{ "@context": { "@vocab": "https://schema.org/", "biolink": "https://w3id.org/biolink/" }, "@type": "Dataset", "@id": "https://robokop.renci.org/graphs/ClinGenVariantPathogenicity/1.0.1/schema.json", "name": "A ROBOKOP Knowledge Graph based on ClinGen - Variant Pathogenicity Schema", "description": "Schema describing the nodes, edges, and attributes in the A ROBOKOP Knowledge Graph based on ClinGen - Variant Pathogenicity knowledge graph", "encodingFormat": "application/ld+json", "isPartOf": { "@type": "Dataset", "@id": "https://robokop.renci.org/graphs/ClinGenVariantPathogenicity/1.0.1/", "name": "A ROBOKOP Knowledge Graph based on ClinGen - Variant Pathogenicity" }, "schema": { "nodes": [ { "category": [ "biolink:Disease" ], "count": 119, "id_prefixes": { "MONDO": 119 }, "attributes": { "name": 119, "equivalent_identifiers": 119, "information_content": 119, "description": 116, "taxon": 12 } }, { "category": [ "biolink:SequenceVariant" ], "count": 12545, "id_prefixes": { "CAID": 12545 }, "attributes": { "name": 12545, "equivalent_identifiers": 12545, "hgvs": 12545, "robokop_variant_id": 12545 } }, { "category": [ "biolink:Gene", "biolink:Protein" ], "count": 663, "id_prefixes": { "NCBIGene": 663 }, "attributes": { "name": 663, "equivalent_identifiers": 663, "description": 663, "taxon": 663, "information_content": 660 } }, { "category": [ "biolink:Gene" ], "count": 706, "id_prefixes": { "ENSEMBL": 372, "NCBIGene": 334 }, "attributes": { "name": 706, "equivalent_identifiers": 706, "description": 334, "taxon": 334, "information_content": 29 } } ], "nodes_summary": { "total_count": 14033, "id_prefixes": { "CAID": 12545, "NCBIGene": 997, "ENSEMBL": 372, "MONDO": 119 }, "attributes": { "name": 14033, "equivalent_identifiers": 14033, "hgvs": 12545, "robokop_variant_id": 12545, "description": 1113, "taxon": 1009, "information_content": 808 } }, "edges": [ { "subject_category": [ "biolink:SequenceVariant" ], "predicate": "biolink:causes", "object_category": [ "biolink:Disease" ], "count": 12552, "primary_knowledge_sources": { "infores:clingen": 12552 }, "qualifiers": {}, "attributes": { "ASSERTION": 12552, "publications": 12552, "EXPERT_PANEL": 12552, "EVIDENCE_REPO_LINK": 12552, "APPROVAL_DATA": 12552, "PUBLISHED_DATE": 12552, "DIRECTION": 12552, "negated": 12552, "original_subject": 12552, "original_object": 12552, "SUMMARY": 12550, "MODE_OF_INHERITANCE": 12535, "HPO_FOR_MODE_OF_INHERITANCE": 12472, "APPLIED_EVIDENCE_CODES_MET": 12293, "APPLIED_EVIDENCE_CODES_NOT_MET": 8874, "GUIDELINE": 3149 }, "subject_id_prefixes": { "CAID": 12552 }, "object_id_prefixes": { "MONDO": 12552 } }, { "subject_category": [ "biolink:SequenceVariant" ], "predicate": "biolink:is_frameshift_variant_of", "object_category": [ "biolink:Gene", "biolink:Protein" ], "count": 1469, "primary_knowledge_sources": { "infores:robokop-snpeff": 1469 }, "qualifiers": {}, "attributes": { "knowledge_level": 1469, "agent_type": 1469, "snpeff_effect": 1469, "original_subject": 1469, "original_object": 1469 }, "subject_id_prefixes": { "CAID": 1469 }, "object_id_prefixes": { "NCBIGene": 1469 } }, { "subject_category": [ "biolink:SequenceVariant" ], "predicate": "biolink:is_non_coding_variant_of", "object_category": [ "biolink:Gene", "biolink:Protein" ], "count": 10197, "primary_knowledge_sources": { "infores:robokop-snpeff": 10197 }, "qualifiers": {}, "attributes": { "knowledge_level": 10197, "agent_type": 10197, "snpeff_effect": 10197, "original_subject": 10197, "original_object": 10197, "distance_to_feature": 3548 }, "subject_id_prefixes": { "CAID": 10197 }, "object_id_prefixes": { "NCBIGene": 10197 } }, { "subject_category": [ "biolink:SequenceVariant" ], "predicate": "biolink:is_nearby_variant_of", "object_category": [ "biolink:Gene" ], "count": 53655, "primary_knowledge_sources": { "infores:robokop-snpeff": 53655 }, "qualifiers": {}, "attributes": { "knowledge_level": 53655, "agent_type": 53655, "snpeff_effect": 53655, "distance_to_feature": 53655, "original_subject": 53655, "original_object": 53655 }, "subject_id_prefixes": { "CAID": 53655 }, "object_id_prefixes": { "NCBIGene": 30758, "ENSEMBL": 22897 } }, { "subject_category": [ "biolink:SequenceVariant" ], "predicate": "biolink:is_nearby_variant_of", "object_category": [ "biolink:Gene", "biolink:Protein" ], "count": 55104, "primary_knowledge_sources": { "infores:robokop-snpeff": 55104 }, "qualifiers": {}, "attributes": { "knowledge_level": 55104, "agent_type": 55104, "snpeff_effect": 55104, "distance_to_feature": 55104, "original_subject": 55104, "original_object": 55104 }, "subject_id_prefixes": { "CAID": 55104 }, "object_id_prefixes": { "NCBIGene": 55104 } }, { "subject_category": [ "biolink:SequenceVariant" ], "predicate": "biolink:is_missense_variant_of", "object_category": [ "biolink:Gene", "biolink:Protein" ], "count": 8154, "primary_knowledge_sources": { "infores:robokop-snpeff": 8154 }, "qualifiers": {}, "attributes": { "knowledge_level": 8154, "agent_type": 8154, "snpeff_effect": 8154, "original_subject": 8154, "original_object": 8154 }, "subject_id_prefixes": { "CAID": 8154 }, "object_id_prefixes": { "NCBIGene": 8154 } }, { "subject_category": [ "biolink:SequenceVariant" ], "predicate": "biolink:is_synonymous_variant_of", "object_category": [ "biolink:Gene", "biolink:Protein" ], "count": 1702, "primary_knowledge_sources": { "infores:robokop-snpeff": 1702 }, "qualifiers": {}, "attributes": { "knowledge_level": 1702, "agent_type": 1702, "snpeff_effect": 1702, "original_subject": 1702, "original_object": 1702 }, "subject_id_prefixes": { "CAID": 1702 }, "object_id_prefixes": { "NCBIGene": 1702 } }, { "subject_category": [ "biolink:SequenceVariant" ], "predicate": "biolink:is_nonsense_variant_of", "object_category": [ "biolink:Gene", "biolink:Protein" ], "count": 920, "primary_knowledge_sources": { "infores:robokop-snpeff": 920 }, "qualifiers": {}, "attributes": { "knowledge_level": 920, "agent_type": 920, "snpeff_effect": 920, "original_subject": 920, "original_object": 920 }, "subject_id_prefixes": { "CAID": 920 }, "object_id_prefixes": { "NCBIGene": 920 } }, { "subject_category": [ "biolink:SequenceVariant" ], "predicate": "biolink:is_splice_site_variant_of", "object_category": [ "biolink:Gene", "biolink:Protein" ], "count": 1613, "primary_knowledge_sources": { "infores:robokop-snpeff": 1613 }, "qualifiers": {}, "attributes": { "knowledge_level": 1613, "agent_type": 1613, "snpeff_effect": 1613, "original_subject": 1613, "original_object": 1613, "distance_to_feature": 19 }, "subject_id_prefixes": { "CAID": 1613 }, "object_id_prefixes": { "NCBIGene": 1613 } }, { "subject_category": [ "biolink:SequenceVariant" ], "predicate": "biolink:related_to", "object_category": [ "biolink:Gene", "biolink:Protein" ], "count": 472, "primary_knowledge_sources": { "infores:robokop-snpeff": 472 }, "qualifiers": {}, "attributes": { "knowledge_level": 472, "agent_type": 472, "snpeff_effect": 472, "original_subject": 472, "original_object": 472 }, "subject_id_prefixes": { "CAID": 472 }, "object_id_prefixes": { "NCBIGene": 472 } }, { "subject_category": [ "biolink:SequenceVariant" ], "predicate": "biolink:is_non_coding_variant_of", "object_category": [ "biolink:Gene" ], "count": 1701, "primary_knowledge_sources": { "infores:robokop-snpeff": 1701 }, "qualifiers": {}, "attributes": { "knowledge_level": 1701, "agent_type": 1701, "snpeff_effect": 1701, "original_subject": 1701, "original_object": 1701, "distance_to_feature": 119 }, "subject_id_prefixes": { "CAID": 1701 }, "object_id_prefixes": { "ENSEMBL": 973, "NCBIGene": 728 } }, { "subject_category": [ "biolink:SequenceVariant" ], "predicate": "biolink:is_splice_site_variant_of", "object_category": [ "biolink:Gene" ], "count": 61, "primary_knowledge_sources": { "infores:robokop-snpeff": 61 }, "qualifiers": {}, "attributes": { "knowledge_level": 61, "agent_type": 61, "snpeff_effect": 61, "original_subject": 61, "original_object": 61 }, "subject_id_prefixes": { "CAID": 61 }, "object_id_prefixes": { "ENSEMBL": 48, "NCBIGene": 13 } }, { "subject_category": [ "biolink:SequenceVariant" ], "predicate": "biolink:is_frameshift_variant_of", "object_category": [ "biolink:Gene" ], "count": 4, "primary_knowledge_sources": { "infores:robokop-snpeff": 4 }, "qualifiers": {}, "attributes": { "knowledge_level": 4, "agent_type": 4, "snpeff_effect": 4, "original_subject": 4, "original_object": 4 }, "subject_id_prefixes": { "CAID": 4 }, "object_id_prefixes": { "NCBIGene": 2, "ENSEMBL": 2 } }, { "subject_category": [ "biolink:SequenceVariant" ], "predicate": "biolink:is_missense_variant_of", "object_category": [ "biolink:Gene" ], "count": 16, "primary_knowledge_sources": { "infores:robokop-snpeff": 16 }, "qualifiers": {}, "attributes": { "knowledge_level": 16, "agent_type": 16, "snpeff_effect": 16, "original_subject": 16, "original_object": 16 }, "subject_id_prefixes": { "CAID": 16 }, "object_id_prefixes": { "ENSEMBL": 11, "NCBIGene": 5 } }, { "subject_category": [ "biolink:SequenceVariant" ], "predicate": "biolink:is_synonymous_variant_of", "object_category": [ "biolink:Gene" ], "count": 5, "primary_knowledge_sources": { "infores:robokop-snpeff": 5 }, "qualifiers": {}, "attributes": { "knowledge_level": 5, "agent_type": 5, "snpeff_effect": 5, "original_subject": 5, "original_object": 5 }, "subject_id_prefixes": { "CAID": 5 }, "object_id_prefixes": { "ENSEMBL": 4, "NCBIGene": 1 } }, { "subject_category": [ "biolink:SequenceVariant" ], "predicate": "biolink:related_to", "object_category": [ "biolink:Gene" ], "count": 2, "primary_knowledge_sources": { "infores:robokop-snpeff": 2 }, "qualifiers": {}, "attributes": { "knowledge_level": 2, "agent_type": 2, "snpeff_effect": 2, "original_subject": 2, "original_object": 2 }, "subject_id_prefixes": { "CAID": 2 }, "object_id_prefixes": { "ENSEMBL": 2 } } ], "edges_summary": { "total_count": 147627, "predicates": { "biolink:is_nearby_variant_of": 108759, "biolink:causes": 12552, "biolink:is_non_coding_variant_of": 11898, "biolink:is_missense_variant_of": 8170, "biolink:is_synonymous_variant_of": 1707, "biolink:is_splice_site_variant_of": 1674, "biolink:is_frameshift_variant_of": 1473, "biolink:is_nonsense_variant_of": 920, "biolink:related_to": 474 }, "primary_knowledge_sources": { "infores:robokop-snpeff": 135075, "infores:clingen": 12552 }, "predicates_by_knowledge_source": { "infores:clingen": { "biolink:causes": 12552 }, "infores:robokop-snpeff": { "biolink:is_nearby_variant_of": 108759, "biolink:is_non_coding_variant_of": 11898, "biolink:is_missense_variant_of": 8170, "biolink:is_synonymous_variant_of": 1707, "biolink:is_splice_site_variant_of": 1674, "biolink:is_frameshift_variant_of": 1473, "biolink:is_nonsense_variant_of": 920, "biolink:related_to": 474 } }, "qualifiers": {}, "attributes": { "original_subject": 147627, "original_object": 147627, "knowledge_level": 135075, "agent_type": 135075, "snpeff_effect": 135075, "distance_to_feature": 112445, "ASSERTION": 12552, "publications": 12552, "EXPERT_PANEL": 12552, "EVIDENCE_REPO_LINK": 12552, "APPROVAL_DATA": 12552, "PUBLISHED_DATE": 12552, "DIRECTION": 12552, "negated": 12552, "SUMMARY": 12550, "MODE_OF_INHERITANCE": 12535, "HPO_FOR_MODE_OF_INHERITANCE": 12472, "APPLIED_EVIDENCE_CODES_MET": 12293, "APPLIED_EVIDENCE_CODES_NOT_MET": 8874, "GUIDELINE": 3149 } } } }