hadPrimarySource", "source": "ctd"}, {"relation_type": "prov:hadPrimarySource", "source": "dictybase"}, {"relation_type": "prov:hadPrimarySource", "source": "go"}, {"relation_type": "prov:hadPrimarySource", "source": "hp"}, {"relation_type": "prov:hadPrimarySource", "source": "kg-monarch"}, {"relation_type": "prov:hadPrimarySource", "source": "maxo"}, {"relation_type": "prov:hadPrimarySource", "source": "panther"}, {"relation_type": "prov:hadPrimarySource", "source": "phenio"}, {"relation_type": "prov:hadPrimarySource", "source": "pombase"}, {"relation_type": "prov:hadPrimarySource", "source": "reactome"}, {"relation_type": "prov:hadPrimarySource", "source": "string"}, {"relation_type": "prov:hadPrimarySource", "source": "xenbase"}, {"relation_type": "prov:hadPrimarySource", "source": "zfin"}], "predicates": ["biolink:actively_involved_in", "biolink:acts_upstream_of", "biolink:acts_upstream_of_negative_effect", "biolink:acts_upstream_of_or_within", "biolink:acts_upstream_of_or_within_negative_effect", "biolink:acts_upstream_of_or_within_positive_effect", "biolink:acts_upstream_of_positive_effect", "biolink:affects", "biolink:applied_to_treat", "biolink:associated_with_increased_likelihood_of", "biolink:capable_of", "biolink:caused_by", "biolink:causes", "biolink:coexists_with", "biolink:colocalizes_with", "biolink:contributes_to", "biolink:correlated_with", "biolink:derives_from", "biolink:develops_from", "biolink:directly_physically_interacts_with", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:expresses", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_adverse_event", "biolink:has_disease", "biolink:has_gene", "biolink:has_input", "biolink:has_mode_of_inheritance", "biolink:has_output", "biolink:has_part", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:homologous_to", "biolink:in_taxon", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_input_of", "biolink:is_output_of", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:location_of", "biolink:model_of", "biolink:occurs_in", "biolink:orthologous_to", "biolink:overlaps", "biolink:part_of", "biolink:participates_in", "biolink:preceded_by", "biolink:precedes", "biolink:produced_by", "biolink:produces", "biolink:regulates", "biolink:related_to", "biolink:same_as", "biolink:subclass_of", "biolink:temporally_related_to", "biolink:treats", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 4386388748, "product_url": "https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg_edges.neo4j.csv"}, {"category": "GraphProduct", "description": "Neo4j Dump of KG-Monarch Nodes", "edge_count": 15211571, "format": "neo4j", "id": "kg-monarch.graph.neo4j.nodes", "name": "Neo4j Dump of KG-Monarch Nodes", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "biolink:Case", "biolink:Cell", "biolink:CellularComponent", "biolink:ChemicalEntity", "biolink:Disease", "biolink:Gene", "biolink:Genotype", "biolink:LifeStage", "biolink:MolecularActivity", "biolink:MolecularEntity", "biolink:NamedThing", "biolink:OrganismTaxon", "biolink:Pathway", "biolink:PhenotypicFeature", "biolink:Protein", "biolink:SequenceVariant"], "node_count": 1462594, "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "alliance"}, {"relation_type": "prov:hadPrimarySource", "source": "bgee"}, {"relation_type": "prov:hadPrimarySource", "source": "biogrid"}, {"relation_type": "prov:hadPrimarySource", "source": "clingen"}, {"relation_type": "prov:hadPrimarySource", "source": "clinvar"}, {"relation_type": "prov:hadPrimarySource", "source": "ctd"}, {"relation_type": "prov:hadPrimarySource", "source": "dictybase"}, {"relation_type": "prov:hadPrimarySource", "source": "go"}, {"relation_type": "prov:hadPrimarySource", "source": "hp"}, {"relation_type": "prov:hadPrimarySource", "source": "kg-monarch"}, {"relation_type": "prov:hadPrimarySource", "source": "maxo"}, {"relation_type": "prov:hadPrimarySource", "source": "panther"}, {"relation_type": "prov:hadPrimarySource", "source": "phenio"}, {"relation_type": "prov:hadPrimarySource", "source": "pombase"}, {"relation_type": "prov:hadPrimarySource", "source": "reactome"}, {"relation_type": "prov:hadPrimarySource", "source": "string"}, {"relation_type": "prov:hadPrimarySource", "source": "xenbase"}, {"relation_type": "prov:hadPrimarySource", "source": "zfin"}], "predicates": ["biolink:actively_involved_in", "biolink:acts_upstream_of", "biolink:acts_upstream_of_negative_effect", "biolink:acts_upstream_of_or_within", "biolink:acts_upstream_of_or_within_negative_effect", "biolink:acts_upstream_of_or_within_positive_effect", "biolink:acts_upstream_of_positive_effect", "biolink:affects", "biolink:applied_to_treat", "biolink:associated_with_increased_likelihood_of", "biolink:capable_of", "biolink:caused_by", "biolink:causes", "biolink:coexists_with", "biolink:colocalizes_with", "biolink:contributes_to", "biolink:correlated_with", "biolink:derives_from", "biolink:develops_from", "biolink:directly_physically_interacts_with", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:expresses", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_adverse_event", "biolink:has_disease", "biolink:has_gene", "biolink:has_input", "biolink:has_mode_of_inheritance", "biolink:has_output", "biolink:has_part", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:homologous_to", "biolink:in_taxon", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_input_of", "biolink:is_output_of", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:location_of", "biolink:model_of", "biolink:occurs_in", "biolink:orthologous_to", "biolink:overlaps", "biolink:part_of", "biolink:participates_in", "biolink:preceded_by", "biolink:precedes", "biolink:produced_by", "biolink:produces", "biolink:regulates", "biolink:related_to", "biolink:same_as", "biolink:subclass_of", "biolink:temporally_related_to", "biolink:treats", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 349573789, "product_url": "https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg_nodes.neo4j.csv"}, {"category": "Product", "description": "Phenio SQLite database in SemSQL format for ontology queries", "format": "sqlite", "id": "kg-monarch.phenio.semsql", "name": "Phenio SQLite (SemSQL)", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "kg-monarch"}, {"relation_type": "prov:hadPrimarySource", "source": "phenio"}], "product_file_size": 3425435914, "product_url": "https://data.monarchinitiative.org/monarch-kg/latest/phenio.db.gz"}, {"category": "GraphProduct", "compression": "targz", "description": "KGX Distribution of KG-Alzheimers", "format": "kgx", "id": "kg-alzheimers.graph", "name": "KGX Distribution of KG-Alzheimers", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "kg-alzheimers"}, {"relation_type": "prov:hadPrimarySource", "source": "monarchinitiative"}, {"relation_type": "prov:hadPrimarySource", "source": "phenio"}, {"relation_type": "prov:hadPrimarySource", "source": "mondo"}, {"relation_type": "prov:hadPrimarySource", "source": "hp"}, {"relation_type": "prov:hadPrimarySource", "source": "alliance"}, {"relation_type": "prov:hadPrimarySource", "source": "bgee"}, {"relation_type": "prov:hadPrimarySource", "source": "biogrid"}, {"relation_type": "prov:hadPrimarySource", "source": "ctd"}, {"relation_type": "prov:hadPrimarySource", "source": "dictybase"}, {"relation_type": "prov:hadPrimarySource", "source": "flybase"}, {"relation_type": "prov:hadPrimarySource", "source": "hgnc"}, {"relation_type": "prov:hadPrimarySource", "source": "mgi"}, {"relation_type": "prov:hadPrimarySource", "source": "ncbigene"}, {"relation_type": "prov:hadPrimarySource", "source": "panther"}, {"relation_type": "prov:hadPrimarySource", "source": "pombase"}, {"relation_type": "prov:hadPrimarySource", "source": "reactome"}, {"relation_type": "prov:hadPrimarySource", "source": "rgd"}, {"relation_type": "prov:hadPrimarySource", "source": "sgd"}, {"relation_type": "prov:hadPrimarySource", "source": "string"}, {"relation_type": "prov:hadPrimarySource", "source": "xenbase"}, {"relation_type": "prov:hadPrimarySource", "source": "zfin"}, {"relation_type": "prov:hadPrimarySource", "source": "chebi"}, {"relation_type": "prov:hadPrimarySource", "source": "mesh"}], "product_file_size": 210868256, "product_url": "https://kg-hub.berkeleybop.io/kg-alzheimers/current/kg-alzheimers.tar.gz", "warnings": ["File was not able to be retrieved when checked on 2026-07-01; no live download location was found (GitHub releases, kghub.io/current, and Zenodo all return 404 or have no published artifact)."]}, {"category": "GraphProduct", "description": "KGX distribution of the SRI-Reference KG", "format": "kgx", "id": "sri-reference-kg.graph", "name": "SRI-Reference KG (KGX distribution)", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "sri-reference-kg"}, {"relation_type": "prov:hadPrimarySource", "source": "alliance"}, {"relation_type": "prov:hadPrimarySource", "source": "bgee"}, {"relation_type": "prov:hadPrimarySource", "source": "biogrid"}, {"relation_type": "prov:hadPrimarySource", "source": "clingen"}, {"relation_type": "prov:hadPrimarySource", "source": "clinvar"}, {"relation_type": "prov:hadPrimarySource", "source": "ctd"}, {"relation_type": "prov:hadPrimarySource", "source": "dictybase"}, {"relation_type": "prov:hadPrimarySource", "source": "flybase"}, {"relation_type": "prov:hadPrimarySource", "source": "goa"}, {"relation_type": "prov:hadPrimarySource", "source": "hgnc"}, {"relation_type": "prov:hadPrimarySource", "source": "mgi"}, {"relation_type": "prov:hadPrimarySource", "source": "ncbigene"}, {"relation_type": "prov:hadPrimarySource", "source": "omim"}, {"relation_type": "prov:hadPrimarySource", "source": "orphanet"}, {"relation_type": "prov:hadPrimarySource", "source": "panther"}, {"relation_type": "prov:hadPrimarySource", "source": "pombase"}, {"relation_type": "prov:hadPrimarySource", "source": "reactome"}, {"relation_type": "prov:hadPrimarySource", "source": "rgd"}, {"relation_type": "prov:hadPrimarySource", "source": "sgd"}, {"relation_type": "prov:hadPrimarySource", "source": "string"}, {"relation_type": "prov:hadPrimarySource", "source": "wormbase"}, {"relation_type": "prov:hadPrimarySource", "source": "xenbase"}, {"relation_type": "prov:hadPrimarySource", "source": "zfin"}, {"relation_type": "prov:hadPrimarySource", "source": "phenio"}, {"relation_type": "prov:hadPrimarySource", "source": "bfo"}, {"relation_type": "prov:hadPrimarySource", "source": "bspo"}, {"relation_type": "prov:hadPrimarySource", "source": "chebi"}, {"relation_type": "prov:hadPrimarySource", "source": "cl"}, {"relation_type": "prov:hadPrimarySource", "source": "ddanat"}, {"relation_type": "prov:hadPrimarySource", "source": "ddpheno"}, {"relation_type": "prov:hadPrimarySource", "source": "doid"}, {"relation_type": "prov:hadPrimarySource", "source": "dpo"}, {"relation_type": "prov:hadPrimarySource", "source": "eco"}, {"relation_type": "prov:hadPrimarySource", "source": "emapa"}, {"relation_type": "prov:hadPrimarySource", "source": "fbbt"}, {"relation_type": "prov:hadPrimarySource", "source": "fbdv"}, {"relation_type": "prov:hadPrimarySource", "source": "foodon"}, {"relation_type": "prov:hadPrimarySource", "source": "fypo"}, {"relation_type": "prov:hadPrimarySource", "source": "go"}, {"relation_type": "prov:hadPrimarySource", "source": "hp"}, {"relation_type": "prov:hadPrimarySource", "source": "hsapdv"}, {"relation_type": "prov:hadPrimarySource", "source": "maxo"}, {"relation_type": "prov:hadPrimarySource", "source": "mondo"}, {"relation_type": "prov:hadPrimarySource", "source": "mp"}, {"relation_type": "prov:hadPrimarySource", "source": "mpath"}, {"relation_type": "prov:hadPrimarySource", "source": "nbo"}, {"relation_type": "prov:hadPrimarySource", "source": "ncbitaxon"}, {"relation_type": "prov:hadPrimarySource", "source": "ncit"}, {"relation_type": "prov:hadPrimarySource", "source": "oba"}, {"relation_type": "prov:hadPrimarySource", "source": "ordo"}, {"relation_type": "prov:hadPrimarySource", "source": "pato"}, {"relation_type": "prov:hadPrimarySource", "source": "pr"}, {"relation_type": "prov:hadPrimarySource", "source": "ro"}, {"relation_type": "prov:hadPrimarySource", "source": "so"}, {"relation_type": "prov:hadPrimarySource", "source": "uberon"}, {"relation_type": "prov:hadPrimarySource", "source": "upheno"}, {"relation_type": "prov:hadPrimarySource", "source": "wbbt"}, {"relation_type": "prov:hadPrimarySource", "source": "wbls"}, {"relation_type": "prov:hadPrimarySource", "source": "wbphenotype"}, {"relation_type": "prov:hadPrimarySource", "source": "xao"}, {"relation_type": "prov:hadPrimarySource", "source": "xpo"}, {"relation_type": "prov:hadPrimarySource", "source": "zfa"}, {"relation_type": "prov:hadPrimarySource", "source": "zfs"}, {"relation_type": "prov:hadPrimarySource", "source": "zp"}, {"relation_type": "prov:hadPrimarySource", "source": "icd10cm"}, {"relation_type": "prov:hadPrimarySource", "source": "icd11"}, {"relation_type": "prov:hadPrimarySource", "source": "decipher"}, {"relation_type": "prov:hadPrimarySource", "source": "mmrrc"}, {"relation_type": "prov:hadPrimarySource", "source": "cureid"}, {"relation_type": "prov:hadPrimarySource", "source": "phenopacket-store"}], "product_file_size": 230046094, "product_url": "https://data.monarchinitiative.org/monarch-kg-dev/latest/monarch-kg.tar.gz"}], "repository": "https://github.com/monarch-initiative/phenio", "usages": [{"description": "PHENIO is used by the Monarch Initiative for cross-species inference. As an example, the disease of Parkinsonism may compared on the basis of its phenotype in humans vs. mouse genes and genotypes known to impact these phenotypes.", "id": "cross-species-inference", "label": "PHENIO is used by the Monarch Initiative for cross-species inference", "publications": [{"doi": "doi:10.1093/nar/gkw1128", "id": "doi:10.1093/nar/gkw1128", "preferred": true, "title": "The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species"}], "type": "actual", "url": "https://monarchinitiative.org/HP:0001300#disease", "users": [{"category": "Organization", "contact_details": [{"contact_type": "url", "value": "https://monarchinitiative.org/"}], "label": "The Monarch Initiative"}]}]}