{ "@id": "https://kgx-storage.rtx.ai/data/gtopdb/2026.1/transform_4d453431/normalization_2025sep1/", "@type": "sc:Dataset", "name": "gtopdb", "description": "A knowledge graph built for the NCATS Biomedical Data Translator project using Translator-Ingests, Biolink Model, and Node Normalizer.", "license": "MIT", "url": "https://kgx-storage.rtx.ai/data/gtopdb/2026.1/transform_4d453431/normalization_2025sep1/", "version": "gtopdb_2026.1_4d453431_2025sep1_4.3.6", "dateCreated": "2026_03_19", "biolinkVersion": "4.3.6", "babelVersion": "2025sep1", "distribution": [ { "@id": "gtopdb.tar.xz", "@type": "cr:FileObject", "contentUrl": "gtopdb.tar.xz", "encodingFormat": "application/x-xz", "description": "Compressed tar archive containing the KGX files: nodes.jsonl and edges.jsonl" } ], "isBasedOn": [ { "id": "gtopdb", "name": "The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb) Reference Ingest Guide", "description": "The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb; https://www.guidetopharmacology.org) is an open-access, expert-curated, online database that provides succinct overviews and key references for pharmacological targets and their recommended experimental ligands. It includes over 3039 protein targets and 12,163 ligand molecules, including approved drugs, small molecules, peptides and antibodies. GtoPdb) was established and developed by the International Union of Basic and Clinical Pharmacology (IUPHAR) and the British Pharmacological Society (BPS). It originated from the IUPHAR-DB, a former resource focused on receptors and channels that was first compiled in 2003 and from the BPS\u2018 Guide to Receptors and Channels\u2019, a compendium of a wider range of targets than those originally covered in IUPHAR-DB", "license": { "license_name": "Creative Commons Attribution 4.0 International", "license_url": "https://creativecommons.org/licenses/by/4.0/legalcode" }, "url": [ "gtoPdb Downloads: https://www.guidetopharmacology.org/download.jsp (this page includes file sizes and simple data dictionaries for each download)" ], "version": "2026.1" } ], "schema": { "nodes": [ { "category": [ "biolink:SmallMolecule" ], "count": 7349, "id_prefixes": { "PUBCHEM.COMPOUND": 4355, "CHEBI": 1817, "UNII": 1177 }, "attributes": { "name": 7349, "equivalent_identifiers": 7349, "information_content": 1817, "description": 897 } }, { "category": [ "biolink:Drug", "biolink:SmallMolecule" ], "count": 965, "id_prefixes": { "CHEBI": 880, "UNII": 79, "PUBCHEM.COMPOUND": 6 }, "attributes": { "name": 965, "equivalent_identifiers": 965, "information_content": 875, "description": 694 } }, { "category": [ "biolink:MolecularMixture", "biolink:SmallMolecule" ], "count": 16, "id_prefixes": { "CHEBI": 13, "UNII": 3 }, "attributes": { "name": 16, "equivalent_identifiers": 16, "information_content": 14, "description": 11 } }, { "category": [ "biolink:MolecularMixture" ], "count": 48, "id_prefixes": { "PUBCHEM.COMPOUND": 36, "CHEBI": 6, "UNII": 6 }, "attributes": { "name": 48, "equivalent_identifiers": 48, "information_content": 6, "description": 5 } }, { "category": [ "biolink:Drug" ], "count": 3, "id_prefixes": { "CHEBI": 2, "PUBCHEM.COMPOUND": 1 }, "attributes": { "name": 3, "equivalent_identifiers": 3, "information_content": 2, "description": 2 } }, { "category": [ "biolink:Protein", "biolink:Gene" ], "count": 2198, "id_prefixes": { "NCBIGene": 2198 }, "attributes": { "name": 2198, "equivalent_identifiers": 2198, "description": 2198, "information_content": 2189 } }, { "category": [ "biolink:ChemicalEntity" ], "count": 5, "id_prefixes": { "PUBCHEM.COMPOUND": 5 }, "attributes": { "name": 5, "equivalent_identifiers": 5 } }, { "category": [ "biolink:Protein" ], "count": 60, "id_prefixes": { "UniProtKB": 60 }, "attributes": { "name": 60, "equivalent_identifiers": 60, "information_content": 55, "description": 55 } } ], "nodes_summary": { "total_count": 10644, "id_prefixes": { "PUBCHEM.COMPOUND": 4403, "CHEBI": 2718, "NCBIGene": 2198, "UNII": 1265, "UniProtKB": 60 }, "attributes": { "name": 10644, "equivalent_identifiers": 10644, "information_content": 4958, "description": 3862 } }, "edges": [ { "subject_category": [ "biolink:SmallMolecule" ], "predicate": "biolink:affects", "object_category": [ "biolink:Protein", "biolink:Gene" ], "count": 14284, "primary_knowledge_sources": { "infores:gtopdb": 14284 }, "qualifiers": { "object_aspect_qualifier": 14284, "qualified_predicate": 13871, "object_direction_qualifier": 13869, "causal_mechanism_qualifier": 13175 }, "attributes": { "id": 14284, "category": 14284, "knowledge_level": 14284, "agent_type": 14284, "original_subject": 14284, "original_object": 14284, "publications": 12643 }, "subject_id_prefixes": { "PUBCHEM.COMPOUND": 7264, "CHEBI": 4641, "UNII": 2379 }, "object_id_prefixes": { "NCBIGene": 14284 } }, { "subject_category": [ "biolink:Drug", "biolink:SmallMolecule" ], "predicate": "biolink:affects", "object_category": [ "biolink:Protein", "biolink:Gene" ], "count": 3013, "primary_knowledge_sources": { "infores:gtopdb": 3013 }, "qualifiers": { "object_aspect_qualifier": 3013, "object_direction_qualifier": 2842, "qualified_predicate": 2842, "causal_mechanism_qualifier": 2737 }, "attributes": { "id": 3013, "category": 3013, "knowledge_level": 3013, "agent_type": 3013, "original_subject": 3013, "original_object": 3013, "publications": 2713 }, "subject_id_prefixes": { "CHEBI": 2818, "UNII": 179, "PUBCHEM.COMPOUND": 16 }, "object_id_prefixes": { "NCBIGene": 3013 } }, { "subject_category": [ "biolink:Drug", "biolink:SmallMolecule" ], "predicate": "biolink:physically_interacts_with", "object_category": [ "biolink:Protein", "biolink:Gene" ], "count": 96, "primary_knowledge_sources": { "infores:gtopdb": 96 }, "qualifiers": { "causal_mechanism_qualifier": 2 }, "attributes": { "id": 96, "category": 96, "knowledge_level": 96, "agent_type": 96, "original_subject": 96, "original_object": 96, "publications": 68 }, "subject_id_prefixes": { "CHEBI": 88, "UNII": 8 }, "object_id_prefixes": { "NCBIGene": 96 } }, { "subject_category": [ "biolink:SmallMolecule" ], "predicate": "biolink:affects", "object_category": [ "biolink:Protein" ], "count": 264, "primary_knowledge_sources": { "infores:gtopdb": 264 }, "qualifiers": { "object_aspect_qualifier": 264, "qualified_predicate": 257, "object_direction_qualifier": 256, "causal_mechanism_qualifier": 246 }, "attributes": { "id": 264, "category": 264, "knowledge_level": 264, "agent_type": 264, "original_subject": 264, "original_object": 264, "publications": 243 }, "subject_id_prefixes": { "PUBCHEM.COMPOUND": 136, "CHEBI": 100, "UNII": 28 }, "object_id_prefixes": { "UniProtKB": 264 } }, { "subject_category": [ "biolink:MolecularMixture" ], "predicate": "biolink:affects", "object_category": [ "biolink:Protein", "biolink:Gene" ], "count": 100, "primary_knowledge_sources": { "infores:gtopdb": 100 }, "qualifiers": { "object_aspect_qualifier": 100, "object_direction_qualifier": 67, "qualified_predicate": 67, "causal_mechanism_qualifier": 65 }, "attributes": { "id": 100, "category": 100, "knowledge_level": 100, "agent_type": 100, "original_subject": 100, "original_object": 100, "publications": 67 }, "subject_id_prefixes": { "PUBCHEM.COMPOUND": 58, "CHEBI": 31, "UNII": 11 }, "object_id_prefixes": { "NCBIGene": 100 } }, { "subject_category": [ "biolink:SmallMolecule" ], "predicate": "biolink:physically_interacts_with", "object_category": [ "biolink:Protein", "biolink:Gene" ], "count": 695, "primary_knowledge_sources": { "infores:gtopdb": 695 }, "qualifiers": { "causal_mechanism_qualifier": 30 }, "attributes": { "id": 695, "category": 695, "knowledge_level": 695, "agent_type": 695, "original_subject": 695, "original_object": 695, "publications": 593 }, "subject_id_prefixes": { "PUBCHEM.COMPOUND": 478, "UNII": 114, "CHEBI": 103 }, "object_id_prefixes": { "NCBIGene": 695 } }, { "subject_category": [ "biolink:Drug", "biolink:SmallMolecule" ], "predicate": "biolink:affects", "object_category": [ "biolink:Protein" ], "count": 62, "primary_knowledge_sources": { "infores:gtopdb": 62 }, "qualifiers": { "object_aspect_qualifier": 62, "object_direction_qualifier": 58, "qualified_predicate": 58, "causal_mechanism_qualifier": 55 }, "attributes": { "id": 62, "category": 62, "knowledge_level": 62, "agent_type": 62, "original_subject": 62, "original_object": 62, "publications": 61 }, "subject_id_prefixes": { "CHEBI": 60, "PUBCHEM.COMPOUND": 2 }, "object_id_prefixes": { "UniProtKB": 62 } }, { "subject_category": [ "biolink:SmallMolecule" ], "predicate": "biolink:physically_interacts_with", "object_category": [ "biolink:Protein" ], "count": 12, "primary_knowledge_sources": { "infores:gtopdb": 12 }, "qualifiers": {}, "attributes": { "id": 12, "category": 12, "publications": 12, "knowledge_level": 12, "agent_type": 12, "original_subject": 12, "original_object": 12 }, "subject_id_prefixes": { "PUBCHEM.COMPOUND": 9, "UNII": 2, "CHEBI": 1 }, "object_id_prefixes": { "UniProtKB": 12 } }, { "subject_category": [ "biolink:Drug" ], "predicate": "biolink:affects", "object_category": [ "biolink:Protein", "biolink:Gene" ], "count": 7, "primary_knowledge_sources": { "infores:gtopdb": 7 }, "qualifiers": { "object_aspect_qualifier": 7, "object_direction_qualifier": 7, "qualified_predicate": 7, "causal_mechanism_qualifier": 3 }, "attributes": { "id": 7, "category": 7, "publications": 7, "knowledge_level": 7, "agent_type": 7, "original_subject": 7, "original_object": 7 }, "subject_id_prefixes": { "CHEBI": 5, "PUBCHEM.COMPOUND": 2 }, "object_id_prefixes": { "NCBIGene": 7 } }, { "subject_category": [ "biolink:Drug", "biolink:SmallMolecule" ], "predicate": "biolink:physically_interacts_with", "object_category": [ "biolink:Protein" ], "count": 2, "primary_knowledge_sources": { "infores:gtopdb": 2 }, "qualifiers": {}, "attributes": { "id": 2, "category": 2, "publications": 2, "knowledge_level": 2, "agent_type": 2, "original_subject": 2, "original_object": 2 }, "subject_id_prefixes": { "CHEBI": 2 }, "object_id_prefixes": { "UniProtKB": 2 } }, { "subject_category": [ "biolink:MolecularMixture", "biolink:SmallMolecule" ], "predicate": "biolink:affects", "object_category": [ "biolink:Protein", "biolink:Gene" ], "count": 28, "primary_knowledge_sources": { "infores:gtopdb": 28 }, "qualifiers": { "object_aspect_qualifier": 28, "object_direction_qualifier": 28, "qualified_predicate": 28, "causal_mechanism_qualifier": 22 }, "attributes": { "id": 28, "category": 28, "knowledge_level": 28, "agent_type": 28, "original_subject": 28, "original_object": 28, "publications": 27 }, "subject_id_prefixes": { "CHEBI": 25, "UNII": 3 }, "object_id_prefixes": { "NCBIGene": 28 } }, { "subject_category": [ "biolink:ChemicalEntity" ], "predicate": "biolink:affects", "object_category": [ "biolink:Protein", "biolink:Gene" ], "count": 8, "primary_knowledge_sources": { "infores:gtopdb": 8 }, "qualifiers": { "object_aspect_qualifier": 8, "object_direction_qualifier": 8, "causal_mechanism_qualifier": 8, "qualified_predicate": 8 }, "attributes": { "id": 8, "category": 8, "publications": 8, "knowledge_level": 8, "agent_type": 8, "original_subject": 8, "original_object": 8 }, "subject_id_prefixes": { "PUBCHEM.COMPOUND": 8 }, "object_id_prefixes": { "NCBIGene": 8 } }, { "subject_category": [ "biolink:MolecularMixture", "biolink:SmallMolecule" ], "predicate": "biolink:physically_interacts_with", "object_category": [ "biolink:Protein", "biolink:Gene" ], "count": 6, "primary_knowledge_sources": { "infores:gtopdb": 6 }, "qualifiers": { "causal_mechanism_qualifier": 1 }, "attributes": { "id": 6, "category": 6, "publications": 6, "knowledge_level": 6, "agent_type": 6, "original_subject": 6, "original_object": 6 }, "subject_id_prefixes": { "CHEBI": 6 }, "object_id_prefixes": { "NCBIGene": 6 } }, { "subject_category": [ "biolink:MolecularMixture" ], "predicate": "biolink:affects", "object_category": [ "biolink:Protein" ], "count": 3, "primary_knowledge_sources": { "infores:gtopdb": 3 }, "qualifiers": { "object_aspect_qualifier": 3, "object_direction_qualifier": 3, "causal_mechanism_qualifier": 3, "qualified_predicate": 3 }, "attributes": { "id": 3, "category": 3, "publications": 3, "knowledge_level": 3, "agent_type": 3, "original_subject": 3, "original_object": 3 }, "subject_id_prefixes": { "PUBCHEM.COMPOUND": 2, "CHEBI": 1 }, "object_id_prefixes": { "UniProtKB": 3 } }, { "subject_category": [ "biolink:MolecularMixture" ], "predicate": "biolink:physically_interacts_with", "object_category": [ "biolink:Protein", "biolink:Gene" ], "count": 1, "primary_knowledge_sources": { "infores:gtopdb": 1 }, "qualifiers": {}, "attributes": { "id": 1, "category": 1, "publications": 1, "knowledge_level": 1, "agent_type": 1, "original_subject": 1, "original_object": 1 }, "subject_id_prefixes": { "PUBCHEM.COMPOUND": 1 }, "object_id_prefixes": { "NCBIGene": 1 } } ], "edges_summary": { "total_count": 18581, "predicates": { "biolink:affects": 17769, "biolink:physically_interacts_with": 812 }, "primary_knowledge_sources": { "infores:gtopdb": 18581 }, "predicates_by_knowledge_source": { "infores:gtopdb": { "biolink:affects": 17769, "biolink:physically_interacts_with": 812 } }, "qualifiers": { "object_aspect_qualifier": 17769, "qualified_predicate": 17141, "object_direction_qualifier": 17138, "causal_mechanism_qualifier": 16347 }, "attributes": { "id": 18581, "category": 18581, "knowledge_level": 18581, "agent_type": 18581, "original_subject": 18581, "original_object": 18581, "publications": 16454 } } } }