ClinVar
ClinVar is a freely accessible, public archive of reports of human genetic variations and their relationships to human health. It collects and presents data on variants found in patient samples, classifications for diseases and drug responses, and supporting evidence. ClinVar enables access to and communication about the clinical significance of genetic variants, providing healthcare professionals, researchers, and the public with vital information for interpreting genetic test results.
[{"category": "Organization", "contact_details": [{"contact_type": "email", "value": "clinvar@ncbi.nlm.nih.gov"}], "id": "ncbi", "label": "ClinVar Team, National Center for Biotechnology Information (NCBI)"}]
[{"category": "Product", "description": "Complete public data set in XML format containing comprehensive variant information, clinical significance classifications, and supporting evidence.", "format": "xml", "id": "clinvar.xml", "name": "ClinVar XML", "product_url": "https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/"}, {"category": "Product", "description": "ClinVar data in VCF format for GRCh37 human genome assembly, containing variant information and clinical significance.", "format": "vcf", "id": "clinvar.vcf.grch37", "name": "ClinVar VCF (GRCh37)", "product_url": "https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/"}, {"category": "Product", "description": "ClinVar data in VCF format for GRCh38 human genome assembly, containing variant information and clinical significance.", "format": "vcf", "id": "clinvar.vcf.grch38", "name": "ClinVar VCF (GRCh38)", "product_url": "https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/"}, {"category": "Product", "description": "Tab-delimited files summarizing variant data, gene-condition relationships, and other aspects of ClinVar data.", "format": "tsv", "id": "clinvar.tab", "name": "ClinVar Tab-Delimited Files", "product_url": "https://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/"}, {"category": "ProgrammingInterface", "description": "API access to ClinVar data through NCBI's E-utilities, supporting programmatic queries and data retrieval.", "format": "http", "id": "clinvar.api", "name": "ClinVar API (E-utilities)", "product_url": "https://www.ncbi.nlm.nih.gov/clinvar/docs/maintenance_use/"}, {"category": "GraphicalInterface", "description": "Web interface for searching and browsing ClinVar data, with detailed variant information and evidence.", "format": "http", "id": "clinvar.web", "name": "ClinVar Web Interface", "product_url": "https://www.ncbi.nlm.nih.gov/clinvar/"}, {"category": "GraphProduct", "description": "Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access.", "dump_format": "neo4j", "id": "ubkg.neo4j", "name": "UBKG Neo4j Docker Distribution", "original_source": ["hgnc", "loinc", "icd10", "snomedct", "uberon", "pato", "cl", "doid", "obi", "obib", "edam", "hsapdv", "sbo", "mi", "chebi", "mp", "ordo", "uniprot", "uo", "mondo", "efo", "pgo", "gencode", "reactome", "hra", "hubmap", "sennet", "stellar", "dct", "clinvar", "connectivitymap", "hp", "mp", "msigdb", "wikipathways", "clingen", "string", "4dn", "erccrbp", "erccreg", "faldo", "glycordf", "glycocoo", "gtex", "kidsfirst", "lincs", "motrpac", "mw", "npo", "sckan", "disgenet", "biomarker", "opentargets"], "product_url": "https://ubkg-downloads.xconsortia.org/", "secondary_source": ["ubkg"]}, {"category": "GraphProduct", "description": "Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access.", "format": "csv", "id": "ubkg.csv", "name": "UBKG Ontology CSV Files", "original_source": ["hgnc", "loinc", "icd10", "snomedct", "uberon", "pato", "cl", "doid", "obi", "obib", "edam", "hsapdv", "sbo", "mi", "chebi", "mp", "ordo", "uniprot", "uo", "mondo", "efo", "pgo", "gencode", "reactome", "hra", "hubmap", "sennet", "stellar", "dct", "clinvar", "connectivitymap", "hp", "mp", "msigdb", "wikipathways", "clingen", "string", "4dn", "erccrbp", "erccreg", "faldo", "glycordf", "glycocoo", "gtex", "kidsfirst", "lincs", "motrpac", "mw", "npo", "sckan", "disgenet", "biomarker", "opentargets"], "product_url": "https://ubkg-downloads.xconsortia.org/", "secondary_source": ["ubkg"]}, {"category": "GraphProduct", "description": "DisGeNET data, including gene to disease associations and variant to disease associations (requires registration and subscription).", "id": "disgenet.data", "name": "DisGeNET Data", "original_source": ["clingen", "clinvar", "mgd", "rgd", "orphanet", "psygenet", "uniprot", "disgenet", "hp", "gwascatalog", "phewascat", "ukbiobank", "finngen", "clinicaltrialsgov"], "product_url": "https://www.disgenet.com/", "secondary_source": ["disgenet"]}, {"category": "GraphProduct", "description": "KGX Distribution of KG-Monarch", "edge_count": 15356321, "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": 1379605, "original_source": ["phenio", "alliance", "bgee", "biogrid", "clingen", "clinvar", "ctd", "dictybase", "go", "hp", "maxo", "panther", "pombase", "reactome", "string", "xenbase", "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:ameliorates_condition", "biolink:associated_with_increased_likelihood_of", "biolink:caused_by", "biolink:causes", "biolink:colocalizes_with", "biolink:contraindicated_in", "biolink:contributes_to", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_disease", "biolink:has_gene", "biolink:has_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:homologous_to", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:model_of", "biolink:orthologous_to", "biolink:part_of", "biolink:participates_in", "biolink:preventative_for_condition", "biolink:related_to", "biolink:same_as", "biolink:subclass_of", "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", "secondary_source": ["kg-monarch"]}, {"category": "GraphProduct", "description": "KGX JSON-Lines Distribution of KG-Monarch", "edge_count": 15356321, "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": 1379605, "original_source": ["phenio", "alliance", "bgee", "biogrid", "clingen", "clinvar", "ctd", "dictybase", "go", "hp", "maxo", "panther", "pombase", "reactome", "string", "xenbase", "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:ameliorates_condition", "biolink:associated_with_increased_likelihood_of", "biolink:caused_by", "biolink:causes", "biolink:colocalizes_with", "biolink:contraindicated_in", "biolink:contributes_to", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_disease", "biolink:has_gene", "biolink:has_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:homologous_to", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:model_of", "biolink:orthologous_to", "biolink:part_of", "biolink:participates_in", "biolink:preventative_for_condition", "biolink:related_to", "biolink:same_as", "biolink:subclass_of", "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", "secondary_source": ["kg-monarch"]}, {"category": "GraphProduct", "description": "RDF Distribution of KG-Monarch", "edge_count": 15356321, "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": 1379605, "original_source": ["phenio", "alliance", "bgee", "biogrid", "clingen", "clinvar", "ctd", "dictybase", "go", "hp", "maxo", "panther", "pombase", "reactome", "string", "xenbase", "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:ameliorates_condition", "biolink:associated_with_increased_likelihood_of", "biolink:caused_by", "biolink:causes", "biolink:colocalizes_with", "biolink:contraindicated_in", "biolink:contributes_to", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_disease", "biolink:has_gene", "biolink:has_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:homologous_to", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:model_of", "biolink:orthologous_to", "biolink:part_of", "biolink:participates_in", "biolink:preventative_for_condition", "biolink:related_to", "biolink:same_as", "biolink:subclass_of", "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", "secondary_source": ["kg-monarch"]}, {"category": "GraphProduct", "description": "Neo4j Dump of KG-Monarch", "dump_format": "neo4j", "edge_count": 15356321, "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": 1379605, "original_source": ["phenio", "alliance", "bgee", "biogrid", "clingen", "clinvar", "ctd", "dictybase", "go", "hp", "maxo", "panther", "pombase", "reactome", "string", "xenbase", "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:ameliorates_condition", "biolink:associated_with_increased_likelihood_of", "biolink:caused_by", "biolink:causes", "biolink:colocalizes_with", "biolink:contraindicated_in", "biolink:contributes_to", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_disease", "biolink:has_gene", "biolink:has_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:homologous_to", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:model_of", "biolink:orthologous_to", "biolink:part_of", "biolink:participates_in", "biolink:preventative_for_condition", "biolink:related_to", "biolink:same_as", "biolink:subclass_of", "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", "secondary_source": ["kg-monarch"], "warnings": []}, {"category": "GraphProduct", "description": "DuckDB database of KG-Monarch", "edge_count": 15356321, "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": 1379605, "original_source": ["phenio", "alliance", "bgee", "biogrid", "clingen", "clinvar", "ctd", "dictybase", "go", "hp", "maxo", "panther", "pombase", "reactome", "string", "xenbase", "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:ameliorates_condition", "biolink:associated_with_increased_likelihood_of", "biolink:caused_by", "biolink:causes", "biolink:colocalizes_with", "biolink:contraindicated_in", "biolink:contributes_to", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_disease", "biolink:has_gene", "biolink:has_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:homologous_to", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:model_of", "biolink:orthologous_to", "biolink:part_of", "biolink:participates_in", "biolink:preventative_for_condition", "biolink:related_to", "biolink:same_as", "biolink:subclass_of", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 6827814912, "product_url": "https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.duckdb", "secondary_source": ["kg-monarch"]}, {"category": "GraphProduct", "description": "PheKnowLator graph files, including subsets with and without inverse relations.", "format": "owl", "id": "pheknowlator.graph", "latest_version": "current_build", "name": "PheKnowLator graph", "original_source": ["cl", "clo", "chebi", "go", "hp", "mondo", "pw", "pr", "ro", "so", "uberon", "vo", "bioportal", "clinvar", "ctd", "disgenet", "ensembl", "genemania", "hgnc", "hpa", "ncbigene", "medgen", "reactome", "string", "uniprot"], "product_url": "https://console.cloud.google.com/storage/browser/pheknowlator/current_build/knowledge_graphs?pageState=(%22StorageObjectListTable%22:(%22f%22:%22%255B%255D%22))&inv=1&invt=Ab5_1Q&project=pheknowlator", "secondary_source": ["pheknowlator"], "versions": ["v1.0.0", "v2.0.0", "v2.1.0", "v3.0.2", "v4.0.0", "current_build"]}, {"category": "GraphProduct", "description": "KGX JSON-Lines Distribution of KG-Monarch (Edges)", "edge_count": 15356321, "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": 1379605, "original_source": ["phenio", "alliance", "bgee", "biogrid", "clingen", "clinvar", "ctd", "dictybase", "go", "hp", "maxo", "panther", "pombase", "reactome", "string", "xenbase", "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:ameliorates_condition", "biolink:associated_with_increased_likelihood_of", "biolink:caused_by", "biolink:causes", "biolink:colocalizes_with", "biolink:contraindicated_in", "biolink:contributes_to", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_disease", "biolink:has_gene", "biolink:has_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:homologous_to", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:model_of", "biolink:orthologous_to", "biolink:part_of", "biolink:participates_in", "biolink:preventative_for_condition", "biolink:related_to", "biolink:same_as", "biolink:subclass_of", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 15279494795, "product_url": "https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg_edges.jsonl", "secondary_source": ["kg-monarch"]}, {"category": "GraphProduct", "description": "KGX JSON-Lines Distribution of KG-Monarch (Nodes)", "edge_count": 15356321, "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": 1379605, "original_source": ["phenio", "alliance", "bgee", "biogrid", "clingen", "clinvar", "ctd", "dictybase", "go", "hp", "maxo", "panther", "pombase", "reactome", "string", "xenbase", "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:ameliorates_condition", "biolink:associated_with_increased_likelihood_of", "biolink:caused_by", "biolink:causes", "biolink:colocalizes_with", "biolink:contraindicated_in", "biolink:contributes_to", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_disease", "biolink:has_gene", "biolink:has_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:homologous_to", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:model_of", "biolink:orthologous_to", "biolink:part_of", "biolink:participates_in", "biolink:preventative_for_condition", "biolink:related_to", "biolink:same_as", "biolink:subclass_of", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 1149505896, "product_url": "https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg_nodes.jsonl", "secondary_source": ["kg-monarch"]}, {"category": "GraphProduct", "description": "Neo4j Dump of KG-Monarch Edges", "edge_count": 15356321, "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": 1379605, "original_source": ["phenio", "alliance", "bgee", "biogrid", "clingen", "clinvar", "ctd", "dictybase", "go", "hp", "maxo", "panther", "pombase", "reactome", "string", "xenbase", "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:ameliorates_condition", "biolink:associated_with_increased_likelihood_of", "biolink:caused_by", "biolink:causes", "biolink:colocalizes_with", "biolink:contraindicated_in", "biolink:contributes_to", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_disease", "biolink:has_gene", "biolink:has_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:homologous_to", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:model_of", "biolink:orthologous_to", "biolink:part_of", "biolink:participates_in", "biolink:preventative_for_condition", "biolink:related_to", "biolink:same_as", "biolink:subclass_of", "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", "secondary_source": ["kg-monarch"]}, {"category": "GraphProduct", "description": "Neo4j Dump of KG-Monarch Nodes", "edge_count": 15356321, "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": 1379605, "original_source": ["phenio", "alliance", "bgee", "biogrid", "clingen", "clinvar", "ctd", "dictybase", "go", "hp", "maxo", "panther", "pombase", "reactome", "string", "xenbase", "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:ameliorates_condition", "biolink:associated_with_increased_likelihood_of", "biolink:caused_by", "biolink:causes", "biolink:colocalizes_with", "biolink:contraindicated_in", "biolink:contributes_to", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_disease", "biolink:has_gene", "biolink:has_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:homologous_to", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:model_of", "biolink:orthologous_to", "biolink:part_of", "biolink:participates_in", "biolink:preventative_for_condition", "biolink:related_to", "biolink:same_as", "biolink:subclass_of", "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", "secondary_source": ["kg-monarch"]}, {"category": "Product", "description": "Disease association data integrated from OMIM, MalaCards, ClinVar, Orphanet, DisGeNET and other disease databases", "format": "http", "id": "genecards.disease.associations", "name": "GeneCards Disease Associations", "original_source": ["omim", "malacards", "clinvar", "orphanet", "disgenet"], "product_url": "https://www.genecards.org/", "warnings": ["File was not able to be retrieved when checked on 2026-04-07: HTTP 403 error when accessing file", "File was not able to be retrieved when checked on 2026-03-30_ HTTP 403 error when accessing file", "File was not able to be retrieved when checked on 2026-04-10: HTTP 403 error when accessing file"]}, {"category": "Product", "description": "Genetic variant data from ClinVar, dbSNP, GWAS Catalog and other variant databases", "format": "http", "id": "genecards.variant.data", "name": "GeneCards Variant Data", "original_source": ["clinvar", "dbsnp", "gwascatalog"], "product_url": "https://www.genecards.org/", "warnings": ["File was not able to be retrieved when checked on 2026-04-07: HTTP 403 error when accessing file", "File was not able to be retrieved when checked on 2026-03-30_ HTTP 403 error when accessing file", "File was not able to be retrieved when checked on 2026-04-10: HTTP 403 error when accessing file"]}]
{"activity_status": "active", "category": "DataSource", "contacts": [{"category": "Organization", "contact_details": [{"contact_type": "email", "value": "clinvar@ncbi.nlm.nih.gov"}], "id": "ncbi", "label": "ClinVar Team, National Center for Biotechnology Information (NCBI)"}], "creation_date": "2025-06-04T00:00:00Z", "description": "ClinVar is a freely accessible, public archive of reports of human genetic variations and their relationships to human health. It collects and presents data on variants found in patient samples, classifications for diseases and drug responses, and supporting evidence. ClinVar enables access to and communication about the clinical significance of genetic variants, providing healthcare professionals, researchers, and the public with vital information for interpreting genetic test results.", "domains": ["biomedical", "genomics", "clinical", "precision medicine", "health", "translational"], "homepage_url": "https://www.ncbi.nlm.nih.gov/clinvar/", "id": "clinvar", "infores_id": "clinvar", "last_modified_date": "2026-02-20T00:00:00Z", "layout": "resource_detail", "license": {"id": "https://www.ncbi.nlm.nih.gov/home/about/policies/", "label": "NCBI and NLM Data Usage Policies and Disclaimers"}, "name": "ClinVar", "products": [{"category": "Product", "description": "Complete public data set in XML format containing comprehensive variant information, clinical significance classifications, and supporting evidence.", "format": "xml", "id": "clinvar.xml", "name": "ClinVar XML", "product_url": "https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/"}, {"category": "Product", "description": "ClinVar data in VCF format for GRCh37 human genome assembly, containing variant information and clinical significance.", "format": "vcf", "id": "clinvar.vcf.grch37", "name": "ClinVar VCF (GRCh37)", "product_url": "https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/"}, {"category": "Product", "description": "ClinVar data in VCF format for GRCh38 human genome assembly, containing variant information and clinical significance.", "format": "vcf", "id": "clinvar.vcf.grch38", "name": "ClinVar VCF (GRCh38)", "product_url": "https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/"}, {"category": "Product", "description": "Tab-delimited files summarizing variant data, gene-condition relationships, and other aspects of ClinVar data.", "format": "tsv", "id": "clinvar.tab", "name": "ClinVar Tab-Delimited Files", "product_url": "https://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/"}, {"category": "ProgrammingInterface", "description": "API access to ClinVar data through NCBI's E-utilities, supporting programmatic queries and data retrieval.", "format": "http", "id": "clinvar.api", "name": "ClinVar API (E-utilities)", "product_url": "https://www.ncbi.nlm.nih.gov/clinvar/docs/maintenance_use/"}, {"category": "GraphicalInterface", "description": "Web interface for searching and browsing ClinVar data, with detailed variant information and evidence.", "format": "http", "id": "clinvar.web", "name": "ClinVar Web Interface", "product_url": "https://www.ncbi.nlm.nih.gov/clinvar/"}, {"category": "GraphProduct", "description": "Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access.", "dump_format": "neo4j", "id": "ubkg.neo4j", "name": "UBKG Neo4j Docker Distribution", "original_source": ["hgnc", "loinc", "icd10", "snomedct", "uberon", "pato", "cl", "doid", "obi", "obib", "edam", "hsapdv", "sbo", "mi", "chebi", "mp", "ordo", "uniprot", "uo", "mondo", "efo", "pgo", "gencode", "reactome", "hra", "hubmap", "sennet", "stellar", "dct", "clinvar", "connectivitymap", "hp", "mp", "msigdb", "wikipathways", "clingen", "string", "4dn", "erccrbp", "erccreg", "faldo", "glycordf", "glycocoo", "gtex", "kidsfirst", "lincs", "motrpac", "mw", "npo", "sckan", "disgenet", "biomarker", "opentargets"], "product_url": "https://ubkg-downloads.xconsortia.org/", "secondary_source": ["ubkg"]}, {"category": "GraphProduct", "description": "Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access.", "format": "csv", "id": "ubkg.csv", "name": "UBKG Ontology CSV Files", "original_source": ["hgnc", "loinc", "icd10", "snomedct", "uberon", "pato", "cl", "doid", "obi", "obib", "edam", "hsapdv", "sbo", "mi", "chebi", "mp", "ordo", "uniprot", "uo", "mondo", "efo", "pgo", "gencode", "reactome", "hra", "hubmap", "sennet", "stellar", "dct", "clinvar", "connectivitymap", "hp", "mp", "msigdb", "wikipathways", "clingen", "string", "4dn", "erccrbp", "erccreg", "faldo", "glycordf", "glycocoo", "gtex", "kidsfirst", "lincs", "motrpac", "mw", "npo", "sckan", "disgenet", "biomarker", "opentargets"], "product_url": "https://ubkg-downloads.xconsortia.org/", "secondary_source": ["ubkg"]}, {"category": "GraphProduct", "description": "DisGeNET data, including gene to disease associations and variant to disease associations (requires registration and subscription).", "id": "disgenet.data", "name": "DisGeNET Data", "original_source": ["clingen", "clinvar", "mgd", "rgd", "orphanet", "psygenet", "uniprot", "disgenet", "hp", "gwascatalog", "phewascat", "ukbiobank", "finngen", "clinicaltrialsgov"], "product_url": "https://www.disgenet.com/", "secondary_source": ["disgenet"]}, {"category": "GraphProduct", "description": "KGX Distribution of KG-Monarch", "edge_count": 15356321, "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": 1379605, "original_source": ["phenio", "alliance", "bgee", "biogrid", "clingen", "clinvar", "ctd", "dictybase", "go", "hp", "maxo", "panther", "pombase", "reactome", "string", "xenbase", "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:ameliorates_condition", "biolink:associated_with_increased_likelihood_of", "biolink:caused_by", "biolink:causes", "biolink:colocalizes_with", "biolink:contraindicated_in", "biolink:contributes_to", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_disease", "biolink:has_gene", "biolink:has_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:homologous_to", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:model_of", "biolink:orthologous_to", "biolink:part_of", "biolink:participates_in", "biolink:preventative_for_condition", "biolink:related_to", "biolink:same_as", "biolink:subclass_of", "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", "secondary_source": ["kg-monarch"]}, {"category": "GraphProduct", "description": "KGX JSON-Lines Distribution of KG-Monarch", "edge_count": 15356321, "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": 1379605, "original_source": ["phenio", "alliance", "bgee", "biogrid", "clingen", "clinvar", "ctd", "dictybase", "go", "hp", "maxo", "panther", "pombase", "reactome", "string", "xenbase", "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:ameliorates_condition", "biolink:associated_with_increased_likelihood_of", "biolink:caused_by", "biolink:causes", "biolink:colocalizes_with", "biolink:contraindicated_in", "biolink:contributes_to", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_disease", "biolink:has_gene", "biolink:has_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:homologous_to", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:model_of", "biolink:orthologous_to", "biolink:part_of", "biolink:participates_in", "biolink:preventative_for_condition", "biolink:related_to", "biolink:same_as", "biolink:subclass_of", "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", "secondary_source": ["kg-monarch"]}, {"category": "GraphProduct", "description": "RDF Distribution of KG-Monarch", "edge_count": 15356321, "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": 1379605, "original_source": ["phenio", "alliance", "bgee", "biogrid", "clingen", "clinvar", "ctd", "dictybase", "go", "hp", "maxo", "panther", "pombase", "reactome", "string", "xenbase", "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:ameliorates_condition", "biolink:associated_with_increased_likelihood_of", "biolink:caused_by", "biolink:causes", "biolink:colocalizes_with", "biolink:contraindicated_in", "biolink:contributes_to", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_disease", "biolink:has_gene", "biolink:has_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:homologous_to", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:model_of", "biolink:orthologous_to", "biolink:part_of", "biolink:participates_in", "biolink:preventative_for_condition", "biolink:related_to", "biolink:same_as", "biolink:subclass_of", "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", "secondary_source": ["kg-monarch"]}, {"category": "GraphProduct", "description": "Neo4j Dump of KG-Monarch", "dump_format": "neo4j", "edge_count": 15356321, "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": 1379605, "original_source": ["phenio", "alliance", "bgee", "biogrid", "clingen", "clinvar", "ctd", "dictybase", "go", "hp", "maxo", "panther", "pombase", "reactome", "string", "xenbase", "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:ameliorates_condition", "biolink:associated_with_increased_likelihood_of", "biolink:caused_by", "biolink:causes", "biolink:colocalizes_with", "biolink:contraindicated_in", "biolink:contributes_to", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_disease", "biolink:has_gene", "biolink:has_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:homologous_to", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:model_of", "biolink:orthologous_to", "biolink:part_of", "biolink:participates_in", "biolink:preventative_for_condition", "biolink:related_to", "biolink:same_as", "biolink:subclass_of", "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", "secondary_source": ["kg-monarch"], "warnings": []}, {"category": "GraphProduct", "description": "DuckDB database of KG-Monarch", "edge_count": 15356321, "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": 1379605, "original_source": ["phenio", "alliance", "bgee", "biogrid", "clingen", "clinvar", "ctd", "dictybase", "go", "hp", "maxo", "panther", "pombase", "reactome", "string", "xenbase", "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:ameliorates_condition", "biolink:associated_with_increased_likelihood_of", "biolink:caused_by", "biolink:causes", "biolink:colocalizes_with", "biolink:contraindicated_in", "biolink:contributes_to", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_disease", "biolink:has_gene", "biolink:has_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:homologous_to", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:model_of", "biolink:orthologous_to", "biolink:part_of", "biolink:participates_in", "biolink:preventative_for_condition", "biolink:related_to", "biolink:same_as", "biolink:subclass_of", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 6827814912, "product_url": "https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.duckdb", "secondary_source": ["kg-monarch"]}, {"category": "GraphProduct", "description": "PheKnowLator graph files, including subsets with and without inverse relations.", "format": "owl", "id": "pheknowlator.graph", "latest_version": "current_build", "name": "PheKnowLator graph", "original_source": ["cl", "clo", "chebi", "go", "hp", "mondo", "pw", "pr", "ro", "so", "uberon", "vo", "bioportal", "clinvar", "ctd", "disgenet", "ensembl", "genemania", "hgnc", "hpa", "ncbigene", "medgen", "reactome", "string", "uniprot"], "product_url": "https://console.cloud.google.com/storage/browser/pheknowlator/current_build/knowledge_graphs?pageState=(%22StorageObjectListTable%22:(%22f%22:%22%255B%255D%22))&inv=1&invt=Ab5_1Q&project=pheknowlator", "secondary_source": ["pheknowlator"], "versions": ["v1.0.0", "v2.0.0", "v2.1.0", "v3.0.2", "v4.0.0", "current_build"]}, {"category": "GraphProduct", "description": "KGX JSON-Lines Distribution of KG-Monarch (Edges)", "edge_count": 15356321, "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": 1379605, "original_source": ["phenio", "alliance", "bgee", "biogrid", "clingen", "clinvar", "ctd", "dictybase", "go", "hp", "maxo", "panther", "pombase", "reactome", "string", "xenbase", "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:ameliorates_condition", "biolink:associated_with_increased_likelihood_of", "biolink:caused_by", "biolink:causes", "biolink:colocalizes_with", "biolink:contraindicated_in", "biolink:contributes_to", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_disease", "biolink:has_gene", "biolink:has_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:homologous_to", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:model_of", "biolink:orthologous_to", "biolink:part_of", "biolink:participates_in", "biolink:preventative_for_condition", "biolink:related_to", "biolink:same_as", "biolink:subclass_of", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 15279494795, "product_url": "https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg_edges.jsonl", "secondary_source": ["kg-monarch"]}, {"category": "GraphProduct", "description": "KGX JSON-Lines Distribution of KG-Monarch (Nodes)", "edge_count": 15356321, "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": 1379605, "original_source": ["phenio", "alliance", "bgee", "biogrid", "clingen", "clinvar", "ctd", "dictybase", "go", "hp", "maxo", "panther", "pombase", "reactome", "string", "xenbase", "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:ameliorates_condition", "biolink:associated_with_increased_likelihood_of", "biolink:caused_by", "biolink:causes", "biolink:colocalizes_with", "biolink:contraindicated_in", "biolink:contributes_to", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_disease", "biolink:has_gene", "biolink:has_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:homologous_to", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:model_of", "biolink:orthologous_to", "biolink:part_of", "biolink:participates_in", "biolink:preventative_for_condition", "biolink:related_to", "biolink:same_as", "biolink:subclass_of", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 1149505896, "product_url": "https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg_nodes.jsonl", "secondary_source": ["kg-monarch"]}, {"category": "GraphProduct", "description": "Neo4j Dump of KG-Monarch Edges", "edge_count": 15356321, "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": 1379605, "original_source": ["phenio", "alliance", "bgee", "biogrid", "clingen", "clinvar", "ctd", "dictybase", "go", "hp", "maxo", "panther", "pombase", "reactome", "string", "xenbase", "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:ameliorates_condition", "biolink:associated_with_increased_likelihood_of", "biolink:caused_by", "biolink:causes", "biolink:colocalizes_with", "biolink:contraindicated_in", "biolink:contributes_to", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_disease", "biolink:has_gene", "biolink:has_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:homologous_to", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:model_of", "biolink:orthologous_to", "biolink:part_of", "biolink:participates_in", "biolink:preventative_for_condition", "biolink:related_to", "biolink:same_as", "biolink:subclass_of", "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", "secondary_source": ["kg-monarch"]}, {"category": "GraphProduct", "description": "Neo4j Dump of KG-Monarch Nodes", "edge_count": 15356321, "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": 1379605, "original_source": ["phenio", "alliance", "bgee", "biogrid", "clingen", "clinvar", "ctd", "dictybase", "go", "hp", "maxo", "panther", "pombase", "reactome", "string", "xenbase", "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:ameliorates_condition", "biolink:associated_with_increased_likelihood_of", "biolink:caused_by", "biolink:causes", "biolink:colocalizes_with", "biolink:contraindicated_in", "biolink:contributes_to", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_disease", "biolink:has_gene", "biolink:has_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:homologous_to", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:model_of", "biolink:orthologous_to", "biolink:part_of", "biolink:participates_in", "biolink:preventative_for_condition", "biolink:related_to", "biolink:same_as", "biolink:subclass_of", "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", "secondary_source": ["kg-monarch"]}, {"category": "Product", "description": "Disease association data integrated from OMIM, MalaCards, ClinVar, Orphanet, DisGeNET and other disease databases", "format": "http", "id": "genecards.disease.associations", "name": "GeneCards Disease Associations", "original_source": ["omim", "malacards", "clinvar", "orphanet", "disgenet"], "product_url": "https://www.genecards.org/", "warnings": ["File was not able to be retrieved when checked on 2026-04-07: HTTP 403 error when accessing file", "File was not able to be retrieved when checked on 2026-03-30_ HTTP 403 error when accessing file", "File was not able to be retrieved when checked on 2026-04-10: HTTP 403 error when accessing file"]}, {"category": "Product", "description": "Genetic variant data from ClinVar, dbSNP, GWAS Catalog and other variant databases", "format": "http", "id": "genecards.variant.data", "name": "GeneCards Variant Data", "original_source": ["clinvar", "dbsnp", "gwascatalog"], "product_url": "https://www.genecards.org/", "warnings": ["File was not able to be retrieved when checked on 2026-04-07: HTTP 403 error when accessing file", "File was not able to be retrieved when checked on 2026-03-30_ HTTP 403 error when accessing file", "File was not able to be retrieved when checked on 2026-04-10: HTTP 403 error when accessing file"]}], "publications": [{"authors": ["Landrum MJ", "Chitipiralla S", "Kaur K", "Brown G", "Chen C", "Hart J", "Hoffman D", "Jang W", "Liu C", "Maddipatla Z", "Maiti R", "Mitchell J", "Rezaie T", "Riley G", "Song G", "Yang J", "Ziyabari L", "Russette A", "Kattman BL"], "doi": "10.1093/nar/gkae1090", "id": "doi:10.1093/nar/gkae1090", "journal": "Nucleic Acids Research", "preferred": true, "title": "ClinVar: updates to support classifications of both germline and somatic variants", "year": "2024"}, {"authors": ["Landrum MJ", "Lee JM", "Benson M", "Brown GR", "Chao C", "Chitipiralla S", "Gu B", "Hart J", "Hoffman D", "Jang W", "Karapetyan K", "Katz K", "Liu C", "Maddipatla Z", "Malheiro A", "McDaniel K", "Ovetsky M", "Riley G", "Zhou G", "Holmes JB", "Kattman BL", "Maglott DR"], "doi": "10.1093/nar/gkx1153", "id": "doi:10.1093/nar/gkx1153", "journal": "Nucleic Acids Research", "title": "ClinVar - improving access to variant interpretations and supporting evidence", "year": "2018"}], "taxon": ["NCBITaxon:9606"]}