name: Bgee - Gene Expression Database
description: Bgee is a database for retrieval and comparison of gene expression patterns across multiple animal species, providing information about gene expression in different anatomical structures, developmental stages, and species.
contacts: [{"category": "Organization", "contact_details": [{"contact_type": "email", "value": "bgee@sib.swiss"}, {"contact_type": "url", "value": "https://www.bgee.org/contact/"}], "label": "Bgee Team - SIB Swiss Institute of Bioinformatics"}]
products: [{"category": "GraphicalInterface", "description": "Web interface for exploring Bgee data", "id": "bgee.site", "is_public": true, "name": "Bgee Web Interface", "original_source": ["bgee"], "product_url": "https://www.bgee.org/", "secondary_source": ["bgee"]}, {"category": "ProgrammingInterface", "description": "SPARQL endpoint for querying Bgee RDF data", "id": "bgee.sparql", "is_public": true, "name": "Bgee SPARQL Endpoint", "original_source": ["bgee"], "product_url": "https://www.bgee.org/sparql/", "secondary_source": ["bgee"]}, {"category": "Product", "compression": "zip", "description": "Complete data dump of Bgee expression data for all species", "format": "tsv", "id": "bgee.expr_calls", "name": "Bgee Expression Calls", "original_source": ["bgee"], "product_url": "https://www.bgee.org/download/data-dumps/current/expr_calls/", "secondary_source": ["bgee"], "warnings": ["File was not able to be retrieved when checked on 2025-09-03: HTTP 404 error when accessing file", "File was not able to be retrieved when checked on 2025-09-02: Timeout connecting to URL", "File was not able to be retrieved when checked on 2025-09-04: HTTP 404 error when accessing file"]}, {"category": "Product", "compression": "zip", "description": "RNA-Seq data processed and formatted for the Bgee database", "format": "tsv", "id": "bgee.rnaseq", "name": "Bgee RNA-Seq Data", "original_source": ["bgee"], "product_url": "https://www.bgee.org/download/data-dumps/current/rna_seq/", "secondary_source": ["bgee"], "warnings": ["File was not able to be retrieved when checked on 2025-09-03: HTTP 404 error when accessing file", "File was not able to be retrieved when checked on 2025-09-02: Timeout connecting to URL", "File was not able to be retrieved when checked on 2025-09-04: HTTP 404 error when accessing file"]}, {"category": "Product", "compression": "zip", "description": "Processed Affymetrix microarray data for the Bgee database", "format": "tsv", "id": "bgee.affymetrix", "name": "Bgee Affymetrix Data", "original_source": ["bgee"], "product_url": "https://www.bgee.org/download/data-dumps/current/affymetrix/", "secondary_source": ["bgee"], "warnings": ["File was not able to be retrieved when checked on 2025-09-03: HTTP 404 error when accessing file", "File was not able to be retrieved when checked on 2025-09-02: Timeout connecting to URL", "File was not able to be retrieved when checked on 2025-09-04: HTTP 404 error when accessing file"]}, {"category": "Product", "compression": "zip", "description": "In Situ Hybridization data in the Bgee database", "format": "tsv", "id": "bgee.in_situ", "name": "Bgee In Situ Hybridization Data", "original_source": ["bgee"], "product_url": "https://www.bgee.org/download/data-dumps/current/in_situ/", "secondary_source": ["bgee"], "warnings": ["File was not able to be retrieved when checked on 2025-09-03: HTTP 404 error when accessing file", "File was not able to be retrieved when checked on 2025-09-02: Timeout connecting to URL", "File was not able to be retrieved when checked on 2025-09-04: HTTP 404 error when accessing file"]}, {"category": "Product", "compression": "zip", "description": "EST (Expressed Sequence Tag) expression data in the Bgee database", "format": "tsv", "id": "bgee.est", "name": "Bgee EST Data", "original_source": ["bgee"], "product_url": "https://www.bgee.org/download/data-dumps/current/est/", "secondary_source": ["bgee"], "warnings": ["File was not able to be retrieved when checked on 2025-09-03: HTTP 404 error when accessing file", "File was not able to be retrieved when checked on 2025-09-02: Timeout connecting to URL", "File was not able to be retrieved when checked on 2025-09-04: HTTP 404 error when accessing file"]}, {"category": "Product", "compression": "zip", "description": "Single-cell RNA-Seq processed data in the Bgee database", "format": "tsv", "id": "bgee.sc_rnaseq", "name": "Bgee Single-cell RNA-Seq Data", "original_source": ["bgee"], "product_url": "https://www.bgee.org/download/data-dumps/current/sc_rnaseq/", "secondary_source": ["bgee"], "warnings": ["File was not able to be retrieved when checked on 2025-09-03: HTTP 404 error when accessing file", "File was not able to be retrieved when checked on 2025-09-02: Timeout connecting to URL", "File was not able to be retrieved when checked on 2025-09-04: HTTP 404 error when accessing file"]}, {"category": "Product", "compression": "zip", "description": "Anatomical homology information used in Bgee", "format": "tsv", "id": "bgee.homology", "name": "Bgee Anatomical Homology Data", "original_source": ["bgee"], "product_url": "https://www.bgee.org/download/data-dumps/current/homology/", "secondary_source": ["bgee"], "warnings": ["File was not able to be retrieved when checked on 2025-09-03: HTTP 404 error when accessing file", "File was not able to be retrieved when checked on 2025-09-02: Timeout connecting to URL", "File was not able to be retrieved when checked on 2025-09-04: HTTP 404 error when accessing file"]}, {"category": "Product", "compression": "zip", "description": "RDF version of the Bgee data for semantic web applications", "format": "ttl", "id": "bgee.rdf", "name": "Bgee RDF Data", "original_source": ["bgee"], "product_url": "https://www.bgee.org/download/data-dumps/current/rdf/", "secondary_source": ["bgee"], "warnings": ["File was not able to be retrieved when checked on 2025-09-03: HTTP 404 error when accessing file", "File was not able to be retrieved when checked on 2025-09-02: Timeout connecting to URL", "File was not able to be retrieved when checked on 2025-09-04: HTTP 404 error when accessing file"]}, {"category": "GraphProduct", "description": "The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources.", "id": "spoke.graph", "name": "SPOKE Graph", "original_source": ["ncbigene", "medline", "mesh", "pid", "do", "diseases", "drugcentral", "go", "gwascatalog", "reactome", "lincs-l1000", "uberon", "wikipathways", "bindingdb", "drugbank", "sider", "bgee", "uniprot", "string", "omim", "chembl", "foodb", "civic", "gdsc", "clinicaltrialsgov", "hpa", "cl", "kegg", "metacyc", "bv-brc", "ncbitaxon", "pathophenodb", "pfam", "interpro", "protcid"], "secondary_source": ["spoke"]}, {"category": "GraphicalInterface", "description": "A browser interface for a knowledge graph for Alzheimer's Disease.", "format": "http", "id": "alzkb.browser", "name": "AlzKB Graph Database Browser", "original_source": ["aop-db", "bgee", "disgenet", "do", "drugbank", "dsstox", "go", "gwascatalog", "hrpimp", "lincs-l1000", "mesh", "ncbigene", "pharmacotherapydb", "pid", "pubchem", "reactome", "sider", "tissues", "uberon", "wikipathways"], "product_url": "https://alzkb.ai:7473/login", "secondary_source": ["alzkb", "hetionet"]}, {"category": "GraphProduct", "description": "Memgraph data release for AlzKB.", "id": "alzkb.data", "name": "AlzKB Data Release (Version 2.0.0)", "original_source": ["aop-db", "bgee", "disgenet", "do", "drugbank", "dsstox", "go", "gwascatalog", "hrpimp", "lincs-l1000", "mesh", "ncbigene", "pharmacotherapydb", "pid", "pubchem", "reactome", "reactome", "sider", "tissues", "uberon", "wikipathways"], "product_url": "https://github.com/EpistasisLab/AlzKB/releases/tag/v2.0.0", "secondary_source": ["alzkb", "hetionet"]}, {"category": "ProcessProduct", "description": "INDRA CoGEx is a graph database integrating causal relations, ontological relations, properties, and data, assembled at scale automatically from the scientific literature and structured sources. This is the code to build the graph.", "id": "indra.cogex.code", "name": "INDRA CoGEx Build Code", "original_source": ["chembl", "sider", "reactome", "wikipathways", "hp", "nihreporter", "disgenet", "pubmed", "gwascatalog", "cellmarker", "go", "bgee", "ccle", "clinicaltrialsgov", "indra"], "product_url": "https://github.com/gyorilab/indra_cogex", "secondary_source": ["indra"]}, {"category": "GraphProduct", "description": "KGX Distribution of KG-Monarch", "edge_count": 14486132, "format": "kgx", "id": "kg-monarch.graph", "name": "KGX Distribution of KG-Monarch", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "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": 1344798, "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_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "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: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": 14486132, "format": "kgx-jsonl", "id": "kg-monarch.graph.jsonl", "name": "KGX JSON-L Distribution of KG-Monarch", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "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": 1344798, "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_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "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: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": 14486132, "format": "rdfxml", "id": "kg-monarch.graph.rdf", "name": "RDF Distribution of KG-Monarch", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "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": 1344798, "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_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "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: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": 14486132, "id": "kg-monarch.graph.neo4j", "name": "Neo4j Dump of KG-Monarch", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "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": 1344798, "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_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "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: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": 14486132, "id": "kg-monarch.graph.duckdb", "name": "DuckDB database of KG-Monarch", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "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": 1344798, "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_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "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: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": "KGX JSON-Lines Distribution of KG-Monarch (Edges)", "edge_count": 14486132, "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: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": 1344798, "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_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "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: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": 14486132, "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: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": 1344798, "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_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "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: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": 14486132, "format": "neo4j", "id": "kg-monarch.graph.neo4j.edges", "name": "Neo4j Dump of KG-Monarch Edges", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "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": 1344798, "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_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "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: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": 14486132, "format": "neo4j", "id": "kg-monarch.graph.neo4j.nodes", "name": "Neo4j Dump of KG-Monarch Nodes", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "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": 1344798, "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_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "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: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"]}]
raw_data: {"activity_status": "active", "category": "DataSource", "contacts": [{"category": "Organization", "contact_details": [{"contact_type": "email", "value": "bgee@sib.swiss"}, {"contact_type": "url", "value": "https://www.bgee.org/contact/"}], "label": "Bgee Team - SIB Swiss Institute of Bioinformatics"}], "description": "Bgee is a database for retrieval and comparison of gene expression patterns across multiple animal species, providing information about gene expression in different anatomical structures, developmental stages, and species.", "domains": ["biological systems", "organisms"], "homepage_url": "https://www.bgee.org/", "id": "bgee", "layout": "resource_detail", "license": {"id": "https://creativecommons.org/licenses/by/4.0/", "label": "CC-BY-4.0", "logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png"}, "name": "Bgee - Gene Expression Database", "products": [{"category": "GraphicalInterface", "description": "Web interface for exploring Bgee data", "id": "bgee.site", "is_public": true, "name": "Bgee Web Interface", "original_source": ["bgee"], "product_url": "https://www.bgee.org/", "secondary_source": ["bgee"]}, {"category": "ProgrammingInterface", "description": "SPARQL endpoint for querying Bgee RDF data", "id": "bgee.sparql", "is_public": true, "name": "Bgee SPARQL Endpoint", "original_source": ["bgee"], "product_url": "https://www.bgee.org/sparql/", "secondary_source": ["bgee"]}, {"category": "Product", "compression": "zip", "description": "Complete data dump of Bgee expression data for all species", "format": "tsv", "id": "bgee.expr_calls", "name": "Bgee Expression Calls", "original_source": ["bgee"], "product_url": "https://www.bgee.org/download/data-dumps/current/expr_calls/", "secondary_source": ["bgee"], "warnings": ["File was not able to be retrieved when checked on 2025-09-03: HTTP 404 error when accessing file", "File was not able to be retrieved when checked on 2025-09-02: Timeout connecting to URL", "File was not able to be retrieved when checked on 2025-09-04: HTTP 404 error when accessing file"]}, {"category": "Product", "compression": "zip", "description": "RNA-Seq data processed and formatted for the Bgee database", "format": "tsv", "id": "bgee.rnaseq", "name": "Bgee RNA-Seq Data", "original_source": ["bgee"], "product_url": "https://www.bgee.org/download/data-dumps/current/rna_seq/", "secondary_source": ["bgee"], "warnings": ["File was not able to be retrieved when checked on 2025-09-03: HTTP 404 error when accessing file", "File was not able to be retrieved when checked on 2025-09-02: Timeout connecting to URL", "File was not able to be retrieved when checked on 2025-09-04: HTTP 404 error when accessing file"]}, {"category": "Product", "compression": "zip", "description": "Processed Affymetrix microarray data for the Bgee database", "format": "tsv", "id": "bgee.affymetrix", "name": "Bgee Affymetrix Data", "original_source": ["bgee"], "product_url": "https://www.bgee.org/download/data-dumps/current/affymetrix/", "secondary_source": ["bgee"], "warnings": ["File was not able to be retrieved when checked on 2025-09-03: HTTP 404 error when accessing file", "File was not able to be retrieved when checked on 2025-09-02: Timeout connecting to URL", "File was not able to be retrieved when checked on 2025-09-04: HTTP 404 error when accessing file"]}, {"category": "Product", "compression": "zip", "description": "In Situ Hybridization data in the Bgee database", "format": "tsv", "id": "bgee.in_situ", "name": "Bgee In Situ Hybridization Data", "original_source": ["bgee"], "product_url": "https://www.bgee.org/download/data-dumps/current/in_situ/", "secondary_source": ["bgee"], "warnings": ["File was not able to be retrieved when checked on 2025-09-03: HTTP 404 error when accessing file", "File was not able to be retrieved when checked on 2025-09-02: Timeout connecting to URL", "File was not able to be retrieved when checked on 2025-09-04: HTTP 404 error when accessing file"]}, {"category": "Product", "compression": "zip", "description": "EST (Expressed Sequence Tag) expression data in the Bgee database", "format": "tsv", "id": "bgee.est", "name": "Bgee EST Data", "original_source": ["bgee"], "product_url": "https://www.bgee.org/download/data-dumps/current/est/", "secondary_source": ["bgee"], "warnings": ["File was not able to be retrieved when checked on 2025-09-03: HTTP 404 error when accessing file", "File was not able to be retrieved when checked on 2025-09-02: Timeout connecting to URL", "File was not able to be retrieved when checked on 2025-09-04: HTTP 404 error when accessing file"]}, {"category": "Product", "compression": "zip", "description": "Single-cell RNA-Seq processed data in the Bgee database", "format": "tsv", "id": "bgee.sc_rnaseq", "name": "Bgee Single-cell RNA-Seq Data", "original_source": ["bgee"], "product_url": "https://www.bgee.org/download/data-dumps/current/sc_rnaseq/", "secondary_source": ["bgee"], "warnings": ["File was not able to be retrieved when checked on 2025-09-03: HTTP 404 error when accessing file", "File was not able to be retrieved when checked on 2025-09-02: Timeout connecting to URL", "File was not able to be retrieved when checked on 2025-09-04: HTTP 404 error when accessing file"]}, {"category": "Product", "compression": "zip", "description": "Anatomical homology information used in Bgee", "format": "tsv", "id": "bgee.homology", "name": "Bgee Anatomical Homology Data", "original_source": ["bgee"], "product_url": "https://www.bgee.org/download/data-dumps/current/homology/", "secondary_source": ["bgee"], "warnings": ["File was not able to be retrieved when checked on 2025-09-03: HTTP 404 error when accessing file", "File was not able to be retrieved when checked on 2025-09-02: Timeout connecting to URL", "File was not able to be retrieved when checked on 2025-09-04: HTTP 404 error when accessing file"]}, {"category": "Product", "compression": "zip", "description": "RDF version of the Bgee data for semantic web applications", "format": "ttl", "id": "bgee.rdf", "name": "Bgee RDF Data", "original_source": ["bgee"], "product_url": "https://www.bgee.org/download/data-dumps/current/rdf/", "secondary_source": ["bgee"], "warnings": ["File was not able to be retrieved when checked on 2025-09-03: HTTP 404 error when accessing file", "File was not able to be retrieved when checked on 2025-09-02: Timeout connecting to URL", "File was not able to be retrieved when checked on 2025-09-04: HTTP 404 error when accessing file"]}, {"category": "GraphProduct", "description": "The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources.", "id": "spoke.graph", "name": "SPOKE Graph", "original_source": ["ncbigene", "medline", "mesh", "pid", "do", "diseases", "drugcentral", "go", "gwascatalog", "reactome", "lincs-l1000", "uberon", "wikipathways", "bindingdb", "drugbank", "sider", "bgee", "uniprot", "string", "omim", "chembl", "foodb", "civic", "gdsc", "clinicaltrialsgov", "hpa", "cl", "kegg", "metacyc", "bv-brc", "ncbitaxon", "pathophenodb", "pfam", "interpro", "protcid"], "secondary_source": ["spoke"]}, {"category": "GraphicalInterface", "description": "A browser interface for a knowledge graph for Alzheimer's Disease.", "format": "http", "id": "alzkb.browser", "name": "AlzKB Graph Database Browser", "original_source": ["aop-db", "bgee", "disgenet", "do", "drugbank", "dsstox", "go", "gwascatalog", "hrpimp", "lincs-l1000", "mesh", "ncbigene", "pharmacotherapydb", "pid", "pubchem", "reactome", "sider", "tissues", "uberon", "wikipathways"], "product_url": "https://alzkb.ai:7473/login", "secondary_source": ["alzkb", "hetionet"]}, {"category": "GraphProduct", "description": "Memgraph data release for AlzKB.", "id": "alzkb.data", "name": "AlzKB Data Release (Version 2.0.0)", "original_source": ["aop-db", "bgee", "disgenet", "do", "drugbank", "dsstox", "go", "gwascatalog", "hrpimp", "lincs-l1000", "mesh", "ncbigene", "pharmacotherapydb", "pid", "pubchem", "reactome", "reactome", "sider", "tissues", "uberon", "wikipathways"], "product_url": "https://github.com/EpistasisLab/AlzKB/releases/tag/v2.0.0", "secondary_source": ["alzkb", "hetionet"]}, {"category": "ProcessProduct", "description": "INDRA CoGEx is a graph database integrating causal relations, ontological relations, properties, and data, assembled at scale automatically from the scientific literature and structured sources. This is the code to build the graph.", "id": "indra.cogex.code", "name": "INDRA CoGEx Build Code", "original_source": ["chembl", "sider", "reactome", "wikipathways", "hp", "nihreporter", "disgenet", "pubmed", "gwascatalog", "cellmarker", "go", "bgee", "ccle", "clinicaltrialsgov", "indra"], "product_url": "https://github.com/gyorilab/indra_cogex", "secondary_source": ["indra"]}, {"category": "GraphProduct", "description": "KGX Distribution of KG-Monarch", "edge_count": 14486132, "format": "kgx", "id": "kg-monarch.graph", "name": "KGX Distribution of KG-Monarch", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "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": 1344798, "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_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "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: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": 14486132, "format": "kgx-jsonl", "id": "kg-monarch.graph.jsonl", "name": "KGX JSON-L Distribution of KG-Monarch", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "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": 1344798, "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_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "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: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": 14486132, "format": "rdfxml", "id": "kg-monarch.graph.rdf", "name": "RDF Distribution of KG-Monarch", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "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": 1344798, "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_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "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: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": 14486132, "id": "kg-monarch.graph.neo4j", "name": "Neo4j Dump of KG-Monarch", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "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": 1344798, "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_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "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: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": 14486132, "id": "kg-monarch.graph.duckdb", "name": "DuckDB database of KG-Monarch", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "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": 1344798, "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_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "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: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": "KGX JSON-Lines Distribution of KG-Monarch (Edges)", "edge_count": 14486132, "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: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": 1344798, "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_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "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: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": 14486132, "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: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": 1344798, "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_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "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: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": 14486132, "format": "neo4j", "id": "kg-monarch.graph.neo4j.edges", "name": "Neo4j Dump of KG-Monarch Edges", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "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": 1344798, "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_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "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: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": 14486132, "format": "neo4j", "id": "kg-monarch.graph.neo4j.nodes", "name": "Neo4j Dump of KG-Monarch Nodes", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "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": 1344798, "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_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "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: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"]}], "publications": [{"authors": ["Bastian FB", "Brandulas Cammarata A", "Carsanaro S", "Detering H", "Huang W-T", "Joye S", "Niknejad A", "Nyamari M", "Mendes de Farias T", "Moretti S", "Tzivanopoulou M", "Wollbrett J", "Robinson-Rechavi M"], "doi": "doi:10.1093/nar/gkae1118", "id": "doi:10.1093/nar/gkae1118", "preferred": true, "title": "Bgee in 2024 - focus on curated single-cell RNA-seq datasets, and query tools", "year": "2025"}, {"authors": ["Bastian FB", "Roux J", "Niknejad A", "Comte A", "Fonseca Costa SS", "de Farias TM", "Moretti S", "Parmentier G", "de Laval VR", "Rosikiewicz M", "Wollbrett J", "Echchiki A", "Escoriza A", "Gharib WH", "Gonzales-Porta M", "Jarosz Y", "Laurenczy B", "Moret P", "Person E", "Roelli P", "Sanjeev K", "Seppey M", "Robinson-Rechavi M"], "doi": "doi:10.1093/nar/gkaa793", "id": "doi:10.1093/nar/gkaa793", "title": "The Bgee suite - integrated curated expression atlas and comparative transcriptomics in animals", "year": "2021"}], "repository": "https://github.com/BgeeDB/bgee_apps"}