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EpiGraphDB meta relationships

BN_GEN_COR

Description:

Study results from “UKBB Genetic Correlation” project by Neale Lab.

Path: (Gwas)-[BN_GEN_COR]->(Gwas)

Schema:

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{'additionalProperties': False,
 'description': 'Study results from "UKBB Genetic Correlation" project\n'
                'by Neale Lab.',
 'properties': {'gcov_int': {'title': 'Gcov Int', 'type': 'number'},
                'gcov_int_se': {'title': 'Gcov Int Se', 'type': 'number'},
                'h2_int': {'title': 'H2 Int', 'type': 'number'},
                'h2_int_se': {'title': 'H2 Int Se', 'type': 'number'},
                'h2_obs': {'title': 'H2 Obs', 'type': 'number'},
                'h2_obs_se': {'title': 'H2 Obs Se', 'type': 'number'},
                'p': {'title': 'P', 'type': 'number'},
                'rg': {'title': 'Rg', 'type': 'number'},
                'se': {'title': 'Se', 'type': 'number'},
                'z': {'title': 'Z', 'type': 'number'}},
 'required': ['rg',
              'se',
              'z',
              'p',
              'h2_obs',
              'h2_obs_se',
              'h2_int',
              'h2_int_se',
              'gcov_int',
              'gcov_int_se'],
 'title': 'BN_GEN_COR',
 'type': 'object'}

CPIC

Path: (Drug)-[CPIC]->(Gene)

Schema:

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{'additionalProperties': False,
 'properties': {'cpic_level': {'title': 'Cpic Level', 'type': 'string'},
                'guideline': {'title': 'Guideline', 'type': 'string'},
                'pgx_on_fda_label': {'title': 'Pgx On Fda Label',
                                     'type': 'string'},
                'pharmgkb_level_of_evidence': {'title': 'Pharmgkb Level Of '
                                                        'Evidence',
                                               'type': 'string'}},
 'required': ['pharmgkb_level_of_evidence',
              'cpic_level',
              'guideline',
              'pgx_on_fda_label'],
 'title': 'CPIC',
 'type': 'object'}

EFO_CHILD_OF

Path: (Efo)-[EFO_CHILD_OF]->(Efo)

Schema:

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{'additionalProperties': False,
 'properties': {},
 'title': 'EFO_CHILD_OF',
 'type': 'object'}

EVENT_IN_PATHWAY

Path: (Pathway)-[EVENT_IN_PATHWAY]->(Event)

Schema:

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{'additionalProperties': False,
 'properties': {},
 'title': 'EVENT_IN_PATHWAY',
 'type': 'object'}

EXPRESSED_IN

Path: (Gene)-[EXPRESSED_IN]->(Tissue)

Schema:

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{'additionalProperties': False,
 'properties': {'tpm': {'title': 'Tpm', 'type': 'number'}},
 'required': ['tpm'],
 'title': 'EXPRESSED_IN',
 'type': 'object'}

GENE_TO_LITERATURE

Path: (Gene)-[GENE_TO_LITERATURE]->(Literature)

Schema:

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{'additionalProperties': False,
 'properties': {},
 'title': 'GENE_TO_LITERATURE',
 'type': 'object'}

GENE_TO_PROTEIN

Path: (Gene)-[GENE_TO_PROTEIN]->(Protein)

Schema:

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{'additionalProperties': False,
 'properties': {},
 'title': 'GENE_TO_PROTEIN',
 'type': 'object'}

GWAS_NLP

Description:

Pairwise semantic similarity of GWAS traits.

Precomputed results from Vectology (BioSentVec model).

Path: (Gwas)-[GWAS_NLP]->(Gwas)

Schema:

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{'additionalProperties': False,
 'description': 'Pairwise semantic similarity of GWAS traits.\n'
                '\n'
                'Precomputed results from Vectology (BioSentVec model).',
 'properties': {'score': {'title': 'Score', 'type': 'number'}},
 'required': ['score'],
 'title': 'GWAS_NLP',
 'type': 'object'}

GWAS_NLP_EFO

Description:

Semantic similarity of a GWAS trait to an EFO term.

Precomputed results from Vectology (BioSentVec model).

Path: (Gwas)-[GWAS_NLP_EFO]->(Efo)

Schema:

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{'additionalProperties': False,
 'description': 'Semantic similarity of a GWAS trait to an EFO term.\n'
                '\n'
                'Precomputed results from Vectology (BioSentVec model).',
 'properties': {'score': {'title': 'Score', 'type': 'number'}},
 'required': ['score'],
 'title': 'GWAS_NLP_EFO',
 'type': 'object'}

GWAS_SEM

Path: (Gwas)-[GWAS_SEM]->(SemmedTriple)

Schema:

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{'additionalProperties': False,
 'properties': {'globalCount': {'title': 'Globalcount', 'type': 'integer'},
                'globalTotal': {'title': 'Globaltotal', 'type': 'integer'},
                'localCount': {'title': 'Localcount', 'type': 'integer'},
                'localTotal': {'title': 'Localtotal', 'type': 'integer'},
                'odds': {'title': 'Odds', 'type': 'number'},
                'pval': {'title': 'Pval', 'type': 'number'}},
 'required': ['localCount',
              'localTotal',
              'globalCount',
              'globalTotal',
              'odds',
              'pval'],
 'title': 'GWAS_SEM',
 'type': 'object'}

GWAS_TO_LIT

Path: (Gwas)-[GWAS_TO_LIT]->(Literature)

Schema:

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{'additionalProperties': False,
 'properties': {},
 'title': 'GWAS_TO_LIT',
 'type': 'object'}

GWAS_TO_VARIANT

Path: (Gwas)-[GWAS_TO_VARIANT]->(Variant)

Schema:

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{'additionalProperties': False,
 'properties': {'beta': {'title': 'Beta', 'type': 'number'},
                'eaf': {'title': 'Eaf', 'type': 'number'},
                'ncase': {'title': 'Ncase', 'type': 'integer'},
                'ncontrol': {'title': 'Ncontrol', 'type': 'integer'},
                'pval': {'title': 'Pval', 'type': 'number'},
                'samplesize': {'title': 'Samplesize', 'type': 'number'},
                'se': {'title': 'Se', 'type': 'number'}},
 'required': ['beta', 'pval', 'samplesize'],
 'title': 'GWAS_TO_VARIANT',
 'type': 'object'}

INTACT_INTERACTS_WITH_GENE_GENE

Path: (Gene)-[INTACT_INTERACTS_WITH_GENE_GENE]->(Gene)

Schema:

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{'additionalProperties': False,
 'properties': {'intact_confidence_score': {'title': 'Intact Confidence Score',
                                            'type': 'number'},
                'intact_detection_method': {'items': {'type': 'string'},
                                            'title': 'Intact Detection Method',
                                            'type': 'array'},
                'intact_identifier': {'items': {'type': 'string'},
                                      'title': 'Intact Identifier',
                                      'type': 'array'},
                'intact_source': {'items': {'type': 'string'},
                                  'title': 'Intact Source',
                                  'type': 'array'},
                'intact_type': {'items': {'type': 'string'},
                                'title': 'Intact Type',
                                'type': 'array'}},
 'required': ['intact_confidence_score',
              'intact_detection_method',
              'intact_type',
              'intact_source',
              'intact_identifier'],
 'title': 'INTACT_INTERACTS_WITH_GENE_GENE',
 'type': 'object'}

INTACT_INTERACTS_WITH_GENE_PROTEIN

Path: (Gene)-[INTACT_INTERACTS_WITH_GENE_PROTEIN]->(Protein)

Schema:

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{'additionalProperties': False,
 'properties': {'intact_confidence_score': {'title': 'Intact Confidence Score',
                                            'type': 'number'},
                'intact_detection_method': {'items': {'type': 'string'},
                                            'title': 'Intact Detection Method',
                                            'type': 'array'},
                'intact_identifier': {'items': {'type': 'string'},
                                      'title': 'Intact Identifier',
                                      'type': 'array'},
                'intact_source': {'items': {'type': 'string'},
                                  'title': 'Intact Source',
                                  'type': 'array'},
                'intact_type': {'items': {'type': 'string'},
                                'title': 'Intact Type',
                                'type': 'array'}},
 'required': ['intact_confidence_score',
              'intact_detection_method',
              'intact_type',
              'intact_source',
              'intact_identifier'],
 'title': 'INTACT_INTERACTS_WITH_GENE_PROTEIN',
 'type': 'object'}

INTACT_INTERACTS_WITH_PROTEIN_PROTEIN

Path: (Protein)-[INTACT_INTERACTS_WITH_PROTEIN_PROTEIN]->(Protein)

Schema:

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{'additionalProperties': False,
 'properties': {'intact_confidence_score': {'title': 'Intact Confidence Score',
                                            'type': 'number'},
                'intact_detection_method': {'items': {'type': 'string'},
                                            'title': 'Intact Detection Method',
                                            'type': 'array'},
                'intact_identifier': {'items': {'type': 'string'},
                                      'title': 'Intact Identifier',
                                      'type': 'array'},
                'intact_source': {'items': {'type': 'string'},
                                  'title': 'Intact Source',
                                  'type': 'array'},
                'intact_type': {'items': {'type': 'string'},
                                'title': 'Intact Type',
                                'type': 'array'}},
 'required': ['intact_confidence_score',
              'intact_detection_method',
              'intact_type',
              'intact_source',
              'intact_identifier'],
 'title': 'INTACT_INTERACTS_WITH_PROTEIN_PROTEIN',
 'type': 'object'}

INTACT_NOT_INTERACTS_WITH

Path: (Protein)-[INTACT_NOT_INTERACTS_WITH]->(Protein)

Schema:

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{'additionalProperties': False,
 'properties': {'intact_confidence_score': {'title': 'Intact Confidence Score',
                                            'type': 'number'},
                'intact_detection_method': {'items': {'type': 'string'},
                                            'title': 'Intact Detection Method',
                                            'type': 'array'},
                'intact_identifier': {'items': {'type': 'string'},
                                      'title': 'Intact Identifier',
                                      'type': 'array'},
                'intact_source': {'items': {'type': 'string'},
                                  'title': 'Intact Source',
                                  'type': 'array'},
                'intact_type': {'items': {'type': 'string'},
                                'title': 'Intact Type',
                                'type': 'array'}},
 'required': ['intact_confidence_score',
              'intact_detection_method',
              'intact_type',
              'intact_source',
              'intact_identifier'],
 'title': 'INTACT_NOT_INTERACTS_WITH',
 'type': 'object'}

METAMAP_LITE

Description:

Mapping between Gwas and SemmedTerm via MetaMap Lite.

Path: (Gwas)-[METAMAP_LITE]->(SemmedTerm)

Schema:

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{'additionalProperties': False,
 'description': 'Mapping between Gwas and SemmedTerm via MetaMap Lite.\n    ',
 'properties': {'mesh': {'title': 'Mesh', 'type': 'string'},
                'mmi_score': {'title': 'Mmi Score', 'type': 'number'}},
 'required': ['mmi_score'],
 'title': 'METAMAP_LITE',
 'type': 'object'}

MONDO_MAP_EFO

Path: (Disease)-[MONDO_MAP_EFO]->(Efo)

Schema:

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{'additionalProperties': False,
 'properties': {},
 'title': 'MONDO_MAP_EFO',
 'type': 'object'}

MONDO_MAP_UMLS

Path: (Disease)-[MONDO_MAP_UMLS]->(SemmedTerm)

Schema:

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{'additionalProperties': False,
 'properties': {},
 'title': 'MONDO_MAP_UMLS',
 'type': 'object'}

MR

Description:

Pairwise Mendelian randomization evidence.

Results from MR-EvE.

Path: (Gwas)-[MR]->(Gwas)

Schema:

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{'additionalProperties': False,
 'description': 'Pairwise Mendelian randomization evidence.\n'
                '\n'
                'Results from MR-EvE.',
 'properties': {'b': {'title': 'B', 'type': 'number'},
                'ci_low': {'title': 'Ci Low', 'type': 'number'},
                'ci_upp': {'title': 'Ci Upp', 'type': 'number'},
                'log10pval': {'title': 'Log10Pval', 'type': 'number'},
                'method': {'title': 'Method', 'type': 'string'},
                'moescore': {'title': 'Moescore', 'type': 'string'},
                'nsnp': {'title': 'Nsnp', 'type': 'number'},
                'pval': {'title': 'Pval', 'type': 'number'},
                'se': {'title': 'Se', 'type': 'number'},
                'selection': {'title': 'Selection', 'type': 'string'}},
 'required': ['method', 'nsnp', 'b', 'selection', 'moescore'],
 'title': 'MR',
 'type': 'object'}

OBS_COR

Description:

Pairwise Spearman rank correlation for UK Biobank GWAS (ukb-b).

Results in-house by Benjamin Elsworth.

Path: (Gwas)-[OBS_COR]->(Gwas)

Schema:

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{'additionalProperties': False,
 'description': 'Pairwise Spearman rank correlation for UK Biobank GWAS '
                '(ukb-b).\n'
                '\n'
                'Results in-house by Benjamin Elsworth.',
 'properties': {'cor': {'title': 'Cor', 'type': 'number'}},
 'required': ['cor'],
 'title': 'OBS_COR',
 'type': 'object'}

OPENTARGETS_DRUG_TO_DISEASE

Path: (Drug)-[OPENTARGETS_DRUG_TO_DISEASE]->(Disease)

Schema:

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{'additionalProperties': False,
 'properties': {},
 'title': 'OPENTARGETS_DRUG_TO_DISEASE',
 'type': 'object'}

OPENTARGETS_DRUG_TO_TARGET

Path: (Drug)-[OPENTARGETS_DRUG_TO_TARGET]->(Gene)

Schema:

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{'additionalProperties': False,
 'properties': {'action_type': {'title': 'Action Type', 'type': 'string'},
                'phase': {'title': 'Phase', 'type': 'string'}},
 'required': ['phase', 'action_type'],
 'title': 'OPENTARGETS_DRUG_TO_TARGET',
 'type': 'object'}

PATHWAY_TO_DISEASE

Path: (Pathway)-[PATHWAY_TO_DISEASE]->(Disease)

Schema:

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{'additionalProperties': False,
 'properties': {},
 'title': 'PATHWAY_TO_DISEASE',
 'type': 'object'}

PATHWAY_TO_LITERATURE

Path: (Pathway)-[PATHWAY_TO_LITERATURE]->(Literature)

Schema:

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{'additionalProperties': False,
 'properties': {},
 'title': 'PATHWAY_TO_LITERATURE',
 'type': 'object'}

PRECEDING_EVENT

Path: (Event)-[PRECEDING_EVENT]->(Event)

Schema:

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{'additionalProperties': False,
 'properties': {},
 'title': 'PRECEDING_EVENT',
 'type': 'object'}

PROTEIN_IN_EVENT

Path: (Protein)-[PROTEIN_IN_EVENT]->(Event)

Schema:

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{'additionalProperties': False,
 'properties': {},
 'title': 'PROTEIN_IN_EVENT',
 'type': 'object'}

PROTEIN_TO_DISEASE

Path: (Protein)-[PROTEIN_TO_DISEASE]->(Disease)

Schema:

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{'additionalProperties': False,
 'properties': {},
 'title': 'PROTEIN_TO_DISEASE',
 'type': 'object'}

PROTEIN_TO_LITERATURE

Path: (Protein)-[PROTEIN_TO_LITERATURE]->(Literature)

Schema:

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{'additionalProperties': False,
 'properties': {},
 'title': 'PROTEIN_TO_LITERATURE',
 'type': 'object'}

PROTEIN_IN_PATHWAY

Path: (Protein)-[PROTEIN_IN_PATHWAY]->(Pathway)

Schema:

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{'additionalProperties': False,
 'properties': {},
 'title': 'PROTEIN_IN_PATHWAY',
 'type': 'object'}

PRS

Description:

Pairwise polygenic risk scores between GWAS.

Results from PRS Atlas.

Path: (Gwas)-[PRS]->(Gwas)

Schema:

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{'additionalProperties': False,
 'description': 'Pairwise polygenic risk scores between GWAS.\n'
                '\n'
                'Results from PRS Atlas.',
 'properties': {'beta': {'title': 'Beta', 'type': 'number'},
                'model': {'title': 'Model', 'type': 'string'},
                'n': {'title': 'N', 'type': 'integer'},
                'nsnps': {'title': 'Nsnps', 'type': 'integer'},
                'p': {'title': 'P', 'type': 'number'},
                'r2': {'title': 'R2', 'type': 'number'},
                'se': {'title': 'Se', 'type': 'number'}},
 'required': ['nsnps', 'model', 'beta', 'se', 'p', 'r2', 'n'],
 'title': 'PRS',
 'type': 'object'}

SEM_GENE

Path: (SemmedTerm)-[SEM_GENE]->(Gene)

Schema:

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{'additionalProperties': False,
 'properties': {},
 'title': 'SEM_GENE',
 'type': 'object'}

SEM_OBJ

Path: (SemmedTriple)-[SEM_OBJ]->(SemmedTerm)

Schema:

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{'additionalProperties': False,
 'properties': {},
 'title': 'SEM_OBJ',
 'type': 'object'}

SEM_PREDICATE

Path: (SemmedTerm)-[SEM_PREDICATE]->(SemmedTerm)

Schema:

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{'additionalProperties': False,
 'properties': {'count': {'title': 'Count', 'type': 'integer'},
                'predicate': {'title': 'Predicate', 'type': 'string'}},
 'required': ['predicate', 'count'],
 'title': 'SEM_PREDICATE',
 'type': 'object'}

SEM_SUB

Path: (SemmedTriple)-[SEM_SUB]->(SemmedTerm)

Schema:

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{'additionalProperties': False,
 'properties': {},
 'title': 'SEM_SUB',
 'type': 'object'}

SEM_TO_LIT

Path: (SemmedTriple)-[SEM_TO_LIT]->(Literature)

Schema:

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{'additionalProperties': False,
 'properties': {},
 'title': 'SEM_TO_LIT',
 'type': 'object'}

STRING_INTERACT_WITH

Path: (Protein)-[STRING_INTERACT_WITH]->(Protein)

Schema:

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{'additionalProperties': False,
 'properties': {'score': {'title': 'Score', 'type': 'number'}},
 'required': ['score'],
 'title': 'STRING_INTERACT_WITH',
 'type': 'object'}

TOPHITS

Path: (Gwas)-[TOPHITS]->(Variant)

Schema:

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{'additionalProperties': False,
 'properties': {'beta': {'title': 'Beta', 'type': 'number'},
                'pval': {'title': 'Pval', 'type': 'number'}},
 'required': ['beta', 'pval'],
 'title': 'TOPHITS',
 'type': 'object'}

VARIANT_TO_GENE

Path: (Variant)-[VARIANT_TO_GENE]->(Gene)

Schema:

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{'additionalProperties': False,
 'properties': {'allele': {'title': 'Allele', 'type': 'string'},
                'amino_acids': {'title': 'Amino Acids', 'type': 'string'},
                'cdna_position': {'title': 'Cdna Position', 'type': 'string'},
                'cds_position': {'title': 'Cds Position', 'type': 'string'},
                'codons': {'title': 'Codons', 'type': 'string'},
                'consequence': {'title': 'Consequence', 'type': 'string'},
                'existing_variation': {'title': 'Existing Variation',
                                       'type': 'string'},
                'extra': {'title': 'Extra', 'type': 'string'},
                'feature': {'title': 'Feature', 'type': 'string'},
                'feature_type': {'title': 'Feature Type', 'type': 'string'},
                'location': {'title': 'Location', 'type': 'string'},
                'protein_position': {'title': 'Protein Position',
                                     'type': 'string'}},
 'required': ['location',
              'allele',
              'feature',
              'feature_type',
              'consequence',
              'cdna_position',
              'cds_position',
              'protein_position',
              'amino_acids',
              'codons',
              'existing_variation',
              'extra'],
 'title': 'VARIANT_TO_GENE',
 'type': 'object'}

XQTL_MULTI_SNP_MR

Description:

Association of exposure gene and outcome phenotype in the multi SNP MR results of xQTL.

Path: (Gene)-[XQTL_MULTI_SNP_MR]->(Gwas)

Schema:

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{'additionalProperties': False,
 'description': 'Association of exposure gene and outcome phenotype in the '
                'multi SNP MR results of xQTL.\n'
                '    ',
 'properties': {'beta': {'title': 'Beta', 'type': 'number'},
                'mr_method': {'title': 'Mr Method', 'type': 'string'},
                'p': {'title': 'P', 'type': 'number'},
                'qtl_type': {'title': 'Qtl Type', 'type': 'string'},
                'se': {'title': 'Se', 'type': 'number'}},
 'required': ['beta', 'se', 'p', 'qtl_type', 'mr_method'],
 'title': 'XQTL_MULTI_SNP_MR',
 'type': 'object'}

XQTL_SINGLE_SNP_MR_GENE_GWAS

Description:

Association of exposure gene and outcome phenotype in the single SNP MR results of xQTL.

Path: (Gene)-[XQTL_SINGLE_SNP_MR_GENE_GWAS]->(Gwas)

Schema:

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{'additionalProperties': False,
 'description': 'Association of exposure gene and outcome phenotype in the '
                'single SNP MR results of xQTL.\n'
                '    ',
 'properties': {'beta': {'title': 'Beta', 'type': 'number'},
                'p': {'title': 'P', 'type': 'number'},
                'qtl_type': {'title': 'Qtl Type', 'type': 'string'},
                'rsid': {'title': 'Rsid', 'type': 'string'},
                'se': {'title': 'Se', 'type': 'number'}},
 'required': ['beta', 'se', 'p', 'rsid', 'qtl_type'],
 'title': 'XQTL_SINGLE_SNP_MR_GENE_GWAS',
 'type': 'object'}

XQTL_SINGLE_SNP_MR_SNP_GENE

Description:

Association of SNP and exposure gene in the single SNP MR results of xQTL.

Path: (Variant)-[XQTL_SINGLE_SNP_MR_SNP_GENE]->(Gene)

Schema:

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{'additionalProperties': False,
 'description': 'Association of SNP and exposure gene in the single SNP MR '
                'results of xQTL.\n'
                '    ',
 'properties': {},
 'title': 'XQTL_SINGLE_SNP_MR_SNP_GENE',
 'type': 'object'}