Skip to content

EpiGraphDB meta relationships

This document shows the current meta relationships (a group of relationship entities) in the EpiGraphDB graph database. For each meta relationship, their available properties are shown, and an example set of relationship entities are shown in the collapsed text box.

BN_GEN_COR

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

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

Properties:

- rg: Genetic correlation (r_g).

- se: Standard error of rg.

- z: z statistic for test of null hypothesis rg = 0.

- p: p-value for test of null hypothesis rg = 0.

- h2_obs: observed scale heritability.

- h2_obs_se: Standard error of h2_obs.

- h2_int: LD score regression intercept for single trait.

- h2_int_se: Standard error of h2_int.

- gcov_int: LD score regression intercept (cross-trait).

- gcov_int_se: Standard error of gcov_int.

Examples

query

 MATCH (n)-[r: BN_GEN_COR]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'access': 'public',
         'author': 'Neale',
         'category': 'NA',
         'consortium': 'Neale Lab',
         'id': 'ukb-a-276',
         'mr': '1',
         'note': 'NA',
         'nsnp': '10894596',
         'population': 'European',
         'priority': '1',
         'sample_size': '331285',
         'sex': 'Males and Females',
         'subcategory': 'NA',
         'trait': 'Leg fat-free mass (right)',
         'unit': 'SD',
         'year': '2017'},
   'n': {'access': 'public',
         'author': 'Ben Elsworth',
         'category': 'Categorical Ordered',
         'consortium': 'MRC-IEU',
         'id': 'ukb-b-9991',
         'mr': '1',
         'note': '991: Output from GWAS pipeline using Phesant derived '
                 'variables from UKBiobank',
         'nsnp': '9851867',
         'population': 'European',
         'priority': '1',
         'sample_size': '46945',
         'sex': 'Males and Females',
         'subcategory': 'NA',
         'trait': 'Frequency of strenuous sports in last 4 weeks',
         'unit': 'SD',
         'year': '2018'},
   'r': {'gcov_int': -0.004741999786347151,
         'gcov_int_se': 0.006558999884873629,
         'h2_int': 1.00600004196167,
         'h2_int_se': 0.006839000154286623,
         'h2_obs': 0.035270001739263535,
         'h2_obs_se': 0.013140000402927399,
         'p': 0.0971900001168251,
         'rg': -0.09010999649763107,
         'se': 0.054329998791217804,
         'z': -1.659000039100647}},
  {'m': {'access': 'public',
         'author': 'Neale',
         'category': 'NA',
         'consortium': 'Neale Lab',
         'id': 'ukb-a-276',
         'mr': '1',
         'note': 'NA',
         'nsnp': '10894596',
         'population': 'European',
         'priority': '1',
         'sample_size': '331285',
         'sex': 'Males and Females',
         'subcategory': 'NA',
         'trait': 'Leg fat-free mass (right)',
         'unit': 'SD',
         'year': '2017'},
   'n': {'access': 'public',
         'author': 'Neale',
         'category': 'NA',
         'consortium': 'Neale Lab',
         'id': 'ukb-a-516',
         'mr': '1',
         'note': 'NA',
         'nsnp': '10894596',
         'population': 'European',
         'priority': '1',
         'sample_size': '240788',
         'sex': 'Males and Females',
         'subcategory': 'NA',
         'trait': 'Duration walking for pleasure',
         'unit': 'SD',
         'year': '2017'},
   'r': {'gcov_int': -0.02484999969601631,
         'gcov_int_se': 0.007089999970048666,
         'h2_int': 1.003999948501587,
         'h2_int_se': 0.006562000140547752,
         'h2_obs': 0.024070000275969505,
         'h2_obs_se': 0.002099999925121665,
         'p': 0.0017529999604448676,
         'rg': -0.09397999942302704,
         'se': 0.03002999909222126,
         'z': -3.128999948501587}},
  {'m': {'access': 'public',
         'author': 'Neale',
         'category': 'NA',
         'consortium': 'Neale Lab',
         'id': 'ukb-a-276',
         'mr': '1',
         'note': 'NA',
         'nsnp': '10894596',
         'population': 'European',
         'priority': '1',
         'sample_size': '331285',
         'sex': 'Males and Females',
         'subcategory': 'NA',
         'trait': 'Leg fat-free mass (right)',
         'unit': 'SD',
         'year': '2017'},
   'n': {'access': 'public',
         'author': 'Ben Elsworth',
         'category': 'Categorical Ordered',
         'consortium': 'MRC-IEU',
         'id': 'ukb-b-703',
         'mr': '1',
         'note': '981: Output from GWAS pipeline using Phesant derived '
                 'variables from UKBiobank',
         'nsnp': '9851867',
         'population': 'European',
         'priority': '1',
         'sample_size': '328153',
         'sex': 'Males and Females',
         'subcategory': 'NA',
         'trait': 'Duration walking for pleasure',
         'unit': 'SD',
         'year': '2018'},
   'r': {'gcov_int': -0.02484999969601631,
         'gcov_int_se': 0.007089999970048666,
         'h2_int': 1.003999948501587,
         'h2_int_se': 0.006562000140547752,
         'h2_obs': 0.024070000275969505,
         'h2_obs_se': 0.002099999925121665,
         'p': 0.0017529999604448676,
         'rg': -0.09397999942302704,
         'se': 0.03002999909222126,
         'z': -3.128999948501587}}]

CPIC

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

Properties:

- pharmgkb_level_of_evidence: PharmGKB level of evidence (https://www.pharmgkb.org/page/clinAnnLevels).

- cpic_level: CPIC level of evidence (https://cpicpgx.org/prioritization/).

- guideline: CPIC guideline for clinicians (cpicpgx.org/guidelines/).

- pgx_on_fda_label: PharmGKB PGx level based on drug label (www.pharmgkb.org/page/drugLabelLegend).

Examples

query

 MATCH (n)-[r: CPIC]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'adme_gene': 'N',
         'bio_druggable': 'N',
         'chr': '16',
         'description': 'NAD(P)H dehydrogenase, quinone 1 [Source:HGNC '
                        'Symbol;Acc:2874]',
         'druggability_tier': 'Tier 1',
         'end': 69760854,
         'ensembl_id': 'ENSG00000181019',
         'name': 'NQO1',
         'reactome_id': '8990858',
         'small_mol_druggable': 'Y',
         'source': 'HGNC Symbol',
         'start': 69740899,
         'type': 'protein_coding'},
   'n': {'label': 'ALKYLATING AGENTS', 'source': ['CPIC']},
   'r': {'cpic_level': 'D',
         'guideline': 'NA',
         'pgx_on_fda_label': 'NA',
         'pharmgkb_level_of_evidence': '2A'}},
  {'m': {'adme_gene': 'N',
         'bio_druggable': 'N',
         'chr': '16',
         'description': 'NAD(P)H dehydrogenase, quinone 1 [Source:HGNC '
                        'Symbol;Acc:2874]',
         'druggability_tier': 'Tier 1',
         'end': 69760854,
         'ensembl_id': 'ENSG00000181019',
         'name': 'NQO1',
         'reactome_id': '8990858',
         'small_mol_druggable': 'Y',
         'source': 'HGNC Symbol',
         'start': 69740899,
         'type': 'protein_coding'},
   'n': {'label': 'PLATINUM COMPOUNDS', 'source': ['CPIC']},
   'r': {'cpic_level': 'D',
         'guideline': 'NA',
         'pgx_on_fda_label': 'NA',
         'pharmgkb_level_of_evidence': '2A'}},
  {'m': {'adme_gene': 'N',
         'bio_druggable': 'N',
         'chr': '16',
         'description': 'NAD(P)H dehydrogenase, quinone 1 [Source:HGNC '
                        'Symbol;Acc:2874]',
         'druggability_tier': 'Tier 1',
         'end': 69760854,
         'ensembl_id': 'ENSG00000181019',
         'name': 'NQO1',
         'reactome_id': '8990858',
         'small_mol_druggable': 'Y',
         'source': 'HGNC Symbol',
         'start': 69740899,
         'type': 'protein_coding'},
   'n': {'label': 'ANTHRACYCLINES AND RELATED SUBSTANCES', 'source': ['CPIC']},
   'r': {'cpic_level': 'D',
         'guideline': 'NA',
         'pgx_on_fda_label': 'NA',
         'pharmgkb_level_of_evidence': '2A'}}]

EFO_CHILD_OF

The source (Efo) term is a child node of the parent target (Efo) term.

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

Examples

query

 MATCH (n)-[r: EFO_CHILD_OF]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'id': 'http://www.orpha.net/ORDO/Orphanet_90342',
         'type': 'typed-literal',
         'value': 'Xeroderma pigmentosum variant'},
   'n': {'id': 'http://www.orpha.net/ORDO/Orphanet_910',
         'type': 'typed-literal',
         'value': 'Xeroderma pigmentosum'},
   'r': {}},
  {'m': {'id': 'http://www.orpha.net/ORDO/Orphanet_910',
         'type': 'typed-literal',
         'value': 'Xeroderma pigmentosum'},
   'n': {'id': 'http://www.orpha.net/ORDO/Orphanet_276267',
         'type': 'typed-literal',
         'value': 'Xeroderma pigmentosum complementation group G'},
   'r': {}},
  {'m': {'id': 'http://www.orpha.net/ORDO/Orphanet_910',
         'type': 'typed-literal',
         'value': 'Xeroderma pigmentosum'},
   'n': {'id': 'http://www.orpha.net/ORDO/Orphanet_276264',
         'type': 'typed-literal',
         'value': 'Xeroderma pigmentosum complementation group F'},
   'r': {}}]

EVENT_IN_PATHWAY

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

Examples

query

 MATCH (n)-[r: EVENT_IN_PATHWAY]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'in_disease': 'FALSE',
         'name': 'Amplification  of signal from unattached  kinetochores via a '
                 'MAD2  inhibitory signal',
         'reactome_id': 'R-HSA-141444'},
   'n': {'in_disease': 'FALSE',
         'name': 'Mad1 binds kinetochore',
         'reactome_id': 'R-HSA-141409'},
   'r': {}},
  {'m': {'in_disease': 'FALSE',
         'name': 'Amplification  of signal from unattached  kinetochores via a '
                 'MAD2  inhibitory signal',
         'reactome_id': 'R-HSA-141444'},
   'n': {'in_disease': 'FALSE',
         'name': 'Release of activated MAD2 from kinetochores',
         'reactome_id': 'R-HSA-141439'},
   'r': {}},
  {'m': {'in_disease': 'FALSE',
         'name': 'Amplification  of signal from unattached  kinetochores via a '
                 'MAD2  inhibitory signal',
         'reactome_id': 'R-HSA-141444'},
   'n': {'in_disease': 'FALSE',
         'name': 'MAD2 associates with the Mad1 kinetochore complex',
         'reactome_id': 'R-HSA-141431'},
   'r': {}}]

EXPRESSED_IN

The source Gene is expressed in the target Tissue in GTEx (https://gtexportal.org).

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

Properties:

- tpm: Gene expression level in transcripts per million (TPM).

Examples

query

 MATCH (n)-[r: EXPRESSED_IN]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'chr': '13',
         'description': 'long intergenic non-protein coding RNA 362 '
                        '[Source:HGNC Symbol;Acc:42682]',
         'end': 23744736,
         'ensembl_id': 'ENSG00000229483',
         'name': 'LINC00362',
         'source': 'HGNC Symbol',
         'start': 23743974,
         'type': 'lincRNA'},
   'n': {'tissue': 'Testis'},
   'r': {'tpm': 2.335}},
  {'m': {'chr': '13',
         'description': 'SACS antisense RNA 1 [Source:HGNC Symbol;Acc:39835]',
         'end': 24002818,
         'ensembl_id': 'ENSG00000229558',
         'name': 'SACS-AS1',
         'source': 'HGNC Symbol',
         'start': 23993110,
         'type': 'lincRNA'},
   'n': {'tissue': 'Testis'},
   'r': {'tpm': 2.955}},
  {'m': {'chr': '13',
         'description': 'long intergenic non-protein coding RNA 327 '
                        '[Source:HGNC Symbol;Acc:42009]',
         'end': 24061603,
         'ensembl_id': 'ENSG00000232977',
         'name': 'LINC00327',
         'source': 'HGNC Symbol',
         'start': 24040710,
         'type': 'lincRNA'},
   'n': {'tissue': 'Nerve - Tibial'},
   'r': {'tpm': 1.7085}}]

GENE_TO_LITERATURE

Association between (Gene) and (Literature).

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

Examples

query

 MATCH (n)-[r: GENE_TO_LITERATURE]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'adme_gene': 'N',
         'bio_druggable': 'N',
         'chr': '2',
         'description': 'ribonuclease H1 [Source:HGNC Symbol;Acc:18466]',
         'druggability_tier': 'Tier 2',
         'end': 3606206,
         'ensembl_id': 'ENSG00000171865',
         'name': 'RNASEH1',
         'small_mol_druggable': 'Y',
         'source': 'HGNC Symbol',
         'start': 3592383,
         'type': 'protein_coding'},
   'n': {'dp': '2012 Dec 11',
         'edat': '2012-12-15',
         'issn': '1878-3686',
         'pubmed_id': '23238014',
         'year': 2012},
   'r': {}},
  {'m': {'chr': '17',
         'description': 'homeobox B5 [Source:HGNC Symbol;Acc:5116]',
         'end': 46671323,
         'ensembl_id': 'ENSG00000120075',
         'name': 'HOXB5',
         'source': 'HGNC Symbol',
         'start': 46668619,
         'type': 'protein_coding'},
   'n': {'dp': '2013 Aug 12',
         'edat': '2013-7-16',
         'issn': '1878-3686',
         'pubmed_id': '23850221',
         'year': 2013},
   'r': {}},
  {'m': {'adme_gene': 'N',
         'bio_druggable': 'N',
         'chr': '12',
         'description': 'MDM2 oncogene, E3 ubiquitin protein ligase '
                        '[Source:HGNC Symbol;Acc:6973]',
         'druggability_tier': 'Tier 1',
         'end': 69239214,
         'ensembl_id': 'ENSG00000135679',
         'name': 'MDM2',
         'reactome_id': '12233126',
         'small_mol_druggable': 'Y',
         'source': 'HGNC Symbol',
         'start': 69201956,
         'type': 'protein_coding'},
   'n': {'dp': '2009 Sep',
         'edat': '2009-6-10',
         'issn': '1535-9484',
         'pubmed_id': '19505873',
         'year': 2009},
   'r': {}}]

GENE_TO_PROTEIN

Mapping between (Gene) and (Protein).

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

Examples

query

 MATCH (n)-[r: GENE_TO_PROTEIN]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'chr': '15',
         'description': 'golgin A6 family-like 6 [Source:HGNC Symbol;Acc:37225]',
         'end': 20747114,
         'ensembl_id': 'ENSG00000215405',
         'name': 'GOLGA6L6',
         'source': 'HGNC Symbol',
         'start': 20737094,
         'type': 'protein_coding'},
   'n': {'uniprot_id': 'A8MZA4'},
   'r': {}},
  {'m': {'chr': '21',
         'description': 'immunoglobulin heavy variable 1/OR21-1 '
                        '(non-functional) [Source:HGNC Symbol;Acc:38040]',
         'end': 10863067,
         'ensembl_id': 'ENSG00000169861',
         'name': 'IGHV1OR21-1',
         'source': 'HGNC Symbol',
         'start': 10862622,
         'type': 'IG_V_gene'},
   'n': {'uniprot_id': 'A6NJS3'},
   'r': {}},
  {'m': {'chr': '15',
         'description': 'POTE ankyrin domain family, member B2 [Source:HGNC '
                        'Symbol;Acc:48327]',
         'end': 21071643,
         'ensembl_id': 'ENSG00000230031',
         'name': 'POTEB2',
         'source': 'HGNC Symbol',
         'start': 21040701,
         'type': 'protein_coding'},
   'n': {'uniprot_id': 'H3BUK9'},
   'r': {}}]

GWAS_NLP

Pairwise semantic similarities of (Gwas) traits. Precomputed results from Vectology (BioSentVec model).

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

Properties:

- score: Similarity score (cosine similarity).

Examples

query

 MATCH (n)-[r: GWAS_NLP]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'access': 'public',
         'author': 'Deloukas',
         'category': 'Disease',
         'consortium': 'NA',
         'id': 'ieu-a-9',
         'mr': '1',
         'ncase': '63746',
         'ncontrol': '130681',
         'nsnp': '79129',
         'pmid': '23202125',
         'population': 'Mixed',
         'priority': '1',
         'sample_size': '194427',
         'sex': 'Males and Females',
         'subcategory': 'Cardiovascular',
         'trait': 'Coronary heart disease',
         'unit': 'NA',
         'year': '2013'},
   'n': {'access': 'public',
         'author': 'Neale',
         'category': 'NA',
         'consortium': 'Neale Lab',
         'id': 'ukb-a-82',
         'mr': '1',
         'ncase': '4611',
         'ncontrol': '332548',
         'note': 'NA',
         'nsnp': '10894596',
         'population': 'European',
         'priority': '1',
         'sample_size': '337159',
         'sex': 'Males and Females',
         'subcategory': 'NA',
         'trait': 'Non-cancer illness code  self-reported: anxiety/panic '
                  'attacks',
         'unit': 'SD',
         'year': '2017'},
   'r': {'score': 0.20381323993206024}},
  {'m': {'access': 'public',
         'author': 'Deloukas',
         'category': 'Disease',
         'consortium': 'NA',
         'id': 'ieu-a-9',
         'mr': '1',
         'ncase': '63746',
         'ncontrol': '130681',
         'nsnp': '79129',
         'pmid': '23202125',
         'population': 'Mixed',
         'priority': '1',
         'sample_size': '194427',
         'sex': 'Males and Females',
         'subcategory': 'Cardiovascular',
         'trait': 'Coronary heart disease',
         'unit': 'NA',
         'year': '2013'},
   'n': {'access': 'public',
         'author': 'Sun BB',
         'category': 'Immune system',
         'consortium': 'NA',
         'id': 'prot-a-903',
         'mr': '1',
         'note': 'NA',
         'nsnp': '10534735',
         'pmid': '29875488',
         'population': 'European',
         'priority': '0',
         'sample_size': '3301',
         'sex': 'Males and Females',
         'subcategory': 'Protein',
         'trait': 'Ephrin-B1',
         'unit': 'NA',
         'year': '2018'},
   'r': {'score': 0.10023094713687897}},
  {'m': {'access': 'public',
         'author': 'Deloukas',
         'category': 'Disease',
         'consortium': 'NA',
         'id': 'ieu-a-9',
         'mr': '1',
         'ncase': '63746',
         'ncontrol': '130681',
         'nsnp': '79129',
         'pmid': '23202125',
         'population': 'Mixed',
         'priority': '1',
         'sample_size': '194427',
         'sex': 'Males and Females',
         'subcategory': 'Cardiovascular',
         'trait': 'Coronary heart disease',
         'unit': 'NA',
         'year': '2013'},
   'n': {'access': 'public',
         'author': 'Ben Elsworth',
         'category': 'Continuous',
         'consortium': 'MRC-IEU',
         'id': 'ukb-b-7478',
         'mr': '1',
         'note': '46: Output from GWAS pipeline using Phesant derived variables '
                 'from UKBiobank',
         'nsnp': '9851867',
         'population': 'European',
         'priority': '1',
         'sample_size': '461026',
         'sex': 'Males and Females',
         'subcategory': 'NA',
         'trait': 'Hand grip strength (left)',
         'unit': 'SD',
         'year': '2018'},
   'r': {'score': 0.1911364644765854}}]

GWAS_NLP_EFO

Semantic similarity mapping of (Gwas) trait to (Efo) term. Precomputed results from Vectology (BioSentVec model).

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

Properties:

- score: Similarity score (cosine similarity).

Examples

query

 MATCH (n)-[r: GWAS_NLP_EFO]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'access': 'public',
         'author': 'Deloukas',
         'category': 'Disease',
         'consortium': 'NA',
         'id': 'ieu-a-9',
         'mr': '1',
         'ncase': '63746',
         'ncontrol': '130681',
         'nsnp': '79129',
         'pmid': '23202125',
         'population': 'Mixed',
         'priority': '1',
         'sample_size': '194427',
         'sex': 'Males and Females',
         'subcategory': 'Cardiovascular',
         'trait': 'Coronary heart disease',
         'unit': 'NA',
         'year': '2013'},
   'n': {'id': 'http://www.ebi.ac.uk/efo/EFO_0000319',
         'type': 'typed-literal',
         'value': 'cardiovascular disease'},
   'r': {'score': 0.711556613445282}},
  {'m': {'access': 'public',
         'author': 'Deloukas',
         'category': 'Disease',
         'consortium': 'NA',
         'id': 'ieu-a-9',
         'mr': '1',
         'ncase': '63746',
         'ncontrol': '130681',
         'nsnp': '79129',
         'pmid': '23202125',
         'population': 'Mixed',
         'priority': '1',
         'sample_size': '194427',
         'sex': 'Males and Females',
         'subcategory': 'Cardiovascular',
         'trait': 'Coronary heart disease',
         'unit': 'NA',
         'year': '2013'},
   'n': {'id': 'http://www.ebi.ac.uk/efo/EFO_0001645',
         'type': 'typed-literal',
         'value': 'coronary heart disease'},
   'r': {'score': 1.0}},
  {'m': {'access': 'public',
         'author': 'Sun BB',
         'category': 'Immune system',
         'consortium': 'NA',
         'id': 'prot-a-7',
         'mr': '1',
         'note': 'NA',
         'nsnp': '10534735',
         'pmid': '29875488',
         'population': 'European',
         'priority': '0',
         'sample_size': '3301',
         'sex': 'Males and Females',
         'subcategory': 'Protein',
         'trait': 'Tyrosine-protein kinase ABL1',
         'unit': 'NA',
         'year': '2018'},
   'n': {'id': 'http://www.ebi.ac.uk/efo/EFO_0008251',
         'type': 'typed-literal',
         'value': 'non-receptor tyrosine-protein kinase TYK2 measurement'},
   'r': {'score': 0.70243901014328}}]

GWAS_SEM

Mapping between (Gwas) and (SemmedTriple).

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

Properties:

- localCount: Count of given triple for given search term.

- localTotal: Count of all triples for given search term.

- globalCount: Count of given triple in database.

- globalTotal: Count of all triples in database.

- odds: Odds ration from Fisher’s Exact Test.

- pval: P-value from Fisher’s Exact Test.

Examples

query

 MATCH (n)-[r: GWAS_SEM]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'access': 'public',
         'author': 'Deloukas',
         'category': 'Disease',
         'consortium': 'NA',
         'id': 'ieu-a-9',
         'mr': '1',
         'ncase': '63746',
         'ncontrol': '130681',
         'nsnp': '79129',
         'pmid': '23202125',
         'population': 'Mixed',
         'priority': '1',
         'sample_size': '194427',
         'sex': 'Males and Females',
         'subcategory': 'Cardiovascular',
         'trait': 'Coronary heart disease',
         'unit': 'NA',
         'year': '2013'},
   'n': {'count': 3,
         'id': 'coumarin:COEXISTS_WITH:Aspirin',
         'object_id': 'C0004057',
         'object_name': 'Aspirin',
         'object_type': 'orch',
         'predicate': 'COEXISTS_WITH',
         'subject_id': 'C0010206',
         'subject_name': 'coumarin',
         'subject_type': 'orch'},
   'r': {'globalCount': 3,
         'globalTotal': 6611441,
         'localCount': 2,
         'localTotal': 109465,
         'odds': 40.265174865722656,
         'pval': 0.0025674477219581604}},
  {'m': {'access': 'public',
         'author': 'Deloukas',
         'category': 'Disease',
         'consortium': 'NA',
         'id': 'ieu-a-9',
         'mr': '1',
         'ncase': '63746',
         'ncontrol': '130681',
         'nsnp': '79129',
         'pmid': '23202125',
         'population': 'Mixed',
         'priority': '1',
         'sample_size': '194427',
         'sex': 'Males and Females',
         'subcategory': 'Cardiovascular',
         'trait': 'Coronary heart disease',
         'unit': 'NA',
         'year': '2013'},
   'n': {'count': 40,
         'id': 'Lipoproteins:AFFECTS:Atherosclerosis',
         'object_id': 'C0004153',
         'object_name': 'Atherosclerosis',
         'object_type': 'dsyn',
         'predicate': 'AFFECTS',
         'subject_id': 'C0023820',
         'subject_name': 'Lipoproteins',
         'subject_type': 'aapp'},
   'r': {'globalCount': 40,
         'globalTotal': 6611441,
         'localCount': 7,
         'localTotal': 109465,
         'odds': 10.569608688354492,
         'pval': 1.0800005838973448e-05}},
  {'m': {'access': 'public',
         'author': 'Deloukas',
         'category': 'Disease',
         'consortium': 'NA',
         'id': 'ieu-a-9',
         'mr': '1',
         'ncase': '63746',
         'ncontrol': '130681',
         'nsnp': '79129',
         'pmid': '23202125',
         'population': 'Mixed',
         'priority': '1',
         'sample_size': '194427',
         'sex': 'Males and Females',
         'subcategory': 'Cardiovascular',
         'trait': 'Coronary heart disease',
         'unit': 'NA',
         'year': '2013'},
   'n': {'count': 9,
         'id': 'Hydroxymethylglutaryl-CoA Reductase '
               'Inhibitors:INTERACTS_WITH:ezetimibe',
         'object_id': 'C1142985',
         'object_name': 'ezetimibe',
         'object_type': 'orch',
         'predicate': 'INTERACTS_WITH',
         'subject_id': 'C0360714',
         'subject_name': 'Hydroxymethylglutaryl-CoA Reductase Inhibitors',
         'subject_type': 'orch'},
   'r': {'globalCount': 9,
         'globalTotal': 6611441,
         'localCount': 2,
         'localTotal': 109465,
         'odds': 13.421725273132324,
         'pval': 0.013232198543846607}}]

GWAS_TO_LIT

Asscociation of the (Gwas) phenotype to a (Literature) PubMed article.

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

Examples

query

 MATCH (n)-[r: GWAS_TO_LIT]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'access': 'public',
         'author': 'Deloukas',
         'category': 'Disease',
         'consortium': 'NA',
         'id': 'ieu-a-9',
         'mr': '1',
         'ncase': '63746',
         'ncontrol': '130681',
         'nsnp': '79129',
         'pmid': '23202125',
         'population': 'Mixed',
         'priority': '1',
         'sample_size': '194427',
         'sex': 'Males and Females',
         'subcategory': 'Cardiovascular',
         'trait': 'Coronary heart disease',
         'unit': 'NA',
         'year': '2013'},
   'n': {'dp': '2008 Dec 01',
         'edat': '2008-11-26',
         'issn': '1879-1913',
         'pubmed_id': '19026302',
         'year': 2008},
   'r': {}},
  {'m': {'access': 'public',
         'author': 'Deloukas',
         'category': 'Disease',
         'consortium': 'NA',
         'id': 'ieu-a-9',
         'mr': '1',
         'ncase': '63746',
         'ncontrol': '130681',
         'nsnp': '79129',
         'pmid': '23202125',
         'population': 'Mixed',
         'priority': '1',
         'sample_size': '194427',
         'sex': 'Males and Females',
         'subcategory': 'Cardiovascular',
         'trait': 'Coronary heart disease',
         'unit': 'NA',
         'year': '2013'},
   'n': {'dp': '2009 Aug 14',
         'edat': '2009-1-22',
         'issn': '1470-8736',
         'pubmed_id': '19154184',
         'year': 2009},
   'r': {}},
  {'m': {'access': 'public',
         'author': 'Deloukas',
         'category': 'Disease',
         'consortium': 'NA',
         'id': 'ieu-a-9',
         'mr': '1',
         'ncase': '63746',
         'ncontrol': '130681',
         'nsnp': '79129',
         'pmid': '23202125',
         'population': 'Mixed',
         'priority': '1',
         'sample_size': '194427',
         'sex': 'Males and Females',
         'subcategory': 'Cardiovascular',
         'trait': 'Coronary heart disease',
         'unit': 'NA',
         'year': '2013'},
   'n': {'dp': '2008 Dec',
         'edat': '2008-11-26',
         'issn': '0277-0008',
         'pubmed_id': '19025436',
         'year': 2008},
   'r': {}}]

GWAS_TO_VARIANT

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

Properties:

- beta

- se

- pval

- eaf

- samplesize

- ncase

- ncontrol

Examples

query

 MATCH (n)-[r: GWAS_TO_VARIANT]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'name': 'rs2292238'},
   'n': {'access': 'public',
         'author': 'Neale',
         'category': 'NA',
         'consortium': 'Neale Lab',
         'id': 'ukb-a-287',
         'mr': '1',
         'note': 'NA',
         'nsnp': '10894596',
         'population': 'European',
         'priority': '1',
         'sample_size': '331164',
         'sex': 'Males and Females',
         'subcategory': 'NA',
         'trait': 'Arm fat mass (left)',
         'unit': 'SD',
         'year': '2017'},
   'r': {'beta': -0.014942600391805172,
         'eaf': 0.4086669981479645,
         'ncase': 0,
         'ncontrol': 0,
         'pval': 7.28215654444142e-10,
         'samplesize': 331164,
         'se': 0.0024257400073111057}},
  {'m': {'name': 'rs2292238'},
   'n': {'access': 'public',
         'author': 'Neale',
         'category': 'NA',
         'consortium': 'Neale Lab',
         'id': 'ukb-a-283',
         'mr': '1',
         'note': 'NA',
         'nsnp': '10894596',
         'population': 'European',
         'priority': '1',
         'sample_size': '331226',
         'sex': 'Males and Females',
         'subcategory': 'NA',
         'trait': 'Arm fat mass (right)',
         'unit': 'SD',
         'year': '2017'},
   'r': {'beta': -0.015376299619674683,
         'eaf': 0.4086669981479645,
         'ncase': 0,
         'ncontrol': 0,
         'pval': 2.291395267972618e-10,
         'samplesize': 331226,
         'se': 0.0024250398855656385}},
  {'m': {'name': 'rs2292238'},
   'n': {'access': 'public',
         'author': 'Neale',
         'category': 'NA',
         'consortium': 'Neale Lab',
         'id': 'ukb-a-279',
         'mr': '1',
         'note': 'NA',
         'nsnp': '10894596',
         'population': 'European',
         'priority': '1',
         'sample_size': '331275',
         'sex': 'Males and Females',
         'subcategory': 'NA',
         'trait': 'Leg fat mass (left)',
         'unit': 'SD',
         'year': '2017'},
   'r': {'beta': -0.012259099632501602,
         'eaf': 0.4086669981479645,
         'ncase': 0,
         'ncontrol': 0,
         'pval': 3.686803640157166e-10,
         'samplesize': 331275,
         'se': 0.001956149935722351}}]

INTACT_INTERACTS_WITH_GENE_GENE

(Gene)-(Gene) interactions from IntAct (www.ebi.ac.uk/intact/). Further details in IntAct reference manual (https://www.ebi.ac.uk/intact/resources/curation_manual)

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

Properties:

- intact_confidence_score: IntAct confidence score.

- intact_detection_method: Method used to detect the interaction.

- intact_type: Type of interaction.

- intact_source

- intact_identifier: IntAct identifier.

Examples

query

 MATCH (n)-[r: INTACT_INTERACTS_WITH_GENE_GENE]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'chr': '2',
         'description': 'BCL2-like 11 (apoptosis facilitator) [Source:HGNC '
                        'Symbol;Acc:994]',
         'end': 111926024,
         'ensembl_id': 'ENSG00000153094',
         'name': 'BCL2L11',
         'reactome_id': '8870690',
         'source': 'HGNC Symbol',
         'start': 111876955,
         'type': 'protein_coding'},
   'n': {'adme_gene': 'N',
         'bio_druggable': 'Y',
         'chr': '1',
         'description': 'Fas ligand (TNF superfamily, member 6) [Source:HGNC '
                        'Symbol;Acc:11936]',
         'druggability_tier': 'Tier 3B',
         'end': 172636014,
         'ensembl_id': 'ENSG00000117560',
         'name': 'FASLG',
         'reactome_id': '12230991',
         'small_mol_druggable': 'N',
         'source': 'HGNC Symbol',
         'start': 172628154,
         'type': 'protein_coding'},
   'r': {'intact_confidence_score': 0.44,
         'intact_detection_method': ['electrophoretic mobility shift assay'],
         'intact_identifier': ['EBI-15098237', 'EBI-15098258'],
         'intact_source': ['NTNU'],
         'intact_type': ['direct interaction']}},
  {'m': {'adme_gene': 'N',
         'bio_druggable': 'Y',
         'chr': '1',
         'description': 'Fas ligand (TNF superfamily, member 6) [Source:HGNC '
                        'Symbol;Acc:11936]',
         'druggability_tier': 'Tier 3B',
         'end': 172636014,
         'ensembl_id': 'ENSG00000117560',
         'name': 'FASLG',
         'reactome_id': '12230991',
         'small_mol_druggable': 'N',
         'source': 'HGNC Symbol',
         'start': 172628154,
         'type': 'protein_coding'},
   'n': {'chr': '2',
         'description': 'BCL2-like 11 (apoptosis facilitator) [Source:HGNC '
                        'Symbol;Acc:994]',
         'end': 111926024,
         'ensembl_id': 'ENSG00000153094',
         'name': 'BCL2L11',
         'reactome_id': '8870690',
         'source': 'HGNC Symbol',
         'start': 111876955,
         'type': 'protein_coding'},
   'r': {'intact_confidence_score': 0.44,
         'intact_detection_method': ['electrophoretic mobility shift assay'],
         'intact_identifier': ['EBI-15098237', 'EBI-15098258'],
         'intact_source': ['NTNU'],
         'intact_type': ['direct interaction']}},
  {'m': {'adme_gene': 'N',
         'bio_druggable': 'Y',
         'chr': '1',
         'description': 'Fas ligand (TNF superfamily, member 6) [Source:HGNC '
                        'Symbol;Acc:11936]',
         'druggability_tier': 'Tier 3B',
         'end': 172636014,
         'ensembl_id': 'ENSG00000117560',
         'name': 'FASLG',
         'reactome_id': '12230991',
         'small_mol_druggable': 'N',
         'source': 'HGNC Symbol',
         'start': 172628154,
         'type': 'protein_coding'},
   'n': {'adme_gene': 'N',
         'bio_druggable': 'Y',
         'chr': '1',
         'description': 'Fas ligand (TNF superfamily, member 6) [Source:HGNC '
                        'Symbol;Acc:11936]',
         'druggability_tier': 'Tier 3B',
         'end': 172636014,
         'ensembl_id': 'ENSG00000117560',
         'name': 'FASLG',
         'reactome_id': '12230991',
         'small_mol_druggable': 'N',
         'source': 'HGNC Symbol',
         'start': 172628154,
         'type': 'protein_coding'},
   'r': {'intact_confidence_score': 0.44,
         'intact_detection_method': ['electrophoretic mobility shift assay'],
         'intact_identifier': ['EBI-15098218'],
         'intact_source': ['NTNU'],
         'intact_type': ['direct interaction']}}]

INTACT_INTERACTS_WITH_GENE_PROTEIN

(Gene)-(Gene) interactions from IntAct (www.ebi.ac.uk/intact/). Further details in IntAct reference manual (https://www.ebi.ac.uk/intact/resources/curation_manual)

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

Properties:

- intact_confidence_score: IntAct confidence score.

- intact_detection_method: Method used to detect the interaction.

- intact_type: Type of interaction.

- intact_source

- intact_identifier: IntAct identifier.

Examples

query

 MATCH (n)-[r: INTACT_INTERACTS_WITH_GENE_PROTEIN]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'adme_gene': 'N',
         'bio_druggable': 'N',
         'chr': '2',
         'description': 'ribonuclease H1 [Source:HGNC Symbol;Acc:18466]',
         'druggability_tier': 'Tier 2',
         'end': 3606206,
         'ensembl_id': 'ENSG00000171865',
         'name': 'RNASEH1',
         'small_mol_druggable': 'Y',
         'source': 'HGNC Symbol',
         'start': 3592383,
         'type': 'protein_coding'},
   'n': {'uniprot_id': 'Q13620'},
   'r': {'intact_confidence_score': 0.35,
         'intact_detection_method': ['chromatin immunoprecipitation assay'],
         'intact_identifier': ['EBI-6469059'],
         'intact_source': ['IntAct'],
         'intact_type': ['association']}},
  {'m': {'adme_gene': 'N',
         'bio_druggable': 'N',
         'chr': '2',
         'description': 'ribonuclease H1 [Source:HGNC Symbol;Acc:18466]',
         'druggability_tier': 'Tier 2',
         'end': 3606206,
         'ensembl_id': 'ENSG00000171865',
         'name': 'RNASEH1',
         'small_mol_druggable': 'Y',
         'source': 'HGNC Symbol',
         'start': 3592383,
         'type': 'protein_coding'},
   'n': {'uniprot_id': 'Q15910'},
   'r': {'intact_confidence_score': 0.35,
         'intact_detection_method': ['chromatin immunoprecipitation assay'],
         'intact_identifier': ['EBI-6469091'],
         'intact_source': ['IntAct'],
         'intact_type': ['association']}},
  {'m': {'chr': '17',
         'description': 'homeobox B5 [Source:HGNC Symbol;Acc:5116]',
         'end': 46671323,
         'ensembl_id': 'ENSG00000120075',
         'name': 'HOXB5',
         'source': 'HGNC Symbol',
         'start': 46668619,
         'type': 'protein_coding'},
   'n': {'uniprot_id': 'P25963'},
   'r': {'intact_confidence_score': 0.35,
         'intact_detection_method': ['chromatin immunoprecipitation assay'],
         'intact_identifier': ['EBI-6930221'],
         'intact_source': ['IntAct'],
         'intact_type': ['association']}}]

INTACT_INTERACTS_WITH_PROTEIN_PROTEIN

(Protein)-(Protein) interactions from IntAct (www.ebi.ac.uk/intact/). Further details in IntAct reference manual (https://www.ebi.ac.uk/intact/resources/curation_manual)

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

Properties:

- intact_confidence_score: IntAct confidence score.

- intact_detection_method: Method used to detect the interaction.

- intact_type: Type of interaction.

- intact_source

- intact_identifier: IntAct identifier.

Examples

query

 MATCH (n)-[r: INTACT_INTERACTS_WITH_PROTEIN_PROTEIN]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'uniprot_id': 'Q93073'},
   'n': {'uniprot_id': 'Q9H871'},
   'r': {'intact_confidence_score': 0.51,
         'intact_detection_method': ['inference by socio-affinity scoring',
                                     'tandem affinity purification'],
         'intact_identifier': ['EBI-11931838', 'EBI-12452026'],
         'intact_source': ['IntAct'],
         'intact_type': ['physical association', 'association']}},
  {'m': {'uniprot_id': 'Q93073'},
   'n': {'uniprot_id': 'Q96FJ2'},
   'r': {'intact_confidence_score': 0.56,
         'intact_detection_method': ['validated two hybrid',
                                     'two hybrid array',
                                     'two hybrid prey pooling approach'],
         'intact_identifier': ['EBI-10602060', 'EBI-10439739', 'EBI-10286044'],
         'intact_source': ['IntAct'],
         'intact_type': ['physical association']}},
  {'m': {'uniprot_id': 'Q93073'},
   'n': {'uniprot_id': 'P63167'},
   'r': {'intact_confidence_score': 0.35,
         'intact_detection_method': ['anti tag coimmunoprecipitation'],
         'intact_identifier': ['EBI-11051725'],
         'intact_source': ['IntAct'],
         'intact_type': ['association']}}]

INTACT_NOT_INTERACTS_WITH

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

Properties:

- intact_confidence_score: IntAct confidence score.

- intact_detection_method: Method used to detect the interaction.

- intact_type: Type of interaction.

- intact_source

- intact_identifier: IntAct identifier.

Examples

query

 MATCH (n)-[r: INTACT_NOT_INTERACTS_WITH]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'uniprot_id': 'Q96K21'},
   'n': {'uniprot_id': 'A0A0S2Z4M1'},
   'r': {'intact_confidence_score': 0.37,
         'intact_detection_method': ['two hybrid array'],
         'intact_identifier': ['EBI-16464481'],
         'intact_source': ['IntAct'],
         'intact_type': ['physical association']}},
  {'m': {'uniprot_id': 'Q9Y3P9'},
   'n': {'uniprot_id': 'P05107'},
   'r': {'intact_confidence_score': 0.44,
         'intact_detection_method': ['pull down'],
         'intact_identifier': ['EBI-8609949'],
         'intact_source': ['MINT'],
         'intact_type': ['direct interaction']}},
  {'m': {'uniprot_id': 'Q8WW34'},
   'n': {'uniprot_id': 'P04271'},
   'r': {'intact_confidence_score': 0.37,
         'intact_detection_method': ['two hybrid array'],
         'intact_identifier': ['EBI-16473652'],
         'intact_source': ['IntAct'],
         'intact_type': ['physical association']}}]

METAMAP_LITE

Mapping between Gwas and SemmedTerm via MetaMap Lite.

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

Properties:

- mmi_score: MetaMap Indexing (MMI) score with a maximum score of 1000.00. The higher the score, the greater the relevance of the UMLS concept according to the MMI algorithm.

Examples

query

 MATCH (n)-[r: METAMAP_LITE]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'access': 'public',
         'author': 'Deloukas',
         'category': 'Disease',
         'consortium': 'NA',
         'id': 'ieu-a-9',
         'mr': '1',
         'ncase': '63746',
         'ncontrol': '130681',
         'nsnp': '79129',
         'pmid': '23202125',
         'population': 'Mixed',
         'priority': '1',
         'sample_size': '194427',
         'sex': 'Males and Females',
         'subcategory': 'Cardiovascular',
         'trait': 'Coronary heart disease',
         'unit': 'NA',
         'year': '2013'},
   'n': {'count': 9827,
         'id': 'C0010068',
         'name': 'Coronary heart disease',
         'type': 'dsyn'},
   'r': {'mmi_score': 3.75}},
  {'m': {'access': 'public',
         'author': 'Deloukas',
         'category': 'Disease',
         'consortium': 'NA',
         'id': 'ieu-a-9',
         'mr': '1',
         'ncase': '63746',
         'ncontrol': '130681',
         'nsnp': '79129',
         'pmid': '23202125',
         'population': 'Mixed',
         'priority': '1',
         'sample_size': '194427',
         'sex': 'Males and Females',
         'subcategory': 'Cardiovascular',
         'trait': 'Coronary heart disease',
         'unit': 'NA',
         'year': '2013'},
   'n': {'count': 14865,
         'id': 'C0010054',
         'name': 'Coronary Arteriosclerosis',
         'type': 'dsyn'},
   'r': {'mmi_score': 3.75}},
  {'m': {'access': 'public',
         'author': 'Sun BB',
         'category': 'Immune system',
         'consortium': 'NA',
         'id': 'prot-a-7',
         'mr': '1',
         'note': 'NA',
         'nsnp': '10534735',
         'pmid': '29875488',
         'population': 'European',
         'priority': '0',
         'sample_size': '3301',
         'sex': 'Males and Females',
         'subcategory': 'Protein',
         'trait': 'Tyrosine-protein kinase ABL1',
         'unit': 'NA',
         'year': '2018'},
   'n': {'count': 39107,
         'id': 'C0031727',
         'name': 'Phosphotransferases',
         'type': 'gngm'},
   'r': {'mmi_score': 1.899999976158142}}]

MONDO_MAP_EFO

Mapping between a (Disease) term and an (Efo) ontology term, based on Mondo.

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

Examples

query

 MATCH (n)-[r: MONDO_MAP_EFO]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'definition': 'A melanoma characterized by the complete absence of '
                       'melanin pigment in the melanoma cells. It occurs more '
                       'frequently on the face and it is often associated with '
                       'desmoplastic reaction.',
         'doid': ['4359'],
         'efo': ['1001937'],
         'icd10': ['NA'],
         'icd9': ['NA'],
         'id': 'http://purl.obolibrary.org/obo/MONDO_0002971',
         'label': 'amelanotic melanoma',
         'mesh': ['D018328'],
         'umls': ['C0206735']},
   'n': {'id': 'http://www.ebi.ac.uk/efo/EFO_1001937',
         'type': 'typed-literal',
         'value': 'amelanotic melanoma'},
   'r': {}},
  {'m': {'definition': 'NA',
         'doid': ['NA'],
         'efo': ['0009158'],
         'icd10': ['NA'],
         'icd9': ['NA'],
         'id': 'http://purl.obolibrary.org/obo/MONDO_0014960',
         'label': 'encephalopathy, progressive, early-onset, with brain edema '
                  'and/or leukoencephalopathy',
         'mesh': ['NA'],
         'umls': ['C4310675']},
   'n': {'id': 'http://www.ebi.ac.uk/efo/EFO_0009158',
         'type': 'typed-literal',
         'value': 'encephalopathy, progressive, early-onset, with brain edema '
                  'and/or leukoencephalopathy'},
   'r': {}},
  {'m': {'definition': 'A condition in which the ocular image of an object as '
                       'seen by one eye differs in size and shape from that '
                       'seen by the other.',
         'doid': ['0050304'],
         'efo': ['1001266'],
         'icd10': ['H52.32'],
         'icd9': ['367.32'],
         'id': 'http://purl.obolibrary.org/obo/MONDO_0000309',
         'label': 'aniseikonia',
         'mesh': ['D000839'],
         'umls': ['NA']},
   'n': {'id': 'http://www.ebi.ac.uk/efo/EFO_1001266',
         'type': 'typed-literal',
         'value': 'Aniseikonia'},
   'r': {}}]

MONDO_MAP_UMLS

Mapping between a (Disease) term and an (SemmedTerm) term, based on Mondo.

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

Examples

query

 MATCH (n)-[r: MONDO_MAP_UMLS]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'definition': 'A hordeolum that results from obstruction and infection '
                       'of an eyelash follicle and adjacent glands of Zeis or '
                       'Moll glands. Follicle obstruction may be associated '
                       'with blepharitis.',
         'doid': ['13134'],
         'efo': ['NA'],
         'icd10': ['H00.03', 'H00.01'],
         'icd9': ['373.11'],
         'id': 'http://purl.obolibrary.org/obo/MONDO_0001642',
         'label': 'hordeolum externum',
         'mesh': ['NA'],
         'umls': ['C0019919']},
   'n': {'count': 1,
         'id': 'C0019919',
         'name': 'Hordeolum externum',
         'type': 'dsyn'},
   'r': {}},
  {'m': {'definition': 'A disorder characterized by the degeneration of the '
                       'nervous system due to autoimmunity. Representative '
                       'examples include multiple sclerosis, Guillain-Barre '
                       'syndrome, and myasthenia gravis.',
         'doid': ['438'],
         'efo': ['NA'],
         'icd10': ['NA'],
         'icd9': ['NA'],
         'id': 'http://purl.obolibrary.org/obo/MONDO_0002977',
         'label': 'autoimmune disease of the nervous system',
         'mesh': ['D020274'],
         'umls': ['C0751871', 'C0751872']},
   'n': {'count': 1,
         'id': 'C0751872',
         'name': 'Immune Disorders, Nervous System',
         'type': 'dsyn'},
   'r': {}},
  {'m': {'definition': 'A disorder characterized by the degeneration of the '
                       'nervous system due to autoimmunity. Representative '
                       'examples include multiple sclerosis, Guillain-Barre '
                       'syndrome, and myasthenia gravis.',
         'doid': ['438'],
         'efo': ['NA'],
         'icd10': ['NA'],
         'icd9': ['NA'],
         'id': 'http://purl.obolibrary.org/obo/MONDO_0002977',
         'label': 'autoimmune disease of the nervous system',
         'mesh': ['D020274'],
         'umls': ['C0751871', 'C0751872']},
   'n': {'count': 5,
         'id': 'C0751871',
         'name': 'Autoimmune Diseases of the Nervous System',
         'type': 'dsyn'},
   'r': {}}]

MR

Pairwise Mendelian randomization evidence between phenotypic traits. Results from MR-EvE (Hemani et al., 2017).

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

Properties:

- method: MR method, e.g. FE IVW etc.

- nsnp: Number of SNPs.

- b: Effect size.

- se: Standard error.

- ci_low: Lower bound of the confidence interval.

- ci_upp: Upper bound of the confidence interval.

- pval: P-value.

- selection

- moescore: Mix of Experts score.

- log10pval: log10 transformed P-Value.

Examples

query

 MATCH (n)-[r: MR]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'access': 'public',
         'author': 'Rietveld CA',
         'category': 'Risk factor',
         'consortium': 'NA',
         'id': 'ieu-a-836',
         'mr': '1',
         'ncase': '20044',
         'ncontrol': '75383',
         'nsnp': '2321511',
         'pmid': '23722424',
         'population': 'European',
         'priority': '1',
         'sample_size': '95427',
         'sex': 'Males and Females',
         'subcategory': 'Education',
         'trait': 'College completion',
         'unit': 'NA',
         'year': '2013'},
   'n': {'access': 'public',
         'author': 'Neale',
         'category': 'NA',
         'consortium': 'Neale Lab',
         'id': 'ukb-a-99',
         'mr': '1',
         'ncase': '8718',
         'ncontrol': '328441',
         'note': 'NA',
         'nsnp': '10894596',
         'population': 'European',
         'priority': '1',
         'sample_size': '337159',
         'sex': 'Males and Females',
         'subcategory': 'NA',
         'trait': 'Non-cancer illness code  self-reported: eczema/dermatitis',
         'unit': 'SD',
         'year': '2017'},
   'r': {'b': 0.006043282803148031,
         'ci_low': 0.00028298949473537505,
         'ci_upp': 0.011803575791418552,
         'log10pval': 1.0,
         'method': 'FE IVW',
         'moescore': 1.0,
         'nsnp': 3,
         'pval': 0.039754558354616165,
         'se': 0.0029389250557869673,
         'selection': 'DF'}},
  {'m': {'access': 'public',
         'author': 'Rietveld CA',
         'category': 'Risk factor',
         'consortium': 'NA',
         'id': 'ieu-a-836',
         'mr': '1',
         'ncase': '20044',
         'ncontrol': '75383',
         'nsnp': '2321511',
         'pmid': '23722424',
         'population': 'European',
         'priority': '1',
         'sample_size': '95427',
         'sex': 'Males and Females',
         'subcategory': 'Education',
         'trait': 'College completion',
         'unit': 'NA',
         'year': '2013'},
   'n': {'access': 'public',
         'author': 'Neale',
         'category': 'NA',
         'consortium': 'Neale Lab',
         'id': 'ukb-a-98',
         'mr': '1',
         'ncase': '118',
         'ncontrol': '337041',
         'note': 'NA',
         'nsnp': '10894596',
         'population': 'European',
         'priority': '1',
         'sample_size': '337159',
         'sex': 'Males and Females',
         'subcategory': 'NA',
         'trait': 'Non-cancer illness code  self-reported: hypopituitarism',
         'unit': 'SD',
         'year': '2017'},
   'r': {'b': -0.0003202843072358519,
         'ci_low': -0.0005827635759487748,
         'ci_upp': -5.780507126473822e-05,
         'log10pval': 2.0,
         'method': 'FE IVW',
         'moescore': 1.0,
         'nsnp': 3,
         'pval': 0.01677304320037365,
         'se': 0.00013391798711381853,
         'selection': 'DF'}},
  {'m': {'access': 'public',
         'author': 'Rietveld CA',
         'category': 'Risk factor',
         'consortium': 'NA',
         'id': 'ieu-a-836',
         'mr': '1',
         'ncase': '20044',
         'ncontrol': '75383',
         'nsnp': '2321511',
         'pmid': '23722424',
         'population': 'European',
         'priority': '1',
         'sample_size': '95427',
         'sex': 'Males and Females',
         'subcategory': 'Education',
         'trait': 'College completion',
         'unit': 'NA',
         'year': '2013'},
   'n': {'access': 'public',
         'author': 'Neale',
         'category': 'NA',
         'consortium': 'Neale Lab',
         'id': 'ukb-a-97',
         'mr': '1',
         'ncase': '1489',
         'ncontrol': '335670',
         'note': 'NA',
         'nsnp': '10894596',
         'population': 'European',
         'priority': '1',
         'sample_size': '337159',
         'sex': 'Males and Females',
         'subcategory': 'NA',
         'trait': 'Non-cancer illness code  self-reported: nasal polyps',
         'unit': 'SD',
         'year': '2017'},
   'r': {'b': -0.00105505611281842,
         'ci_low': -0.002489469014108181,
         'ci_upp': 0.00037935684667900205,
         'log10pval': 1.0,
         'method': 'FE IVW',
         'moescore': 1.0,
         'nsnp': 3,
         'pval': 0.1494033932685852,
         'se': 0.000731843349058181,
         'selection': 'DF'}}]

OBS_COR

Pairwise Spearman rank correlation for UK Biobank (Gwas) (ukb-b). Results in-house by Benjamin Elsworth.

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

Properties:

- cor: Correlation coefficient.

Examples

query

 MATCH (n)-[r: OBS_COR]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'access': 'public',
         'author': 'Ben Elsworth',
         'category': 'Categorical Ordered',
         'consortium': 'MRC-IEU',
         'id': 'ukb-b-2035',
         'mr': '1',
         'note': '102020: Output from GWAS pipeline using Phesant derived '
                 'variables from UKBiobank',
         'nsnp': '9851867',
         'population': 'European',
         'priority': '1',
         'sample_size': '64949',
         'sex': 'Males and Females',
         'subcategory': 'NA',
         'trait': 'Scotch pancake intake',
         'unit': 'SD',
         'year': '2018'},
   'n': {'access': 'public',
         'author': 'Ben Elsworth',
         'category': 'Binary',
         'consortium': 'MRC-IEU',
         'id': 'ukb-b-57',
         'mr': '1',
         'ncase': '8022',
         'ncontrol': '56927',
         'note': '20090#354: Output from GWAS pipeline using Phesant derived '
                 'variables from UKBiobank',
         'nsnp': '9851867',
         'population': 'European',
         'priority': '1',
         'sample_size': '64949',
         'sex': 'Males and Females',
         'subcategory': 'NA',
         'trait': 'Type of fat/oil used in cooking: Sunflower oil',
         'unit': 'SD',
         'year': '2018'},
   'r': {'cor': 0.7267494201660156}},
  {'m': {'access': 'public',
         'author': 'Ben Elsworth',
         'category': 'Categorical Ordered',
         'consortium': 'MRC-IEU',
         'id': 'ukb-b-2035',
         'mr': '1',
         'note': '102020: Output from GWAS pipeline using Phesant derived '
                 'variables from UKBiobank',
         'nsnp': '9851867',
         'population': 'European',
         'priority': '1',
         'sample_size': '64949',
         'sex': 'Males and Females',
         'subcategory': 'NA',
         'trait': 'Scotch pancake intake',
         'unit': 'SD',
         'year': '2018'},
   'n': {'access': 'public',
         'author': 'Ben Elsworth',
         'category': 'Categorical Ordered',
         'consortium': 'MRC-IEU',
         'id': 'ukb-b-5627',
         'mr': '1',
         'note': '102070: Output from GWAS pipeline using Phesant derived '
                 'variables from UKBiobank',
         'nsnp': '9851867',
         'population': 'European',
         'priority': '1',
         'sample_size': '64949',
         'sex': 'Males and Females',
         'subcategory': 'NA',
         'trait': 'Scone intake',
         'unit': 'SD',
         'year': '2018'},
   'r': {'cor': 0.9074811339378357}},
  {'m': {'access': 'public',
         'author': 'Ben Elsworth',
         'category': 'Categorical Ordered',
         'consortium': 'MRC-IEU',
         'id': 'ukb-b-2035',
         'mr': '1',
         'note': '102020: Output from GWAS pipeline using Phesant derived '
                 'variables from UKBiobank',
         'nsnp': '9851867',
         'population': 'European',
         'priority': '1',
         'sample_size': '64949',
         'sex': 'Males and Females',
         'subcategory': 'NA',
         'trait': 'Scotch pancake intake',
         'unit': 'SD',
         'year': '2018'},
   'n': {'access': 'public',
         'author': 'Ben Elsworth',
         'category': 'Categorical Ordered',
         'consortium': 'MRC-IEU',
         'id': 'ukb-b-5605',
         'mr': '1',
         'note': '102030: Output from GWAS pipeline using Phesant derived '
                 'variables from UKBiobank',
         'nsnp': '9851867',
         'population': 'European',
         'priority': '1',
         'sample_size': '64949',
         'sex': 'Males and Females',
         'subcategory': 'NA',
         'trait': 'Yorkshire pudding intake',
         'unit': 'SD',
         'year': '2018'},
   'r': {'cor': 0.9347252249717712}}]

OPENTARGETS_DRUG_TO_DISEASE

The association evidence of a (Drug) in the treatment of a (Disease) from Open Targets.

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

Examples

query

 MATCH (n)-[r: OPENTARGETS_DRUG_TO_DISEASE]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'definition': 'A sleep disorder characterized by difficulty in falling '
                       'asleep and/or remaining asleep.',
         'doid': ['NA'],
         'efo': ['0004698'],
         'icd10': ['G47.0'],
         'icd9': ['780.52'],
         'id': 'http://purl.obolibrary.org/obo/MONDO_0013600',
         'label': 'insomnia (disease)',
         'mesh': ['D007319'],
         'umls': ['NA']},
   'n': {'chembl_uri': 'http://identifiers.org/chembl.compound/CHEMBL2103791',
         'label': 'ADIPIPLON',
         'molecule_type': 'Small molecule',
         'source': ['CHEMBL']},
   'r': {}},
  {'m': {'definition': 'A sleep disorder characterized by difficulty in falling '
                       'asleep and/or remaining asleep.',
         'doid': ['NA'],
         'efo': ['0004698'],
         'icd10': ['G47.0'],
         'icd9': ['780.52'],
         'id': 'http://purl.obolibrary.org/obo/MONDO_0013600',
         'label': 'insomnia (disease)',
         'mesh': ['D007319'],
         'umls': ['NA']},
   'n': {'chembl_uri': 'http://identifiers.org/chembl.compound/CHEMBL74355',
         'label': 'VOLINANSERIN',
         'molecule_type': 'Small molecule',
         'source': ['CHEMBL']},
   'r': {}},
  {'m': {'definition': 'A sleep disorder characterized by difficulty in falling '
                       'asleep and/or remaining asleep.',
         'doid': ['NA'],
         'efo': ['0004698'],
         'icd10': ['G47.0'],
         'icd9': ['780.52'],
         'id': 'http://purl.obolibrary.org/obo/MONDO_0013600',
         'label': 'insomnia (disease)',
         'mesh': ['D007319'],
         'umls': ['NA']},
   'n': {'chembl_uri': 'http://identifiers.org/chembl.compound/CHEMBL1215661',
         'label': 'PRUVANSERIN',
         'molecule_type': 'Small molecule',
         'source': ['CHEMBL']},
   'r': {}}]

OPENTARGETS_DRUG_TO_TARGET

The association evidence of a (Drug) in the treatment of a target (Gene) from Open Targets.

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

Properties:

- phase: Phase of the target drug.

- action_type: Type of the mechanism, e.g. inhibitor, etc.

Examples

query

 MATCH (n)-[r: OPENTARGETS_DRUG_TO_TARGET]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'adme_gene': 'N',
         'bio_druggable': 'Y',
         'chr': '1',
         'description': 'Rh blood group, D antigen [Source:HGNC '
                        'Symbol;Acc:10009]',
         'druggability_tier': 'Tier 1',
         'end': 25656936,
         'ensembl_id': 'ENSG00000187010',
         'name': 'RHD',
         'small_mol_druggable': 'N',
         'source': 'HGNC Symbol',
         'start': 25598884,
         'type': 'protein_coding'},
   'n': {'chembl_uri': 'http://identifiers.org/chembl.compound/CHEMBL2107859',
         'label': 'ROZROLIMUPAB',
         'molecule_type': 'Unknown',
         'source': ['CHEMBL']},
   'r': {'action_type': 'INHIBITOR', 'phase': '2'}},
  {'m': {'adme_gene': 'N',
         'bio_druggable': 'Y',
         'chr': '1',
         'description': 'Rh blood group, D antigen [Source:HGNC '
                        'Symbol;Acc:10009]',
         'druggability_tier': 'Tier 1',
         'end': 25656936,
         'ensembl_id': 'ENSG00000187010',
         'name': 'RHD',
         'small_mol_druggable': 'N',
         'source': 'HGNC Symbol',
         'start': 25598884,
         'type': 'protein_coding'},
   'n': {'chembl_uri': 'http://identifiers.org/chembl.compound/CHEMBL1743065',
         'label': 'ROLEDUMAB',
         'molecule_type': 'Antibody',
         'source': ['CHEMBL']},
   'r': {'action_type': 'INHIBITOR', 'phase': '2'}},
  {'m': {'chr': '2',
         'description': 'proteasome (prosome, macropain) 26S subunit, '
                        'non-ATPase, 1 [Source:HGNC Symbol;Acc:9554]',
         'end': 232037541,
         'ensembl_id': 'ENSG00000173692',
         'name': 'PSMD1',
         'reactome_id': '8958517',
         'source': 'HGNC Symbol',
         'start': 231921578,
         'type': 'protein_coding'},
   'n': {'chembl_uri': 'http://identifiers.org/chembl.compound/CHEMBL2103884',
         'label': 'OPROZOMIB',
         'molecule_type': 'Small molecule',
         'source': ['CHEMBL']},
   'r': {'action_type': 'INHIBITOR', 'phase': '1'}}]

PATHWAY_TO_DISEASE

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

Examples

query

 MATCH (n)-[r: PATHWAY_TO_DISEASE]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'definition': 'NA',
         'doid': ['0050338'],
         'efo': ['NA'],
         'icd10': ['NA'],
         'icd9': ['NA'],
         'id': 'http://purl.obolibrary.org/obo/MONDO_0000314',
         'label': 'primary bacterial infectious disease',
         'mesh': ['NA'],
         'umls': ['NA']},
   'n': {'in_disease': 'TRUE',
         'name': 'Uptake and actions of bacterial toxins',
         'reactome_id': 'R-HSA-5339562'},
   'r': {}},
  {'m': {'definition': 'Lower than normal levels of phosphates in the '
                       'circulating blood.',
         'doid': ['0050336'],
         'efo': ['NA'],
         'icd10': ['NA'],
         'icd9': ['NA'],
         'id': 'http://purl.obolibrary.org/obo/MONDO_0000313',
         'label': 'hypophosphatemia (disease)',
         'mesh': ['D017674'],
         'umls': ['C0085682']},
   'n': {'in_disease': 'TRUE',
         'name': 'Defective SLC34A1 causes hypophosphatemic '
                 'nephrolithiasis/osteoporosis 1 (NPHLOP1)',
         'reactome_id': 'R-HSA-5619040'},
   'r': {}},
  {'m': {'definition': 'Spondylocostal dysplasia is a rare genetic disorder '
                       'characterized by defects of the bones of the spine '
                       '(vertebrae) and abnormalities of the ribs. Ribs can be '
                       'fused or missing in chaotic patterns. These '
                       'malformations are present at birth (congenital).',
         'doid': ['0050568'],
         'efo': ['NA'],
         'icd10': ['NA'],
         'icd9': ['NA'],
         'id': 'http://purl.obolibrary.org/obo/MONDO_0000359',
         'label': 'spondylocostal dysostosis',
         'mesh': ['C537565'],
         'umls': ['CN201467']},
   'n': {'in_disease': 'TRUE',
         'name': 'Defective LFNG causes SCDO3',
         'reactome_id': 'R-HSA-5083630'},
   'r': {}}]

PATHWAY_TO_LITERATURE

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

Examples

query

 MATCH (n)-[r: PATHWAY_TO_LITERATURE]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'dp': '2003 Aug 01',
         'edat': '2003-6-28',
         'issn': '0021-9533',
         'pubmed_id': '12829738',
         'year': 2003},
   'n': {'in_disease': 'FALSE',
         'name': 'Oligomerization of connexins into connexons',
         'reactome_id': 'R-HSA-190704'},
   'r': {}},
  {'m': {'dp': '2003 Jul 25',
         'edat': '2003-5-10',
         'issn': '0021-9258',
         'pubmed_id': '12738770',
         'year': 2003},
   'n': {'in_disease': 'FALSE',
         'name': 'Regulation of RUNX2 expression and activity',
         'reactome_id': 'R-HSA-8939902'},
   'r': {}},
  {'m': {'dp': '1999 Mar 08',
         'edat': '1999-3-23',
         'issn': '0021-9525',
         'pubmed_id': '10085299',
         'year': 1999},
   'n': {'in_disease': 'FALSE',
         'name': 'c-src mediated regulation of Cx43 function and closure of gap '
                 'junctions',
         'reactome_id': 'R-HSA-191647'},
   'r': {}}]

PRECEDING_EVENT

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

Examples

query

 MATCH (n)-[r: PRECEDING_EVENT]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'in_disease': 'FALSE',
         'name': 'CYP21A2 oxidises 17HPROG',
         'reactome_id': 'R-HSA-193981'},
   'n': {'in_disease': 'FALSE',
         'name': 'Pregn-5-ene-3,20-dione-17-ol isomerizes to '
                 '17-hydroxyprogesterone',
         'reactome_id': 'R-HSA-193961'},
   'r': {}},
  {'m': {'in_disease': 'FALSE',
         'name': 'CYP21A2 oxidises 17HPROG',
         'reactome_id': 'R-HSA-193981'},
   'n': {'in_disease': 'FALSE',
         'name': '11-deoxycortisol translocates to the mitochondrion',
         'reactome_id': 'R-HSA-194025'},
   'r': {}},
  {'m': {'in_disease': 'FALSE',
         'name': '11-deoxycortisol translocates to the mitochondrion',
         'reactome_id': 'R-HSA-194025'},
   'n': {'in_disease': 'FALSE',
         'name': 'CYP11B1 oxidises 11DCORT',
         'reactome_id': 'R-HSA-193997'},
   'r': {}}]

PROTEIN_IN_EVENT

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

Examples

query

 MATCH (n)-[r: PROTEIN_IN_EVENT]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'uniprot_id': 'Q8NGB6'},
   'n': {'in_disease': 'FALSE',
         'name': 'Olfactory Receptor - G Protein olfactory trimer complex '
                 'formation',
         'reactome_id': 'R-HSA-381750'},
   'r': {}},
  {'m': {'uniprot_id': 'Q8N0Y3'},
   'n': {'in_disease': 'FALSE',
         'name': 'Olfactory Receptor - G Protein olfactory trimer complex '
                 'formation',
         'reactome_id': 'R-HSA-381750'},
   'r': {}},
  {'m': {'uniprot_id': 'P48552'},
   'n': {'in_disease': 'FALSE',
         'name': 'RORA,EP300,PPARGC1A bind NR1D1 gene',
         'reactome_id': 'R-HSA-5663273'},
   'r': {}}]

PROTEIN_TO_DISEASE

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

Examples

query

 MATCH (n)-[r: PROTEIN_TO_DISEASE]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'uniprot_id': 'Q15796'},
   'n': {'definition': 'Primary or metastatic malignant neoplasm involving the '
                       'kidney.',
         'doid': ['263'],
         'efo': ['NA'],
         'icd10': ['C64'],
         'icd9': ['189.0'],
         'id': 'http://purl.obolibrary.org/obo/MONDO_0002367',
         'label': 'kidney cancer',
         'mesh': ['D007680'],
         'umls': ['CN881103']},
   'r': {}},
  {'m': {'uniprot_id': 'Q15796'},
   'n': {'definition': 'A malignant neoplasm involving the lung.',
         'doid': ['1324'],
         'efo': ['NA'],
         'icd10': ['C34.3', 'C34.2', 'C34.1'],
         'icd9': ['162.5', '162.4', '162.3', '162.9', '162.8'],
         'id': 'http://purl.obolibrary.org/obo/MONDO_0008903',
         'label': 'lung cancer',
         'mesh': ['NA'],
         'umls': ['NA']},
   'r': {}},
  {'m': {'uniprot_id': 'Q15796'},
   'n': {'definition': 'A tumor composed of atypical neoplastic, often '
                       'pleomorphic cells that invade other tissues. Malignant '
                       'neoplasms often metastasize to distant anatomic sites '
                       'and may recur after excision. The most common malignant '
                       'neoplasms are carcinomas (adenocarcinomas or squamous '
                       'cell carcinomas), Hodgkin and non-Hodgkin lymphomas, '
                       'leukemias, melanomas, and sarcomas.',
         'doid': ['162', '0050687', '0050686'],
         'efo': ['0000311'],
         'icd10': ['C80.1', 'C80'],
         'icd9': ['195.8', '199.1', '199'],
         'id': 'http://purl.obolibrary.org/obo/MONDO_0004992',
         'label': 'cancer',
         'mesh': ['NA'],
         'umls': ['C0006826']},
   'r': {}}]

PROTEIN_TO_LITERATURE

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

Examples

query

 MATCH (n)-[r: PROTEIN_TO_LITERATURE]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'uniprot_id': 'Q93073'},
   'n': {'dp': '2015 Oct 22',
         'edat': '2015-10-27',
         'issn': '1097-4172',
         'pubmed_id': '26496610',
         'year': 2015},
   'r': {}},
  {'m': {'uniprot_id': 'Q93073'},
   'n': {'dp': '2018 Oct',
         'edat': '2018-7-20',
         'issn': '1535-9484',
         'pubmed_id': '30021884',
         'year': 2018},
   'r': {}},
  {'m': {'uniprot_id': 'Q93073'},
   'n': {'dp': '2014 Nov 20',
         'edat': '2014-11-24',
         'issn': '1097-4172',
         'pubmed_id': '25416956',
         'year': 2014},
   'r': {}}]

PROTEIN_IN_PATHWAY

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

Examples

query

 MATCH (n)-[r: PROTEIN_IN_PATHWAY]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'uniprot_id': 'Q8NGB6'},
   'n': {'in_disease': 'FALSE',
         'name': 'Olfactory Signaling Pathway',
         'reactome_id': 'R-HSA-381753'},
   'r': {}},
  {'m': {'uniprot_id': 'Q8N0Y3'},
   'n': {'in_disease': 'FALSE',
         'name': 'Olfactory Signaling Pathway',
         'reactome_id': 'R-HSA-381753'},
   'r': {}},
  {'m': {'uniprot_id': 'P48552'},
   'n': {'in_disease': 'FALSE',
         'name': 'Circadian Clock',
         'reactome_id': 'R-HSA-400253'},
   'r': {}}]

PRS

Pairwise polygenic risk scores between GWAS. Results from PRS Atlas ( Richardson et al., 2019 ).

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

Properties:

- nsnps: Number of SNPs.

- model: Name of the model used, e.g. lm, glm, etc.

- beta: Effect size.

- se: Standard error.

- p: P-value.

- r2: R2 metric.

- n: Sample size.

Examples

query

 MATCH (n)-[r: PRS]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'access': 'public',
         'author': 'Rietveld CA',
         'category': 'Risk factor',
         'consortium': 'NA',
         'id': 'ieu-a-836',
         'mr': '1',
         'ncase': '20044',
         'ncontrol': '75383',
         'nsnp': '2321511',
         'pmid': '23722424',
         'population': 'European',
         'priority': '1',
         'sample_size': '95427',
         'sex': 'Males and Females',
         'subcategory': 'Education',
         'trait': 'College completion',
         'unit': 'NA',
         'year': '2013'},
   'n': {'access': 'public',
         'author': 'Neale',
         'category': 'NA',
         'consortium': 'Neale Lab',
         'id': 'ukb-a-557',
         'mr': '1',
         'ncase': '9853',
         'ncontrol': '327346',
         'note': 'NA',
         'nsnp': '10894596',
         'population': 'European',
         'priority': '1',
         'sample_size': '337199',
         'sex': 'Males and Females',
         'subcategory': 'NA',
         'trait': 'Diagnoses - main ICD10: K62 Other diseases of anus and '
                  'rectum',
         'unit': 'SD',
         'year': '2017'},
   'r': {'beta': 0.00015730000450275838,
         'model': 'glm',
         'n': 334970,
         'nsnps': 117,
         'p': 0.9873520135879517,
         'r2': 0.043225452303886414,
         'se': 0.009922645054757595}},
  {'m': {'access': 'public',
         'author': 'Rietveld CA',
         'category': 'Risk factor',
         'consortium': 'NA',
         'id': 'ieu-a-836',
         'mr': '1',
         'ncase': '20044',
         'ncontrol': '75383',
         'nsnp': '2321511',
         'pmid': '23722424',
         'population': 'European',
         'priority': '1',
         'sample_size': '95427',
         'sex': 'Males and Females',
         'subcategory': 'Education',
         'trait': 'College completion',
         'unit': 'NA',
         'year': '2013'},
   'n': {'access': 'public',
         'author': 'Neale',
         'category': 'NA',
         'consortium': 'Neale Lab',
         'id': 'ukb-a-511',
         'mr': '1',
         'note': 'NA',
         'nsnp': '10894596',
         'population': 'European',
         'priority': '1',
         'sample_size': '321533',
         'sex': 'Males and Females',
         'subcategory': 'NA',
         'trait': 'Number of days/week of vigorous physical activity 10+ '
                  'minutes',
         'unit': 'SD',
         'year': '2017'},
   'r': {'beta': 6.549999670824036e-05,
         'model': 'lm',
         'n': 319417,
         'nsnps': 117,
         'p': 0.9846966862678528,
         'r2': 5.41000019893545e-07,
         'se': 0.003414108883589506}},
  {'m': {'access': 'public',
         'author': 'Rietveld CA',
         'category': 'Risk factor',
         'consortium': 'NA',
         'id': 'ieu-a-836',
         'mr': '1',
         'ncase': '20044',
         'ncontrol': '75383',
         'nsnp': '2321511',
         'pmid': '23722424',
         'population': 'European',
         'priority': '1',
         'sample_size': '95427',
         'sex': 'Males and Females',
         'subcategory': 'Education',
         'trait': 'College completion',
         'unit': 'NA',
         'year': '2013'},
   'n': {'access': 'public',
         'author': 'Ben Elsworth',
         'category': 'Categorical Ordered',
         'consortium': 'MRC-IEU',
         'id': 'ukb-b-151',
         'mr': '1',
         'note': '904: Output from GWAS pipeline using Phesant derived '
                 'variables from UKBiobank',
         'nsnp': '9851867',
         'population': 'European',
         'priority': '1',
         'sample_size': '440512',
         'sex': 'Males and Females',
         'subcategory': 'NA',
         'trait': 'Number of days/week of vigorous physical activity 10+ '
                  'minutes',
         'unit': 'SD',
         'year': '2018'},
   'r': {'beta': 6.549999670824036e-05,
         'model': 'lm',
         'n': 319417,
         'nsnps': 117,
         'p': 0.9846966862678528,
         'r2': 5.41000019893545e-07,
         'se': 0.003414108883589506}}]

SEM_GENE

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

Examples

query

 MATCH (n)-[r: SEM_GENE]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'chr': '13',
         'description': 'Small nucleolar RNA SNORD22 [Source:RFAM;Acc:RF00099]',
         'end': 94021213,
         'ensembl_id': 'ENSG00000252365',
         'name': 'SNORD22',
         'source': 'RFAM',
         'start': 94021100,
         'type': 'snoRNA'},
   'n': {'count': 1, 'id': '9304', 'name': 'SNORD22', 'type': 'gngm'},
   'r': {}},
  {'m': {'chr': '13',
         'description': 'SOX21 antisense RNA 1 (head to head) [Source:HGNC '
                        'Symbol;Acc:39807]',
         'end': 95368500,
         'ensembl_id': 'ENSG00000227640',
         'name': 'SOX21-AS1',
         'source': 'HGNC Symbol',
         'start': 95364970,
         'type': 'lincRNA'},
   'n': {'count': 5, 'id': '100507533', 'name': 'SOX21-AS1', 'type': 'gngm'},
   'r': {}},
  {'m': {'chr': '13',
         'description': 'DAOA antisense RNA 1 [Source:HGNC Symbol;Acc:30243]',
         'end': 106158030,
         'ensembl_id': 'ENSG00000232307',
         'name': 'DAOA-AS1',
         'source': 'HGNC Symbol',
         'start': 106111404,
         'type': 'antisense'},
   'n': {'count': 23, 'id': '282706', 'name': 'DAOA-AS1', 'type': 'gngm'},
   'r': {}}]

SEM_OBJ

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

Examples

query

 MATCH (n)-[r: SEM_OBJ]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'count': 3,
         'id': 'XS:PRODUCES:homocysteine',
         'object_id': 'C0019878',
         'object_name': 'homocysteine',
         'object_type': 'aapp',
         'predicate': 'PRODUCES',
         'subject_id': '7523',
         'subject_name': 'XS',
         'subject_type': 'gngm'},
   'n': {'count': 9746,
         'id': 'C0019878',
         'name': 'homocysteine',
         'type': 'aapp'},
   'r': {}},
  {'m': {'count': 12,
         'id': 'Genes:COEXISTS_WITH:Estrogens',
         'object_id': 'C0014939',
         'object_name': 'Estrogens',
         'object_type': 'horm',
         'predicate': 'COEXISTS_WITH',
         'subject_id': 'C0017337',
         'subject_name': 'Genes',
         'subject_type': 'gngm'},
   'n': {'count': 29126, 'id': 'C0014939', 'name': 'Estrogens', 'type': 'horm'},
   'r': {}},
  {'m': {'count': 2,
         'id': 'ESR2 gene|ESR2:INTERACTS_WITH:ESR1 gene|ESR1',
         'object_id': 'C1414461|2099',
         'object_name': 'ESR1 gene|ESR1',
         'object_type': 'gngm',
         'predicate': 'INTERACTS_WITH',
         'subject_id': 'C1414462|2100',
         'subject_name': 'ESR2 gene|ESR2',
         'subject_type': 'gngm'},
   'n': {'count': 1358,
         'id': 'C1414461|2099',
         'name': 'ESR1 gene|ESR1',
         'type': 'gngm'},
   'r': {}}]

SEM_PREDICATE

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

Properties:

- predicate: The string representation of each predicate (for example TREATS, PROCESS_OF)

- count: The total predicate count

Examples

query

 MATCH (n)-[r: SEM_PREDICATE]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'count': 241, 'id': '7523', 'name': 'XS', 'type': 'gngm'},
   'n': {'count': 223,
         'id': 'C0038180',
         'name': 'Starch (Bacterial Glycogen) Synthase',
         'type': 'aapp'},
   'r': {'count': 1, 'predicate': 'INTERACTS_WITH'}},
  {'m': {'count': 241, 'id': '7523', 'name': 'XS', 'type': 'gngm'},
   'n': {'count': 223,
         'id': 'C0038180',
         'name': 'Starch (Bacterial Glycogen) Synthase',
         'type': 'aapp'},
   'r': {'count': 1, 'predicate': 'COEXISTS_WITH'}},
  {'m': {'count': 241, 'id': '7523', 'name': 'XS', 'type': 'gngm'},
   'n': {'count': 7538, 'id': 'C0025646', 'name': 'Methionine', 'type': 'aapp'},
   'r': {'count': 1, 'predicate': 'STIMULATES'}}]

SEM_SUB

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

Examples

query

 MATCH (n)-[r: SEM_SUB]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'count': 3,
         'id': 'XS:PRODUCES:homocysteine',
         'object_id': 'C0019878',
         'object_name': 'homocysteine',
         'object_type': 'aapp',
         'predicate': 'PRODUCES',
         'subject_id': '7523',
         'subject_name': 'XS',
         'subject_type': 'gngm'},
   'n': {'count': 241, 'id': '7523', 'name': 'XS', 'type': 'gngm'},
   'r': {}},
  {'m': {'count': 12,
         'id': 'Genes:COEXISTS_WITH:Estrogens',
         'object_id': 'C0014939',
         'object_name': 'Estrogens',
         'object_type': 'horm',
         'predicate': 'COEXISTS_WITH',
         'subject_id': 'C0017337',
         'subject_name': 'Genes',
         'subject_type': 'gngm'},
   'n': {'count': 98630, 'id': 'C0017337', 'name': 'Genes', 'type': 'gngm'},
   'r': {}},
  {'m': {'count': 2,
         'id': 'ESR2 gene|ESR2:INTERACTS_WITH:ESR1 gene|ESR1',
         'object_id': 'C1414461|2099',
         'object_name': 'ESR1 gene|ESR1',
         'object_type': 'gngm',
         'predicate': 'INTERACTS_WITH',
         'subject_id': 'C1414462|2100',
         'subject_name': 'ESR2 gene|ESR2',
         'subject_type': 'gngm'},
   'n': {'count': 291,
         'id': 'C1414462|2100',
         'name': 'ESR2 gene|ESR2',
         'type': 'gngm'},
   'r': {}}]

SEM_TO_LIT

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

Examples

query

 MATCH (n)-[r: SEM_TO_LIT]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'count': 3,
         'id': 'XS:PRODUCES:homocysteine',
         'object_id': 'C0019878',
         'object_name': 'homocysteine',
         'object_type': 'aapp',
         'predicate': 'PRODUCES',
         'subject_id': '7523',
         'subject_name': 'XS',
         'subject_type': 'gngm'},
   'n': {'dp': '2005 May',
         'edat': '2005-4-20',
         'issn': '0021-9193',
         'pubmed_id': '15838035',
         'year': 2005},
   'r': {}},
  {'m': {'count': 3,
         'id': 'XS:PRODUCES:homocysteine',
         'object_id': 'C0019878',
         'object_name': 'homocysteine',
         'object_type': 'aapp',
         'predicate': 'PRODUCES',
         'subject_id': '7523',
         'subject_name': 'XS',
         'subject_type': 'gngm'},
   'n': {'dp': '2015 Apr',
         'edat': '2015-1-22',
         'issn': '1098-5522',
         'pubmed_id': '25605770',
         'year': 2015},
   'r': {}},
  {'m': {'count': 3,
         'id': 'XS:PRODUCES:homocysteine',
         'object_id': 'C0019878',
         'object_name': 'homocysteine',
         'object_type': 'aapp',
         'predicate': 'PRODUCES',
         'subject_id': '7523',
         'subject_name': 'XS',
         'subject_type': 'gngm'},
   'n': {'dp': '2006 May',
         'edat': '2006-3-15',
         'issn': '1438-4221',
         'pubmed_id': '16530477',
         'year': 2006},
   'r': {}}]

STRING_INTERACT_WITH

(Protein)-(Protein) interactions from STRING (https://string-db.org).

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

Properties:

- score

Examples

query

 MATCH (n)-[r: STRING_INTERACT_WITH]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'uniprot_id': 'A8MZA4'},
   'n': {'uniprot_id': 'A0A0A6YYL3'},
   'r': {'score': 711}},
  {'m': {'uniprot_id': 'A8MZA4'},
   'n': {'uniprot_id': 'H3BUK9'},
   'r': {'score': 718}},
  {'m': {'uniprot_id': 'A8MZA4'},
   'n': {'uniprot_id': 'Q96M34'},
   'r': {'score': 734}}]

TOPHITS

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

Properties:

- beta: Effect size.

- pval: P-Value.

Examples

query

 MATCH (n)-[r: TOPHITS]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'name': 'rs553741'},
   'n': {'access': 'public',
         'author': 'Kettunen',
         'category': 'Metabolites',
         'consortium': 'NA',
         'id': 'met-c-895',
         'mr': '1',
         'note': 'LDL.C; SD value comes from the original untransformed '
                 'distribution of the ERF cohort',
         'nsnp': '11871461',
         'pmid': '27005778',
         'population': 'European',
         'priority': '1',
         'sample_size': '21559',
         'sd': '0.27',
         'sex': 'Males and Females',
         'subcategory': 'Lipid',
         'trait': 'Total cholesterol in LDL',
         'unit': 'NA',
         'year': '2016'},
   'r': {'beta': '0.06927', 'pval': 1.03001e-10}},
  {'m': {'name': 'rs553741'},
   'n': {'access': 'public',
         'author': 'Kettunen',
         'category': 'Metabolites',
         'consortium': 'NA',
         'id': 'met-c-880',
         'mr': '1',
         'note': 'L.LDL.C; SD value comes from the original untransformed '
                 'distribution of the ERF cohort',
         'nsnp': '11871461',
         'pmid': '27005778',
         'population': 'European',
         'priority': '1',
         'sample_size': '21552',
         'sd': '0.19',
         'sex': 'Males and Females',
         'subcategory': 'Lipid',
         'trait': 'Total cholesterol in large LDL',
         'unit': 'NA',
         'year': '2016'},
   'r': {'beta': '0.073671', 'pval': 6.18016e-12}},
  {'m': {'name': 'rs553741'},
   'n': {'access': 'public',
         'author': 'Kettunen',
         'category': 'Metabolites',
         'consortium': 'NA',
         'id': 'met-c-885',
         'mr': '1',
         'note': 'L.LDL.PL; SD value comes from the original untransformed '
                 'distribution of the ERF cohort',
         'nsnp': '11871461',
         'pmid': '27005778',
         'population': 'European',
         'priority': '1',
         'sample_size': '21550',
         'sd': '0.3',
         'sex': 'Males and Females',
         'subcategory': 'Lipid',
         'trait': 'Phospholipids in large LDL',
         'unit': 'NA',
         'year': '2016'},
   'r': {'beta': '0.068023', 'pval': 2.17e-10}}]

VARIANT_TO_GENE

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

Properties:

- location: In standard coordinate format (chr:start or chr:start-end).

- allele: The variant allele used to calculate the consequence.

- feature: Ensembl stable ID of feature.

- feature_type: Type of feature. Currently one of Transcript, RegulatoryFeature, MotifFeature.

- consequence: Consequence type of this variant (see https://www.ensembl.org/info/genome/variation/prediction/predicted_data.html#consequences).

- cdna_position: Relative position of base pair in cDNA sequence.

- cds_position: Relative position of base pair in coding sequence.

- protein_position: Relative position of amino acid in protein.

- amino_acids: Only given if the variant affects the protein-coding sequence.

- codons: The alternative codons with the variant base in upper case.

- existing_variation: Known identifier of existing variant.

- extra: This column contains extra information as key=value pairs separated by “;” (see https://www.ensembl.org/info/docs/tools/vep/vep_formats.html#other_fields).

Examples

query

 MATCH (n)-[r: VARIANT_TO_GENE]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'name': 'rs553741'},
   'n': {'adme_gene': 'N',
         'bio_druggable': 'Y',
         'chr': '1',
         'description': 'proprotein convertase subtilisin/kexin type 9 '
                        '[Source:HGNC Symbol;Acc:20001]',
         'druggability_tier': 'Tier 1',
         'end': 55530525,
         'ensembl_id': 'ENSG00000169174',
         'name': 'PCSK9',
         'reactome_id': '9004307',
         'small_mol_druggable': 'N',
         'source': 'HGNC Symbol',
         'start': 55505221,
         'type': 'protein_coding'},
   'r': {'allele': 'A',
         'amino_acids': '-',
         'cdna_position': '-',
         'cds_position': '-',
         'codons': '-',
         'consequence': 'intron_variant',
         'existing_variation': '-',
         'extra': 'IMPACT=MODIFIER;STRAND=1',
         'feature': 'ENST00000302118',
         'feature_type': 'Transcript',
         'location': '1:55520408',
         'protein_position': '-'}},
  {'m': {'name': 'rs2292238'},
   'n': {'chr': '12',
         'description': 'proliferation-associated 2G4, 38kDa [Source:HGNC '
                        'Symbol;Acc:8550]',
         'end': 56507691,
         'ensembl_id': 'ENSG00000170515',
         'name': 'PA2G4',
         'reactome_id': '12232094',
         'source': 'HGNC Symbol',
         'start': 56498103,
         'type': 'protein_coding'},
   'r': {'allele': 'C',
         'amino_acids': '-',
         'cdna_position': '-',
         'cds_position': '-',
         'codons': '-',
         'consequence': 'upstream_gene_variant',
         'existing_variation': '-',
         'extra': 'IMPACT=MODIFIER;DISTANCE=4281;STRAND=1',
         'feature': 'ENST00000303305',
         'feature_type': 'Transcript',
         'location': '12:56493822',
         'protein_position': '-'}},
  {'m': {'name': 'rs2292238'},
   'n': {'chr': '12',
         'description': 'Uncharacterized protein  '
                        '[Source:UniProtKB/TrEMBL;Acc:H0YIN7]',
         'end': 56503073,
         'ensembl_id': 'ENSG00000257411',
         'name': 'RP11-603J24.9',
         'source': 'Clone-based (Vega) gene',
         'start': 56495115,
         'type': 'protein_coding'},
   'r': {'allele': 'C',
         'amino_acids': '-',
         'cdna_position': '-',
         'cds_position': '-',
         'codons': '-',
         'consequence': 'upstream_gene_variant',
         'existing_variation': '-',
         'extra': 'IMPACT=MODIFIER;DISTANCE=1293;STRAND=1;FLAGS=cds_start_NF,cds_end_NF',
         'feature': 'ENST00000548861',
         'feature_type': 'Transcript',
         'location': '12:56493822',
         'protein_position': '-'}}]

XQTL_MULTI_SNP_MR

Association of exposure gene and outcome phenotype of xQTL (Zheng et al. 2020), multi SNP MR methods.

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

Properties:

- beta: Effect size.

- se: Standard error.

- p: P-Value.

- qtl_type: pQTL, or eQTL.

- mr_method: underlying Mendelian randomization method, e.g. IVW, Egger, etc.

Examples

query

 MATCH (n)-[r: XQTL_MULTI_SNP_MR]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'access': 'public',
         'author': 'Ben Elsworth',
         'category': 'Binary',
         'consortium': 'MRC-IEU',
         'id': 'ukb-b-2964',
         'mr': '1',
         'ncase': '1483',
         'ncontrol': '461527',
         'note': '41204#F171: Output from GWAS pipeline using Phesant derived '
                 'variables from UKBiobank',
         'nsnp': '9851867',
         'population': 'European',
         'priority': '1',
         'sample_size': '463010',
         'sex': 'Males and Females',
         'subcategory': 'NA',
         'trait': 'Diagnoses - secondary ICD10: F17.1 Harmful use',
         'unit': 'SD',
         'year': '2018'},
   'n': {'chr': '15',
         'description': 'electron-transfer-flavoprotein, alpha polypeptide '
                        '[Source:HGNC Symbol;Acc:3481]',
         'end': 76603813,
         'ensembl_id': 'ENSG00000140374',
         'name': 'ETFA',
         'reactome_id': '9004675',
         'source': 'HGNC Symbol',
         'start': 76507696,
         'type': 'protein_coding'},
   'r': {'beta': -6.925854904693551e-06,
         'mr_method': 'IVW',
         'p': 0.9846875667572021,
         'qtl_type': 'eQTL',
         'se': 0.0003608631668612361}},
  {'m': {'access': 'public',
         'author': 'Ben Elsworth',
         'category': 'Binary',
         'consortium': 'MRC-IEU',
         'id': 'ukb-b-2964',
         'mr': '1',
         'ncase': '1483',
         'ncontrol': '461527',
         'note': '41204#F171: Output from GWAS pipeline using Phesant derived '
                 'variables from UKBiobank',
         'nsnp': '9851867',
         'population': 'European',
         'priority': '1',
         'sample_size': '463010',
         'sex': 'Males and Females',
         'subcategory': 'NA',
         'trait': 'Diagnoses - secondary ICD10: F17.1 Harmful use',
         'unit': 'SD',
         'year': '2018'},
   'n': {'adme_gene': 'N',
         'bio_druggable': 'Y',
         'chr': '5',
         'description': 'adrenoceptor beta 2, surface [Source:HGNC '
                        'Symbol;Acc:286]',
         'druggability_tier': 'Tier 1',
         'end': 148208196,
         'ensembl_id': 'ENSG00000169252',
         'name': 'ADRB2',
         'reactome_id': '8999895',
         'small_mol_druggable': 'Y',
         'source': 'HGNC Symbol',
         'start': 148206156,
         'type': 'protein_coding'},
   'r': {'beta': -1.688985685177613e-05,
         'mr_method': 'IVW',
         'p': 0.9845685362815857,
         'qtl_type': 'eQTL',
         'se': 0.000873236043844372}},
  {'m': {'access': 'public',
         'author': 'Ben Elsworth',
         'category': 'Binary',
         'consortium': 'MRC-IEU',
         'id': 'ukb-b-2964',
         'mr': '1',
         'ncase': '1483',
         'ncontrol': '461527',
         'note': '41204#F171: Output from GWAS pipeline using Phesant derived '
                 'variables from UKBiobank',
         'nsnp': '9851867',
         'population': 'European',
         'priority': '1',
         'sample_size': '463010',
         'sex': 'Males and Females',
         'subcategory': 'NA',
         'trait': 'Diagnoses - secondary ICD10: F17.1 Harmful use',
         'unit': 'SD',
         'year': '2018'},
   'n': {'chr': '4',
         'end': 47846356,
         'ensembl_id': 'ENSG00000259959',
         'name': 'RP11-121C2.2',
         'source': 'Clone-based (Vega) gene',
         'start': 47842139,
         'type': 'lincRNA'},
   'r': {'beta': 3.2280931918649003e-06,
         'mr_method': 'IVW',
         'p': 0.9845654964447021,
         'qtl_type': 'eQTL',
         'se': 0.00016686526942066848}}]

XQTL_SINGLE_SNP_MR_GENE_GWAS

Association of exposure gene and outcome phenotype of xQTL (Zheng et al. 2020), single SNP MR methods.

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

Properties:

- beta: Effect size

- se: Standard error

- p: P-Value

- rsid: SNP rsID

- qtl_type: pQTL, or eQTL

Examples

query

 MATCH (n)-[r: XQTL_SINGLE_SNP_MR_GENE_GWAS]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'access': 'public',
         'author': 'Ben Elsworth',
         'category': 'Binary',
         'consortium': 'MRC-IEU',
         'id': 'ukb-b-2964',
         'mr': '1',
         'ncase': '1483',
         'ncontrol': '461527',
         'note': '41204#F171: Output from GWAS pipeline using Phesant derived '
                 'variables from UKBiobank',
         'nsnp': '9851867',
         'population': 'European',
         'priority': '1',
         'sample_size': '463010',
         'sex': 'Males and Females',
         'subcategory': 'NA',
         'trait': 'Diagnoses - secondary ICD10: F17.1 Harmful use',
         'unit': 'SD',
         'year': '2018'},
   'n': {'adme_gene': 'N',
         'bio_druggable': 'Y',
         'chr': '1',
         'description': 'hexose-6-phosphate dehydrogenase (glucose '
                        '1-dehydrogenase) [Source:HGNC Symbol;Acc:4795]',
         'druggability_tier': 'Tier 3B',
         'end': 9331396,
         'ensembl_id': 'ENSG00000049239',
         'name': 'H6PD',
         'small_mol_druggable': 'N',
         'source': 'HGNC Symbol',
         'start': 9294834,
         'type': 'protein_coding'},
   'r': {'beta': -4.0220958908321336e-05,
         'p': 0.9852237701416016,
         'qtl_type': 'eQTL',
         'rsid': 'rs2275457',
         'se': 0.002171725034713745}},
  {'m': {'access': 'public',
         'author': 'Ben Elsworth',
         'category': 'Binary',
         'consortium': 'MRC-IEU',
         'id': 'ukb-b-2964',
         'mr': '1',
         'ncase': '1483',
         'ncontrol': '461527',
         'note': '41204#F171: Output from GWAS pipeline using Phesant derived '
                 'variables from UKBiobank',
         'nsnp': '9851867',
         'population': 'European',
         'priority': '1',
         'sample_size': '463010',
         'sex': 'Males and Females',
         'subcategory': 'NA',
         'trait': 'Diagnoses - secondary ICD10: F17.1 Harmful use',
         'unit': 'SD',
         'year': '2018'},
   'n': {'chr': '7',
         'description': 'alkylglycerol monooxygenase [Source:HGNC '
                        'Symbol;Acc:33784]',
         'end': 15601640,
         'ensembl_id': 'ENSG00000187546',
         'name': 'AGMO',
         'reactome_id': '9002795',
         'source': 'HGNC Symbol',
         'start': 15239943,
         'type': 'protein_coding'},
   'r': {'beta': 1.6428259186795913e-05,
         'p': 0.9851876497268677,
         'qtl_type': 'eQTL',
         'rsid': 'rs7812160',
         'se': 0.0008848753059282899}},
  {'m': {'access': 'public',
         'author': 'Ben Elsworth',
         'category': 'Binary',
         'consortium': 'MRC-IEU',
         'id': 'ukb-b-2964',
         'mr': '1',
         'ncase': '1483',
         'ncontrol': '461527',
         'note': '41204#F171: Output from GWAS pipeline using Phesant derived '
                 'variables from UKBiobank',
         'nsnp': '9851867',
         'population': 'European',
         'priority': '1',
         'sample_size': '463010',
         'sex': 'Males and Females',
         'subcategory': 'NA',
         'trait': 'Diagnoses - secondary ICD10: F17.1 Harmful use',
         'unit': 'SD',
         'year': '2018'},
   'n': {'chr': '12',
         'description': 'UDP-N-acetyl-alpha-D-galactosamine:polypeptide '
                        'N-acetylgalactosaminyltransferase 6 (GalNAc-T6) '
                        '[Source:HGNC Symbol;Acc:4128]',
         'end': 51786651,
         'ensembl_id': 'ENSG00000139629',
         'name': 'GALNT6',
         'reactome_id': '9003540',
         'source': 'HGNC Symbol',
         'start': 51745031,
         'type': 'protein_coding'},
   'r': {'beta': -3.593823566916399e-05,
         'p': 0.9851584434509277,
         'qtl_type': 'eQTL',
         'rsid': 'rs140740520',
         'se': 0.0019319361308589578}}]

XQTL_SINGLE_SNP_MR_SNP_GENE

Association of SNP and exposure gene of xQTL (Zheng et al. 2020), single SNP MR methods.

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

Examples

query

 MATCH (n)-[r: XQTL_SINGLE_SNP_MR_SNP_GENE]-(m) RETURN n, r, m SKIP 0 LIMIT 3

data

 [{'m': {'name': 'rs140428865'},
   'n': {'chr': '8',
         'description': 'tRNA methyltransferase 12 homolog (S. cerevisiae) '
                        '[Source:HGNC Symbol;Acc:26091]',
         'end': 125474391,
         'ensembl_id': 'ENSG00000183665',
         'name': 'TRMT12',
         'reactome_id': '12232479',
         'source': 'HGNC Symbol',
         'start': 125463048,
         'type': 'protein_coding'},
   'r': {}},
  {'m': {'name': 'rs6100162'},
   'n': {'chr': '20',
         'description': 'aminopeptidase-like 1 [Source:HGNC Symbol;Acc:16244]',
         'end': 57294294,
         'ensembl_id': 'ENSG00000215440',
         'name': 'NPEPL1',
         'source': 'HGNC Symbol',
         'start': 57264187,
         'type': 'protein_coding'},
   'r': {}},
  {'m': {'name': 'rs58729822'},
   'n': {'chr': '16',
         'description': 'rogdi homolog (Drosophila) [Source:HGNC '
                        'Symbol;Acc:29478]',
         'end': 4852951,
         'ensembl_id': 'ENSG00000067836',
         'name': 'ROGDI',
         'source': 'HGNC Symbol',
         'start': 4846969,
         'type': 'protein_coding'},
   'r': {}}]