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.
BIORXIV_OBJ
Link between
(LiteratureTriple)object and(LiteratureTerm)for BioRxiv SemRep triples.
Path: (LiteratureTriple)-[BIORXIV_OBJ]->(LiteratureTerm)
Examples
query
MATCH (n)-[r: BIORXIV_OBJ]-(m) RETURN n, r, m SKIP 0 LIMIT 3
data
[{'m': {'_id': 'C0239946:COEXISTS_WITH:C0341439',
'_name': 'Fibrosis, Liver COEXISTS_WITH Chronic liver disease NOS',
'_source': ['SemMedDB_VER42_2020_R', 'bioRxiv-2020-10-06'],
'id': 'C0239946:COEXISTS_WITH:C0341439',
'name': 'Fibrosis, Liver COEXISTS_WITH Chronic liver disease NOS',
'object_id': 'C0341439',
'predicate': 'COEXISTS_WITH',
'subject_id': 'C0239946'},
'n': {'_id': 'C0341439',
'_name': 'Chronic liver disease',
'_source': ['SemMedDB_VER42_2020_R',
'bioRxiv-2020-10-06',
'medRxiv-2020-10-06'],
'id': 'C0341439',
'name': 'Chronic liver disease',
'type': ['dsyn']},
'r': {'_source': ['bioRxiv-2020-10-06']}},
{'m': {'_id': 'C0069717:CAUSES:C0442874',
'_name': 'oxaliplatin CAUSES Neuropathy',
'_source': ['SemMedDB_VER42_2020_R', 'bioRxiv-2020-10-06'],
'id': 'C0069717:CAUSES:C0442874',
'name': 'oxaliplatin CAUSES Neuropathy',
'object_id': 'C0442874',
'predicate': 'CAUSES',
'subject_id': 'C0069717'},
'n': {'_id': 'C0442874',
'_name': 'Neuropathy',
'_source': ['SemMedDB_VER42_2020_R',
'bioRxiv-2020-10-06',
'medRxiv-2020-10-06'],
'id': 'C0442874',
'name': 'Neuropathy',
'type': ['dsyn']},
'r': {'_source': ['bioRxiv-2020-10-06']}},
{'m': {'_id': 'C0036720:PRODUCES:C0070861',
'_name': 'Serine PRODUCES Phosphoglycerate dehydrogenase',
'_source': ['SemMedDB_VER42_2020_R', 'bioRxiv-2020-10-06'],
'id': 'C0036720:PRODUCES:C0070861',
'name': 'Serine PRODUCES Phosphoglycerate dehydrogenase',
'object_id': 'C0070861',
'predicate': 'PRODUCES',
'subject_id': 'C0036720'},
'n': {'_id': 'C0070861',
'_name': 'Phosphoglycerate dehydrogenase',
'_source': ['SemMedDB_VER42_2020_R', 'bioRxiv-2020-10-06'],
'id': 'C0070861',
'name': 'Phosphoglycerate dehydrogenase',
'type': ['aapp', 'gngm', 'enzy']},
'r': {'_source': ['bioRxiv-2020-10-06']}}]
BIORXIV_PREDICATE
Link between
(LiteratureTerm)and(LiteratureTerm)for BioRxiv SemRep triples.
Path: (LiteratureTerm)-[BIORXIV_PREDICATE]->(LiteratureTerm)
Properties:
count:int, required; Number of triples.
predicate:str, required; The string representation of each predicate (for example TREATS, PROCESS_OF).
Examples
query
MATCH (n)-[r: BIORXIV_PREDICATE]-(m) RETURN n, r, m SKIP 0 LIMIT 3
data
[{'m': {'_id': 'C1425620',
'_name': 'LPHN2 gene',
'_source': ['SemMedDB_VER42_2020_R', 'bioRxiv-2020-10-06'],
'id': 'C1425620',
'name': 'LPHN2 gene',
'type': ['aapp']},
'n': {'_id': 'C3146409',
'_name': 'ARHGAP44 gene',
'_source': ['bioRxiv-2020-10-06'],
'id': 'C3146409',
'name': 'ARHGAP44 gene',
'type': ['gngm']},
'r': {'_source': ['bioRxiv-2020-10-06'],
'count': 1,
'predicate': 'INTERACTS_WITH'}},
{'m': {'_id': 'C1416472',
'_name': 'IQGAP2 gene',
'_source': ['SemMedDB_VER42_2020_R', 'bioRxiv-2020-10-06'],
'id': 'C1416472',
'name': 'IQGAP2 gene',
'type': ['gngm']},
'n': {'_id': 'C1567665',
'_name': 'ITK protein, human',
'_source': ['SemMedDB_VER42_2020_R',
'bioRxiv-2020-10-06',
'medRxiv-2020-10-06'],
'id': 'C1567665',
'name': 'ITK protein, human',
'type': ['aapp', 'gngm']},
'r': {'_source': ['bioRxiv-2020-10-06'],
'count': 1,
'predicate': 'INTERACTS_WITH'}},
{'m': {'_id': 'C1135979',
'_name': 'Mitochondrial Membrane Transport Proteins',
'_source': ['SemMedDB_VER42_2020_R', 'bioRxiv-2020-10-06'],
'id': 'C1135979',
'name': 'Mitochondrial Membrane Transport Proteins',
'type': ['aapp', 'gngm']},
'n': {'_id': 'C0949610',
'_name': 'Mitochondrial Proteins',
'_source': ['SemMedDB_VER42_2020_R', 'bioRxiv-2020-10-06'],
'id': 'C0949610',
'name': 'Mitochondrial Proteins',
'type': ['aapp', 'gngm']},
'r': {'_source': ['bioRxiv-2020-10-06'],
'count': 1,
'predicate': 'INTERACTS_WITH'}}]
BIORXIV_SUB
Link between
(LiteratureTriple)subject and(LiteratureTerm)for BioRxiv SemRep triples.
Path: (LiteratureTriple)-[BIORXIV_SUB]->(LiteratureTerm)
Examples
query
MATCH (n)-[r: BIORXIV_SUB]-(m) RETURN n, r, m SKIP 0 LIMIT 3
data
[{'m': {'_id': 'C0239946:COEXISTS_WITH:C0341439',
'_name': 'Fibrosis, Liver COEXISTS_WITH Chronic liver disease NOS',
'_source': ['SemMedDB_VER42_2020_R', 'bioRxiv-2020-10-06'],
'id': 'C0239946:COEXISTS_WITH:C0341439',
'name': 'Fibrosis, Liver COEXISTS_WITH Chronic liver disease NOS',
'object_id': 'C0341439',
'predicate': 'COEXISTS_WITH',
'subject_id': 'C0239946'},
'n': {'_id': 'C0239946',
'_name': 'Fibrosis, Liver',
'_source': ['SemMedDB_VER42_2020_R',
'bioRxiv-2020-10-06',
'medRxiv-2020-10-06'],
'id': 'C0239946',
'name': 'Fibrosis, Liver',
'type': ['dsyn']},
'r': {'_source': ['bioRxiv-2020-10-06']}},
{'m': {'_id': 'C0069717:CAUSES:C0442874',
'_name': 'oxaliplatin CAUSES Neuropathy',
'_source': ['SemMedDB_VER42_2020_R', 'bioRxiv-2020-10-06'],
'id': 'C0069717:CAUSES:C0442874',
'name': 'oxaliplatin CAUSES Neuropathy',
'object_id': 'C0442874',
'predicate': 'CAUSES',
'subject_id': 'C0069717'},
'n': {'_id': 'C0069717',
'_name': 'oxaliplatin',
'_source': ['SemMedDB_VER42_2020_R', 'bioRxiv-2020-10-06'],
'id': 'C0069717',
'name': 'oxaliplatin',
'type': ['orch', 'phsu']},
'r': {'_source': ['bioRxiv-2020-10-06']}},
{'m': {'_id': 'C0036720:PRODUCES:C0070861',
'_name': 'Serine PRODUCES Phosphoglycerate dehydrogenase',
'_source': ['SemMedDB_VER42_2020_R', 'bioRxiv-2020-10-06'],
'id': 'C0036720:PRODUCES:C0070861',
'name': 'Serine PRODUCES Phosphoglycerate dehydrogenase',
'object_id': 'C0070861',
'predicate': 'PRODUCES',
'subject_id': 'C0036720'},
'n': {'_id': 'C0036720',
'_name': 'serine',
'_source': ['SemMedDB_VER42_2020_R', 'bioRxiv-2020-10-06'],
'id': 'C0036720',
'name': 'serine',
'type': ['aapp', 'gngm', 'phsu']},
'r': {'_source': ['bioRxiv-2020-10-06']}}]
BIORXIV_TO_LIT
Link between
(LiteratureTriple)object and(Literature)for BioRxiv SemRep triples.
Path: (LiteratureTriple)-[BIORXIV_TO_LIT]->(Literature)
Examples
query
MATCH (n)-[r: BIORXIV_TO_LIT]-(m) RETURN n, r, m SKIP 0 LIMIT 3
data
[{'m': {'_id': '10.1101/2020.06.11.146472',
'_name': '10.1101/2020.06.11.146472',
'_source': ['bioRxiv-2020-10-06'],
'doi': '10.1101/2020.06.11.146472',
'id': '10.1101/2020.06.11.146472',
'issn': 'biorxiv',
'title': 'The C. elegans proteasome subunit RPN-12 is required for '
'hermaphrodite germline sex determination and oocyte quality',
'year': 2020},
'n': {'_id': 'C0208355:INHIBITS:C0599220',
'_name': 'multicatalytic endopeptidase complex INHIBITS Protein '
'Subunits',
'_source': ['SemMedDB_VER42_2020_R', 'bioRxiv-2020-10-06'],
'id': 'C0208355:INHIBITS:C0599220',
'name': 'multicatalytic endopeptidase complex INHIBITS Protein '
'Subunits',
'object_id': 'C0599220',
'predicate': 'INHIBITS',
'subject_id': 'C0208355'},
'r': {'_source': ['bioRxiv-2020-10-06']}},
{'m': {'_id': '10.1101/2020.05.12.091678',
'_name': '10.1101/2020.05.12.091678',
'_source': ['bioRxiv-2020-10-06'],
'doi': '10.1101/2020.05.12.091678',
'id': '10.1101/2020.05.12.091678',
'issn': 'biorxiv',
'title': 'Mu-opioids suppress GABAergic synaptic transmission onto '
'orbitofrontal cortex pyramidal neurons with subregional '
'selectivity.',
'year': 2020},
'n': {'_id': 'C0242402:STIMULATES:C0027410',
'_name': 'Opioids STIMULATES Narcotic Antagonists',
'_source': ['SemMedDB_VER42_2020_R', 'bioRxiv-2020-10-06'],
'id': 'C0242402:STIMULATES:C0027410',
'name': 'Opioids STIMULATES Narcotic Antagonists',
'object_id': 'C0027410',
'predicate': 'STIMULATES',
'subject_id': 'C0242402'},
'r': {'_source': ['bioRxiv-2020-10-06']}},
{'m': {'_id': '10.1101/2020.05.12.091678',
'_name': '10.1101/2020.05.12.091678',
'_source': ['bioRxiv-2020-10-06'],
'doi': '10.1101/2020.05.12.091678',
'id': '10.1101/2020.05.12.091678',
'issn': 'biorxiv',
'title': 'Mu-opioids suppress GABAergic synaptic transmission onto '
'orbitofrontal cortex pyramidal neurons with subregional '
'selectivity.',
'year': 2020},
'n': {'_id': 'C0066908:STIMULATES:C0030616',
'_name': 'Receptors, Opioid, mu STIMULATES Parvalbumins',
'_source': ['bioRxiv-2020-10-06'],
'id': 'C0066908:STIMULATES:C0030616',
'name': 'Receptors, Opioid, mu STIMULATES Parvalbumins',
'object_id': 'C0030616',
'predicate': 'STIMULATES',
'subject_id': 'C0066908'},
'r': {'_source': ['bioRxiv-2020-10-06']}}]
GEN_COR
Study results from the "UKBB Genetic Correlation" project by Neale Lab.
Path: (Gwas)-[GEN_COR]->(Gwas)
Properties:
h2:float, optional; SNP heritability.
h2_SE:float, optional; Standard error of SNP heritability.
h2_intercept:float, optional; Intercept term of the SNP heritability model.
h2_intercept_SE:float, optional; Standard error of the intercept term of the SNP heritability.
rpheno:float, optional; Phenotypic correlation.
rg:float, required; Genetic correlation.
rg_SE:float, optional; Standard error of the genetic correlation
Z:float, optional; Z score of the genetic correlation.
p:float, required; P value of the genetic correlation.
rg_intercept:float, optional; Intercept term of the genetic correlation model.
rg_intercept_SE:float, optional; Standard error of the intercept term of the genetic correlation model
Examples
query
MATCH (n)-[r: GEN_COR]-(m) RETURN n, r, m SKIP 0 LIMIT 3
data
[{'m': {'_id': 'ukb-b-9433',
'_name': 'Age started oral contraceptive pill',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Ben Elsworth',
'build': 'HG19/GRCh37',
'category': 'Continuous',
'consortium': 'MRC-IEU',
'id': 'ukb-b-9433',
'mr': '1',
'note': '2794: Output from GWAS pipeline using Phesant derived '
'variables from UKBiobank',
'nsnp': '9851867',
'population': 'European',
'sample_size': '198213.0',
'sex': 'Males and Females',
'trait': 'Age started oral contraceptive pill',
'unit': 'SD',
'year': '2018.0'},
'n': {'_id': 'ukb-d-XVIII_MISCFINDINGS',
'_name': 'Symptoms, signs and abnormal clinical and laboratory '
'findings, not elsewhere classified',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Neale lab',
'build': 'HG19/GRCh37',
'category': 'Binary',
'id': 'ukb-d-XVIII_MISCFINDINGS',
'mr': '1',
'ncase': '97602.0',
'ncontrol': '263592.0',
'nsnp': '13586589',
'population': 'European',
'sample_size': '361194.0',
'sex': 'Males and Females',
'trait': 'Symptoms, signs and abnormal clinical and laboratory '
'findings, not elsewhere classified',
'year': '2018.0'},
'r': {'Z': -11.91,
'_source': ['http://www.nealelab.is/blog/2019/10/10/genetic-correlation-results-for-heritable-phenotypes-in-the-uk-biobank'],
'h2': 0.06577999999999999,
'h2_SE': 0.004484,
'h2_intercept': 1.005,
'h2_intercept_SE': 0.007405,
'p': 1.11e-32,
'rg': -0.5056,
'rg_SE': 0.042460000000000005,
'rg_intercept': -0.03193,
'rg_intercept_SE': 0.0057740000000000005,
'rpheno': -0.0392602046205207}},
{'m': {'_id': 'ukb-b-9433',
'_name': 'Age started oral contraceptive pill',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Ben Elsworth',
'build': 'HG19/GRCh37',
'category': 'Continuous',
'consortium': 'MRC-IEU',
'id': 'ukb-b-9433',
'mr': '1',
'note': '2794: Output from GWAS pipeline using Phesant derived '
'variables from UKBiobank',
'nsnp': '9851867',
'population': 'European',
'sample_size': '198213.0',
'sex': 'Males and Females',
'trait': 'Age started oral contraceptive pill',
'unit': 'SD',
'year': '2018.0'},
'n': {'_id': 'ukb-a-566',
'_name': 'Diagnoses - main ICD10: M23 Internal derangement of knee',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Neale',
'build': 'HG19/GRCh37',
'consortium': 'Neale Lab',
'id': 'ukb-a-566',
'mr': '1',
'ncase': '7489.0',
'ncontrol': '329710.0',
'nsnp': '10894596',
'population': 'European',
'sample_size': '337199.0',
'sex': 'Males and Females',
'trait': 'Diagnoses - main ICD10: M23 Internal derangement of knee',
'unit': 'SD',
'year': '2017.0'},
'r': {'Z': -5.66,
'_source': ['http://www.nealelab.is/blog/2019/10/10/genetic-correlation-results-for-heritable-phenotypes-in-the-uk-biobank'],
'h2': 0.06577999999999999,
'h2_SE': 0.004484,
'h2_intercept': 1.005,
'h2_intercept_SE': 0.007405,
'p': 1.5109999999999998e-08,
'rg': -0.3677,
'rg_SE': 0.06496,
'rg_intercept': -0.00176,
'rg_intercept_SE': 0.005464,
'rpheno': -0.0138199991524957}},
{'m': {'_id': 'ukb-b-9433',
'_name': 'Age started oral contraceptive pill',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Ben Elsworth',
'build': 'HG19/GRCh37',
'category': 'Continuous',
'consortium': 'MRC-IEU',
'id': 'ukb-b-9433',
'mr': '1',
'note': '2794: Output from GWAS pipeline using Phesant derived '
'variables from UKBiobank',
'nsnp': '9851867',
'population': 'European',
'sample_size': '198213.0',
'sex': 'Males and Females',
'trait': 'Age started oral contraceptive pill',
'unit': 'SD',
'year': '2018.0'},
'n': {'_id': 'ukb-d-XI_DIGESTIVE',
'_name': 'Diseases of the digestive system',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Neale lab',
'build': 'HG19/GRCh37',
'category': 'Binary',
'id': 'ukb-d-XI_DIGESTIVE',
'mr': '1',
'ncase': '115893.0',
'ncontrol': '245301.0',
'nsnp': '13586589',
'population': 'European',
'sample_size': '361194.0',
'sex': 'Males and Females',
'trait': 'Diseases of the digestive system',
'year': '2018.0'},
'r': {'Z': -12.28,
'_source': ['http://www.nealelab.is/blog/2019/10/10/genetic-correlation-results-for-heritable-phenotypes-in-the-uk-biobank'],
'h2': 0.06577999999999999,
'h2_SE': 0.004484,
'h2_intercept': 1.005,
'h2_intercept_SE': 0.007405,
'p': 1.19e-34,
'rg': -0.4772,
'rg_SE': 0.03887,
'rg_intercept': -0.02484,
'rg_intercept_SE': 0.005297,
'rpheno': -0.0335643994012311}}]
CPIC
Evidence of drug to target gene by CPIC.
Path: (Drug)-[CPIC]->(Gene)
Properties:
cpic_level:str, required; CPIC level of evidence (https://cpicpgx.org/prioritization/).
guideline:str, required; CPIC guideline for clinicians (cpicpgx.org/guidelines/).
pgx_on_fda_label:str, required; PharmGKB PGx level based on drug label (www.pharmgkb.org/page/drugLabelLegend).
pharmgkb_level_of_evidence:str, required; PharmGKB level of evidence (https://www.pharmgkb.org/page/clinAnnLevels).
Examples
query
MATCH (n)-[r: CPIC]-(m) RETURN n, r, m SKIP 0 LIMIT 3
data
[{'m': {'_id': 'CARVEDILOL',
'_name': 'CARVEDILOL',
'_source': ['Opentargets-2020-10-19', 'CPIC-2020-06-12'],
'chembl_uri': 'http://identifiers.org/chembl.compound/CHEMBL723',
'label': 'CARVEDILOL',
'molecule_type': 'Small molecule'},
'n': {'_id': 'ENSG00000100197',
'_name': 'CYP2D6',
'_source': ['BioMart-2020-10-13', 'Finan_et_al'],
'adme_gene': 'Y',
'bio_druggable': 'N',
'biomart_source': 'HGNC Symbol',
'chr': '22',
'description': 'cytochrome P450, family 2, subfamily D, polypeptide 6 '
'[Source:HGNC Symbol;Acc:2625]',
'druggability_tier': 'Tier 1',
'end': 42526908,
'ensembl_id': 'ENSG00000100197',
'name': 'CYP2D6',
'small_mol_druggable': 'Y',
'start': 42522501,
'type': 'protein_coding'},
'r': {'_source': ['CPIC'],
'cpic_level': 'C',
'guideline': 'NA',
'pgx_on_fda_label': 'Actionable PGx',
'pharmgkb_level_of_evidence': '3'}},
{'m': {'_id': 'METOPROLOL',
'_name': 'METOPROLOL',
'_source': ['Opentargets-2020-10-19', 'CPIC-2020-06-12'],
'chembl_uri': 'http://identifiers.org/chembl.compound/CHEMBL13',
'label': 'METOPROLOL',
'molecule_type': 'Small molecule'},
'n': {'_id': 'ENSG00000100197',
'_name': 'CYP2D6',
'_source': ['BioMart-2020-10-13', 'Finan_et_al'],
'adme_gene': 'Y',
'bio_druggable': 'N',
'biomart_source': 'HGNC Symbol',
'chr': '22',
'description': 'cytochrome P450, family 2, subfamily D, polypeptide 6 '
'[Source:HGNC Symbol;Acc:2625]',
'druggability_tier': 'Tier 1',
'end': 42526908,
'ensembl_id': 'ENSG00000100197',
'name': 'CYP2D6',
'small_mol_druggable': 'Y',
'start': 42522501,
'type': 'protein_coding'},
'r': {'_source': ['CPIC'],
'cpic_level': 'C',
'guideline': 'NA',
'pgx_on_fda_label': 'Informative PGx',
'pharmgkb_level_of_evidence': '2A'}},
{'m': {'_id': 'PROPAFENONE',
'_name': 'PROPAFENONE',
'_source': ['Opentargets-2020-10-19', 'CPIC-2020-06-12'],
'chembl_uri': 'http://identifiers.org/chembl.compound/CHEMBL631',
'label': 'PROPAFENONE',
'molecule_type': 'Small molecule'},
'n': {'_id': 'ENSG00000100197',
'_name': 'CYP2D6',
'_source': ['BioMart-2020-10-13', 'Finan_et_al'],
'adme_gene': 'Y',
'bio_druggable': 'N',
'biomart_source': 'HGNC Symbol',
'chr': '22',
'description': 'cytochrome P450, family 2, subfamily D, polypeptide 6 '
'[Source:HGNC Symbol;Acc:2625]',
'druggability_tier': 'Tier 1',
'end': 42526908,
'ensembl_id': 'ENSG00000100197',
'name': 'CYP2D6',
'small_mol_druggable': 'Y',
'start': 42522501,
'type': 'protein_coding'},
'r': {'_source': ['CPIC'],
'cpic_level': 'C',
'guideline': 'NA',
'pgx_on_fda_label': 'Actionable PGx',
'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_99939',
'_name': 'Autosomal dominant Charcot-Marie-Tooth disease type 2E',
'_source': ['EpiGraphDB v0.3'],
'id': 'http://www.orpha.net/ORDO/Orphanet_99939',
'type': 'typed-literal',
'value': 'Autosomal dominant Charcot-Marie-Tooth disease type 2E'},
'n': {'_id': 'http://www.orpha.net/ORDO/Orphanet_64746',
'_name': 'Autosomal dominant Charcot-Marie-Tooth disease type 2',
'_source': ['EpiGraphDB v0.3'],
'id': 'http://www.orpha.net/ORDO/Orphanet_64746',
'type': 'typed-literal',
'value': 'Autosomal dominant Charcot-Marie-Tooth disease type 2'},
'r': {'_source': ['EpiGraphDB v0.3']}},
{'m': {'_id': 'http://www.orpha.net/ORDO/Orphanet_99940',
'_name': 'Autosomal dominant Charcot-Marie-Tooth disease type 2F',
'_source': ['EpiGraphDB v0.3'],
'id': 'http://www.orpha.net/ORDO/Orphanet_99940',
'type': 'typed-literal',
'value': 'Autosomal dominant Charcot-Marie-Tooth disease type 2F'},
'n': {'_id': 'http://www.orpha.net/ORDO/Orphanet_64746',
'_name': 'Autosomal dominant Charcot-Marie-Tooth disease type 2',
'_source': ['EpiGraphDB v0.3'],
'id': 'http://www.orpha.net/ORDO/Orphanet_64746',
'type': 'typed-literal',
'value': 'Autosomal dominant Charcot-Marie-Tooth disease type 2'},
'r': {'_source': ['EpiGraphDB v0.3']}},
{'m': {'_id': 'http://www.orpha.net/ORDO/Orphanet_99941',
'_name': 'Autosomal dominant Charcot-Marie-Tooth disease type 2G',
'_source': ['EpiGraphDB v0.3'],
'id': 'http://www.orpha.net/ORDO/Orphanet_99941',
'type': 'typed-literal',
'value': 'Autosomal dominant Charcot-Marie-Tooth disease type 2G'},
'n': {'_id': 'http://www.orpha.net/ORDO/Orphanet_64746',
'_name': 'Autosomal dominant Charcot-Marie-Tooth disease type 2',
'_source': ['EpiGraphDB v0.3'],
'id': 'http://www.orpha.net/ORDO/Orphanet_64746',
'type': 'typed-literal',
'value': 'Autosomal dominant Charcot-Marie-Tooth disease type 2'},
'r': {'_source': ['EpiGraphDB v0.3']}}]
EXPRESSED_IN
The source Gene is expressed in the target Tissue in GTEx (https://gtexportal.org).
Path: (Gene)-[EXPRESSED_IN]->(Tissue)
Properties:
tpm:float, required; 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': {'_id': 'Adipose - Subcutaneous',
'_name': 'Adipose - Subcutaneous',
'_source': ['GTEx-2016-01-15_v7_RNASeQCv1.1.8'],
'id': 'Adipose - Subcutaneous',
'name': 'Adipose - Subcutaneous'},
'n': {'_id': 'ENSG00000270499',
'_name': 'MKI67P1',
'_source': ['BioMart-2020-10-13'],
'biomart_source': 'HGNC Symbol',
'chr': 'X',
'description': 'marker of proliferation Ki-67 pseudogene 1 '
'[Source:HGNC Symbol;Acc:49230]',
'end': 46422184,
'ensembl_id': 'ENSG00000270499',
'name': 'MKI67P1',
'start': 46420363,
'type': 'pseudogene'},
'r': {'_source': ['GTEx-2016-01-15_v7_RNASeQCv1.1.8'], 'tpm': 0.032365}},
{'m': {'_id': 'Adipose - Subcutaneous',
'_name': 'Adipose - Subcutaneous',
'_source': ['GTEx-2016-01-15_v7_RNASeQCv1.1.8'],
'id': 'Adipose - Subcutaneous',
'name': 'Adipose - Subcutaneous'},
'n': {'_id': 'ENSG00000230844',
'_name': 'ZNF674-AS1',
'_source': ['BioMart-2020-10-13'],
'biomart_source': 'HGNC Symbol',
'chr': 'X',
'description': 'ZNF674 antisense RNA 1 (head to head) [Source:HGNC '
'Symbol;Acc:44266]',
'end': 46407843,
'ensembl_id': 'ENSG00000230844',
'name': 'ZNF674-AS1',
'start': 46404928,
'type': 'lincRNA'},
'r': {'_source': ['GTEx-2016-01-15_v7_RNASeQCv1.1.8'], 'tpm': 4.9855}},
{'m': {'_id': 'Adipose - Subcutaneous',
'_name': 'Adipose - Subcutaneous',
'_source': ['GTEx-2016-01-15_v7_RNASeQCv1.1.8'],
'id': 'Adipose - Subcutaneous',
'name': 'Adipose - Subcutaneous'},
'n': {'_id': 'ENSG00000199226',
'_name': 'RNU6-50P',
'_source': ['BioMart-2020-10-13'],
'biomart_source': 'HGNC Symbol',
'chr': 'X',
'description': 'RNA, U6 small nuclear 50, pseudogene [Source:HGNC '
'Symbol;Acc:10229]',
'end': 46377303,
'ensembl_id': 'ENSG00000199226',
'name': 'RNU6-50P',
'start': 46377201,
'type': 'snRNA'},
'r': {'_source': ['GTEx-2016-01-15_v7_RNASeQCv1.1.8'], 'tpm': 0.0}}]
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': {'_id': 'ENSG00000109519',
'_name': 'GRPEL1',
'_source': ['BioMart-2020-10-13'],
'biomart_source': 'HGNC Symbol',
'chr': '4',
'description': 'GrpE-like 1, mitochondrial (E. coli) [Source:HGNC '
'Symbol;Acc:19696]',
'end': 7069924,
'ensembl_id': 'ENSG00000109519',
'name': 'GRPEL1',
'start': 7060633,
'type': 'protein_coding'},
'n': {'_id': 'Q9HAV7',
'_name': 'Q9HAV7',
'_source': ['BioMart-2020-10-13', 'Reactome-2020-10-13', 'STRING-v11'],
'name': 'Q9HAV7',
'uniprot_id': 'Q9HAV7'},
'r': {'_source': ['BioMart-2020-10-13']}},
{'m': {'_id': 'ENSG00000167434',
'_name': 'CA4',
'_source': ['BioMart-2020-10-13', 'Finan_et_al'],
'adme_gene': 'N',
'bio_druggable': 'Y',
'biomart_source': 'HGNC Symbol',
'chr': '17',
'description': 'carbonic anhydrase IV [Source:HGNC Symbol;Acc:1375]',
'druggability_tier': 'Tier 1',
'end': 58248260,
'ensembl_id': 'ENSG00000167434',
'name': 'CA4',
'small_mol_druggable': 'Y',
'start': 58227297,
'type': 'protein_coding'},
'n': {'_id': 'P22748',
'_name': 'P22748',
'_source': ['BioMart-2020-10-13', 'Reactome-2020-10-13', 'STRING-v11'],
'name': 'P22748',
'uniprot_id': 'P22748'},
'r': {'_source': ['BioMart-2020-10-13']}},
{'m': {'_id': 'ENSG00000109182',
'_name': 'CWH43',
'_source': ['BioMart-2020-10-13'],
'biomart_source': 'HGNC Symbol',
'chr': '4',
'description': 'cell wall biogenesis 43 C-terminal homolog (S. '
'cerevisiae) [Source:HGNC Symbol;Acc:26133]',
'end': 49064098,
'ensembl_id': 'ENSG00000109182',
'name': 'CWH43',
'start': 48988264,
'type': 'protein_coding'},
'n': {'_id': 'Q9H720',
'_name': 'Q9H720',
'_source': ['BioMart-2020-10-13'],
'name': 'Q9H720',
'uniprot_id': 'Q9H720'},
'r': {'_source': ['BioMart-2020-10-13']}}]
GWAS_EFO_EBI
Vectology mapping between GWAS traits and EFO terms
Path: (Gwas)-[GWAS_EFO_EBI]->(Efo)
Examples
query
MATCH (n)-[r: GWAS_EFO_EBI]-(m) RETURN n, r, m SKIP 0 LIMIT 3
data
[{'m': {'_id': 'ebi-a-GCST006357',
'_name': 'IgG levels',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Scepanovic P',
'build': 'HG19/GRCh37',
'id': 'ebi-a-GCST006357',
'mr': '1',
'nsnp': '5278042',
'pmid': '30053915.0',
'population': 'European',
'sample_size': '1000.0',
'trait': 'IgG levels',
'year': '2018.0'},
'n': {'_id': 'http://www.ebi.ac.uk/efo/EFO_0004565',
'_name': 'serum IgG measurement',
'_source': ['EpiGraphDB v0.3'],
'id': 'http://www.ebi.ac.uk/efo/EFO_0004565',
'type': 'typed-literal',
'value': 'serum IgG measurement'},
'r': {'_source': ['gwas_catalog_v1.0.2-studies_r2020-11-03.tsv']}},
{'m': {'_id': 'ebi-a-GCST004076',
'_name': 'Optic disc area',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Springelkamp H',
'build': 'HG19/GRCh37',
'id': 'ebi-a-GCST004076',
'mr': '1',
'nsnp': '11962854',
'pmid': '28073927.0',
'population': 'European',
'sample_size': '22504.0',
'trait': 'Optic disc area',
'year': '2017.0'},
'n': {'_id': 'http://www.ebi.ac.uk/efo/EFO_0006937',
'_name': 'optic disc area measurement',
'_source': ['EpiGraphDB v0.3'],
'id': 'http://www.ebi.ac.uk/efo/EFO_0006937',
'type': 'typed-literal',
'value': 'optic disc area measurement'},
'r': {'_source': ['gwas_catalog_v1.0.2-studies_r2020-11-03.tsv']}},
{'m': {'_id': 'ebi-a-GCST002222',
'_name': 'LDL cholesterol',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Willer CJ',
'build': 'HG19/GRCh37',
'id': 'ebi-a-GCST002222',
'mr': '1',
'nsnp': '2409690',
'pmid': '24097068.0',
'population': 'European',
'sample_size': '94595.0',
'trait': 'LDL cholesterol',
'year': '2013.0'},
'n': {'_id': 'http://www.ebi.ac.uk/efo/EFO_0004611',
'_name': 'low density lipoprotein cholesterol measurement',
'_source': ['EpiGraphDB v0.3'],
'id': 'http://www.ebi.ac.uk/efo/EFO_0004611',
'type': 'typed-literal',
'value': 'low density lipoprotein cholesterol measurement'},
'r': {'_source': ['gwas_catalog_v1.0.2-studies_r2020-11-03.tsv']}}]
GWAS_NLP
Pairwise semantic similarities of
(Gwas)traits.Precomputed results from Vectology (BioSentVec model).
Path: (Gwas)-[GWAS_NLP]->(Gwas)
Properties:
score:float, required; Similarity score (cosine similarity).
Examples
query
MATCH (n)-[r: GWAS_NLP]-(m) RETURN n, r, m SKIP 0 LIMIT 3
data
[{'m': {'_id': 'ieu-b-43',
'_name': 'frontotemporal dementia (TDP subtype)',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Van Deerlin,V',
'build': 'HG19/GRCh37',
'category': 'Binary',
'id': 'ieu-b-43',
'mr': '1',
'ncase': '515.0',
'ncontrol': '2509.0',
'nsnp': '494577',
'pmid': '20154673.0',
'population': 'European',
'sample_size': '3024.0',
'sex': 'Males and Females',
'subcategory': 'Psychiatric / neurological',
'trait': 'frontotemporal dementia (TDP subtype)',
'unit': 'log odds ratio',
'year': '2010.0'},
'n': {'_id': 'met-c-936',
'_name': 'Total fatty acids',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Kettunen',
'build': 'HG19/GRCh37',
'category': 'Metabolites',
'id': 'met-c-936',
'mr': '1',
'nsnp': '11412092',
'pmid': '27005778.0',
'population': 'European',
'sample_size': '13505.0',
'sex': 'Males and Females',
'subcategory': 'Fatty acid',
'trait': 'Total fatty acids',
'year': '2016.0'},
'r': {'_source': ['Vectology-2020-11-30'], 'score': 0.036393511423545084}},
{'m': {'_id': 'ieu-b-43',
'_name': 'frontotemporal dementia (TDP subtype)',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Van Deerlin,V',
'build': 'HG19/GRCh37',
'category': 'Binary',
'id': 'ieu-b-43',
'mr': '1',
'ncase': '515.0',
'ncontrol': '2509.0',
'nsnp': '494577',
'pmid': '20154673.0',
'population': 'European',
'sample_size': '3024.0',
'sex': 'Males and Females',
'subcategory': 'Psychiatric / neurological',
'trait': 'frontotemporal dementia (TDP subtype)',
'unit': 'log odds ratio',
'year': '2010.0'},
'n': {'_id': 'ukb-b-3768',
'_name': 'Age when periods started (menarche)',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Ben Elsworth',
'build': 'HG19/GRCh37',
'category': 'Categorical Ordered',
'consortium': 'MRC-IEU',
'id': 'ukb-b-3768',
'mr': '1',
'note': '2714: Output from GWAS pipeline using Phesant derived '
'variables from UKBiobank',
'nsnp': '9851867',
'population': 'European',
'sample_size': '243944.0',
'sex': 'Males and Females',
'trait': 'Age when periods started (menarche)',
'unit': 'SD',
'year': '2018.0'},
'r': {'_source': ['Vectology-2020-11-30'], 'score': 0.14343192335039467}},
{'m': {'_id': 'ieu-b-43',
'_name': 'frontotemporal dementia (TDP subtype)',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Van Deerlin,V',
'build': 'HG19/GRCh37',
'category': 'Binary',
'id': 'ieu-b-43',
'mr': '1',
'ncase': '515.0',
'ncontrol': '2509.0',
'nsnp': '494577',
'pmid': '20154673.0',
'population': 'European',
'sample_size': '3024.0',
'sex': 'Males and Females',
'subcategory': 'Psychiatric / neurological',
'trait': 'frontotemporal dementia (TDP subtype)',
'unit': 'log odds ratio',
'year': '2010.0'},
'n': {'_id': 'ubm-a-2723',
'_name': 'DKTatlas lh lateraloccipital area',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Elliott LT',
'build': 'HG19/GRCh37',
'category': 'Continuous',
'id': 'ubm-a-2723',
'mr': '1',
'nsnp': '11734354',
'pmid': '30305740.0',
'population': 'European',
'sample_size': '8411.0',
'sex': 'Males',
'subcategory': 'Psychiatric / neurological',
'trait': 'DKTatlas lh lateraloccipital area',
'year': '2018.0'},
'r': {'_source': ['Vectology-2020-11-30'], 'score': 0.11822513468052298}}]
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:float, required; Similarity score (cosine similarity).
Examples
query
MATCH (n)-[r: GWAS_NLP_EFO]-(m) RETURN n, r, m SKIP 0 LIMIT 3
data
[{'m': {'_id': 'met-c-919',
'_name': 'Phenylalanine',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Kettunen',
'build': 'HG19/GRCh37',
'category': 'Metabolites',
'id': 'met-c-919',
'mr': '1',
'note': 'SD value comes from the original untransformed distribution '
'of the ERF cohort',
'nsnp': '12042964',
'pmid': '27005778.0',
'population': 'European',
'sample_size': '22663.0',
'sd': '0.21',
'sex': 'Males and Females',
'subcategory': 'Amino acid',
'trait': 'Phenylalanine',
'year': '2016.0'},
'n': {'_id': 'http://www.ebi.ac.uk/efo/EFO_0005001',
'_name': 'phenylalanine measurement',
'_source': ['EpiGraphDB v0.3'],
'id': 'http://www.ebi.ac.uk/efo/EFO_0005001',
'type': 'typed-literal',
'value': 'phenylalanine measurement'},
'r': {'_source': ['Vectology'], 'score': 0.7713243000000001}},
{'m': {'_id': 'met-c-919',
'_name': 'Phenylalanine',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Kettunen',
'build': 'HG19/GRCh37',
'category': 'Metabolites',
'id': 'met-c-919',
'mr': '1',
'note': 'SD value comes from the original untransformed distribution '
'of the ERF cohort',
'nsnp': '12042964',
'pmid': '27005778.0',
'population': 'European',
'sample_size': '22663.0',
'sd': '0.21',
'sex': 'Males and Females',
'subcategory': 'Amino acid',
'trait': 'Phenylalanine',
'year': '2016.0'},
'n': {'_id': 'http://purl.obolibrary.org/obo/CHEBI_28044',
'_name': 'phenylalanine',
'_source': ['EpiGraphDB v0.3'],
'id': 'http://purl.obolibrary.org/obo/CHEBI_28044',
'type': 'typed-literal',
'value': 'phenylalanine'},
'r': {'_source': ['Vectology'], 'score': 1.0}},
{'m': {'_id': 'ukb-d-Z30',
'_name': 'Diagnoses - main ICD10: Z30 Contraceptive management',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Neale lab',
'build': 'HG19/GRCh37',
'category': 'Binary',
'id': 'ukb-d-Z30',
'mr': '1',
'ncase': '6392.0',
'ncontrol': '354802.0',
'nsnp': '12475388',
'population': 'European',
'sample_size': '361194.0',
'sex': 'Males and Females',
'trait': 'Diagnoses - main ICD10: Z30 Contraceptive management',
'year': '2018.0'},
'n': {'_id': 'http://www.ebi.ac.uk/efo/EFO_0009520',
'_name': 'contraception',
'_source': ['EpiGraphDB v0.3'],
'id': 'http://www.ebi.ac.uk/efo/EFO_0009520',
'type': 'typed-literal',
'value': 'contraception'},
'r': {'_source': ['Vectology'], 'score': 0.7510756999999999}}]
GWAS_TO_LITERATURE_TRIPLE
Mapping between
(Gwas)and(LiteratureTriple).
Path: (Gwas)-[GWAS_TO_LITERATURE_TRIPLE]->(LiteratureTriple)
Properties:
globalCount:int, required; Count of given triple in database.
globalTotal:int, required; Count of all triples in database.
localCount:int, required; Count of given triple for given search term.
localTotal:int, required; Count of all triples for given search term.
odds:float, required; Odds ration from Fisher's Exact Test.
pval:float, required; P-value from Fisher's Exact Test.
Examples
query
MATCH (n)-[r: GWAS_TO_LITERATURE_TRIPLE]-(m) RETURN n, r, m SKIP 0 LIMIT 3
data
[{'m': {'_id': 'ieu-b-43',
'_name': 'frontotemporal dementia (TDP subtype)',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Van Deerlin,V',
'build': 'HG19/GRCh37',
'category': 'Binary',
'id': 'ieu-b-43',
'mr': '1',
'ncase': '515.0',
'ncontrol': '2509.0',
'nsnp': '494577',
'pmid': '20154673.0',
'population': 'European',
'sample_size': '3024.0',
'sex': 'Males and Females',
'subcategory': 'Psychiatric / neurological',
'trait': 'frontotemporal dementia (TDP subtype)',
'unit': 'log odds ratio',
'year': '2010.0'},
'n': {'_id': '23435:INTERACTS_WITH:55997',
'_name': 'TARDBP INTERACTS_WITH CFC1 gene|CFC1',
'_source': ['SemMedDB_VER42_2020_R'],
'id': '23435:INTERACTS_WITH:55997',
'name': 'TARDBP INTERACTS_WITH CFC1 gene|CFC1',
'object_id': '55997',
'predicate': 'INTERACTS_WITH',
'subject_id': '23435'},
'r': {'_source': ['MELODI-Presto-2020-11-30'],
'globalCount': 2,
'globalTotal': 8600311,
'localCount': 2,
'localTotal': 4332,
'odds': 1986.21454965358,
'pval': 1.519395320049507e-06}},
{'m': {'_id': 'ieu-b-43',
'_name': 'frontotemporal dementia (TDP subtype)',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Van Deerlin,V',
'build': 'HG19/GRCh37',
'category': 'Binary',
'id': 'ieu-b-43',
'mr': '1',
'ncase': '515.0',
'ncontrol': '2509.0',
'nsnp': '494577',
'pmid': '20154673.0',
'population': 'European',
'sample_size': '3024.0',
'sex': 'Males and Females',
'subcategory': 'Psychiatric / neurological',
'trait': 'frontotemporal dementia (TDP subtype)',
'unit': 'log odds ratio',
'year': '2010.0'},
'n': {'_id': '23435:INTERACTS_WITH:C1332788',
'_name': 'TARDBP INTERACTS_WITH CFC1 gene|CFC1',
'_source': ['SemMedDB_VER42_2020_R'],
'id': '23435:INTERACTS_WITH:C1332788',
'name': 'TARDBP INTERACTS_WITH CFC1 gene|CFC1',
'object_id': 'C1332788',
'predicate': 'INTERACTS_WITH',
'subject_id': '23435'},
'r': {'_source': ['MELODI-Presto-2020-11-30'],
'globalCount': 2,
'globalTotal': 8600311,
'localCount': 2,
'localTotal': 4332,
'odds': 1986.21454965358,
'pval': 1.519395320049507e-06}},
{'m': {'_id': 'ieu-b-43',
'_name': 'frontotemporal dementia (TDP subtype)',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Van Deerlin,V',
'build': 'HG19/GRCh37',
'category': 'Binary',
'id': 'ieu-b-43',
'mr': '1',
'ncase': '515.0',
'ncontrol': '2509.0',
'nsnp': '494577',
'pmid': '20154673.0',
'population': 'European',
'sample_size': '3024.0',
'sex': 'Males and Females',
'subcategory': 'Psychiatric / neurological',
'trait': 'frontotemporal dementia (TDP subtype)',
'unit': 'log odds ratio',
'year': '2010.0'},
'n': {'_id': 'C0006772:PREDISPOSES:C0002395',
'_name': "Calmodulin PREDISPOSES Alzheimer's Disease",
'_source': ['SemMedDB_VER42_2020_R'],
'id': 'C0006772:PREDISPOSES:C0002395',
'name': "Calmodulin PREDISPOSES Alzheimer's Disease",
'object_id': 'C0002395',
'predicate': 'PREDISPOSES',
'subject_id': 'C0006772'},
'r': {'_source': ['MELODI-Presto-2020-11-30'],
'globalCount': 2,
'globalTotal': 8600311,
'localCount': 2,
'localTotal': 4332,
'odds': 1986.21454965358,
'pval': 1.519395320049507e-06}}]
GWAS_TO_LITERATURE
Association of the
(Gwas)phenotype to a(Literature)PubMed article.
Path: (Gwas)-[GWAS_TO_LITERATURE]->(Literature)
Examples
query
MATCH (n)-[r: GWAS_TO_LITERATURE]-(m) RETURN n, r, m SKIP 0 LIMIT 3
data
[{'m': {'_id': 'ieu-b-43',
'_name': 'frontotemporal dementia (TDP subtype)',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Van Deerlin,V',
'build': 'HG19/GRCh37',
'category': 'Binary',
'id': 'ieu-b-43',
'mr': '1',
'ncase': '515.0',
'ncontrol': '2509.0',
'nsnp': '494577',
'pmid': '20154673.0',
'population': 'European',
'sample_size': '3024.0',
'sex': 'Males and Females',
'subcategory': 'Psychiatric / neurological',
'trait': 'frontotemporal dementia (TDP subtype)',
'unit': 'log odds ratio',
'year': '2010.0'},
'n': {'_id': '24499616',
'_name': '24499616',
'_source': ['SemMedDB_VER42_2020_R'],
'dp': '2013 Nov 07',
'edat': '2014-2-7',
'id': '24499616',
'issn': '1758-9193',
'year': 2013},
'r': {'_source': ['MELODI-Presto-2020-11-30']}},
{'m': {'_id': 'ieu-b-43',
'_name': 'frontotemporal dementia (TDP subtype)',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Van Deerlin,V',
'build': 'HG19/GRCh37',
'category': 'Binary',
'id': 'ieu-b-43',
'mr': '1',
'ncase': '515.0',
'ncontrol': '2509.0',
'nsnp': '494577',
'pmid': '20154673.0',
'population': 'European',
'sample_size': '3024.0',
'sex': 'Males and Females',
'subcategory': 'Psychiatric / neurological',
'trait': 'frontotemporal dementia (TDP subtype)',
'unit': 'log odds ratio',
'year': '2010.0'},
'n': {'_id': '18852354',
'_name': '18852354',
'_source': ['SemMedDB_VER42_2020_R'],
'dp': '2008 Oct',
'edat': '2008-10-15',
'id': '18852354',
'issn': '1538-3687',
'year': 2008},
'r': {'_source': ['MELODI-Presto-2020-11-30']}},
{'m': {'_id': 'ieu-b-43',
'_name': 'frontotemporal dementia (TDP subtype)',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Van Deerlin,V',
'build': 'HG19/GRCh37',
'category': 'Binary',
'id': 'ieu-b-43',
'mr': '1',
'ncase': '515.0',
'ncontrol': '2509.0',
'nsnp': '494577',
'pmid': '20154673.0',
'population': 'European',
'sample_size': '3024.0',
'sex': 'Males and Females',
'subcategory': 'Psychiatric / neurological',
'trait': 'frontotemporal dementia (TDP subtype)',
'unit': 'log odds ratio',
'year': '2010.0'},
'n': {'_id': '12873851',
'_name': '12873851',
'_source': ['SemMedDB_VER42_2020_R'],
'dp': '2003 Jul',
'edat': '2003-7-23',
'id': '12873851',
'issn': '0003-9942',
'year': 2003},
'r': {'_source': ['MELODI-Presto-2020-11-30']}}]
GWAS_TO_VARIANT
Association of the
(Gwas)phenotype to a(Variant).Instrument data from MR-EvE (Hemani et al., 2017).
Path: (Gwas)-[GWAS_TO_VARIANT]->(Variant)
Properties:
beta:float, required; Effect size.
eaf:float, optional; Effect allele frequency.
ncase:int, optional; Number of cases.
ncontrol:int, optional; Number of controls.
pval:float, required; P-value.
samplesize:int, required; Sample size.
se:float, optional; Standard error.
Examples
query
MATCH (n)-[r: GWAS_TO_VARIANT]-(m) RETURN n, r, m SKIP 0 LIMIT 3
data
[{'m': {'_id': 'rs2642438',
'_name': 'rs2642438',
'_source': ['OpenGWAS-2020-10-13', 'MR-EvE-2019-02-21'],
'alt': 'G',
'build': 'b37',
'chr': '1',
'name': 'rs2642438',
'pos': 220970028,
'ref': 'A'},
'n': {'_id': 'ieu-a-782',
'_name': 'Total cholesterol',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Willer CJ',
'build': 'HG19/GRCh37',
'category': 'Risk factor',
'id': 'ieu-a-782',
'mr': '1',
'note': 'Metabo-chip',
'nsnp': '120794',
'pmid': '24097068.0',
'population': 'Mixed',
'sample_size': '92260.0',
'sd': '41.75071927',
'sex': 'Males and Females',
'subcategory': 'Lipid',
'trait': 'Total cholesterol',
'year': '2013.0'},
'r': {'_source': ['MR-EvE-2019-02-21'],
'beta': 0.0365,
'eaf': 0.7454,
'pval': 1.51900778621703e-10,
'samplesize': 85004,
'se': 0.0056}},
{'m': {'_id': 'rs2642438',
'_name': 'rs2642438',
'_source': ['OpenGWAS-2020-10-13', 'MR-EvE-2019-02-21'],
'alt': 'G',
'build': 'b37',
'chr': '1',
'name': 'rs2642438',
'pos': 220970028,
'ref': 'A'},
'n': {'_id': 'ieu-a-781',
'_name': 'LDL cholesterol',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Willer CJ',
'build': 'HG19/GRCh37',
'category': 'Risk factor',
'id': 'ieu-a-781',
'mr': '1',
'note': 'Metabo-chip',
'nsnp': '120251',
'pmid': '24097068.0',
'population': 'Mixed',
'sample_size': '83198.0',
'sd': '38.6745912',
'sex': 'Males and Females',
'subcategory': 'Lipid',
'trait': 'LDL cholesterol',
'year': '2013.0'},
'r': {'_source': ['MR-EvE-2019-02-21'],
'beta': 0.0364,
'eaf': 0.7454,
'pval': 4.34300170639973e-09,
'samplesize': 75582,
'se': 0.0059}},
{'m': {'_id': 'rs2642438',
'_name': 'rs2642438',
'_source': ['OpenGWAS-2020-10-13', 'MR-EvE-2019-02-21'],
'alt': 'G',
'build': 'b37',
'chr': '1',
'name': 'rs2642438',
'pos': 220970028,
'ref': 'A'},
'n': {'_id': 'ieu-a-780',
'_name': 'HDL cholesterol',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Willer CJ',
'build': 'HG19/GRCh37',
'category': 'Risk factor',
'id': 'ieu-a-780',
'mr': '1',
'note': 'Metabo-chip',
'nsnp': '120672',
'pmid': '24097068.0',
'population': 'Mixed',
'sample_size': '92860.0',
'sd': '15.51018433',
'sex': 'Males and Females',
'subcategory': 'Lipid',
'trait': 'HDL cholesterol',
'year': '2013.0'},
'r': {'_source': ['MR-EvE-2019-02-21'],
'beta': 0.0384,
'eaf': 0.7454,
'pval': 4.85623841391425e-11,
'samplesize': 85128,
'se': 0.0055}}]
MEDRXIV_OBJ
Link between
(LiteratureTriple)object and(LiteratureTerm)for MedRxiv SemRep triples.
Path: (LiteratureTriple)-[MEDRXIV_OBJ]->(LiteratureTerm)
Examples
query
MATCH (n)-[r: MEDRXIV_OBJ]-(m) RETURN n, r, m SKIP 0 LIMIT 3
data
[{'m': {'_id': 'C0042210:TREATS:C0012634',
'_name': 'Vaccines TREATS Disease',
'_source': ['SemMedDB_VER42_2020_R',
'bioRxiv-2020-10-06',
'medRxiv-2020-10-06'],
'id': 'C0042210:TREATS:C0012634',
'name': 'Vaccines TREATS Disease',
'object_id': 'C0012634',
'predicate': 'TREATS',
'subject_id': 'C0042210'},
'n': {'_id': 'C0012634',
'_name': 'Disease',
'_source': ['SemMedDB_VER42_2020_R',
'bioRxiv-2020-10-06',
'medRxiv-2020-10-06'],
'id': 'C0012634',
'name': 'Disease',
'type': ['dsyn']},
'r': {'_source': ['medRxiv-2020-10-06']}},
{'m': {'_id': 'C0455829:PREDISPOSES:C0020538',
'_name': 'Waist Circumference PREDISPOSES Hypertensive disease',
'_source': ['SemMedDB_VER42_2020_R', 'medRxiv-2020-10-06'],
'id': 'C0455829:PREDISPOSES:C0020538',
'name': 'Waist Circumference PREDISPOSES Hypertensive disease',
'object_id': 'C0020538',
'predicate': 'PREDISPOSES',
'subject_id': 'C0455829'},
'n': {'_id': 'C0020538',
'_name': 'Hypertensive disease',
'_source': ['SemMedDB_VER42_2020_R',
'bioRxiv-2020-10-06',
'medRxiv-2020-10-06'],
'id': 'C0020538',
'name': 'Hypertensive disease',
'type': ['dsyn']},
'r': {'_source': ['medRxiv-2020-10-06']}},
{'m': {'_id': 'C0017337:COEXISTS_WITH:C0043047',
'_name': 'Genes COEXISTS_WITH water',
'_source': ['SemMedDB_VER42_2020_R',
'bioRxiv-2020-10-06',
'medRxiv-2020-10-06'],
'id': 'C0017337:COEXISTS_WITH:C0043047',
'name': 'Genes COEXISTS_WITH water',
'object_id': 'C0043047',
'predicate': 'COEXISTS_WITH',
'subject_id': 'C0017337'},
'n': {'_id': 'C0043047',
'_name': 'water',
'_source': ['SemMedDB_VER42_2020_R',
'bioRxiv-2020-10-06',
'medRxiv-2020-10-06'],
'id': 'C0043047',
'name': 'water',
'type': ['inch', 'phsu']},
'r': {'_source': ['medRxiv-2020-10-06']}}]
MEDRXIV_PREDICATE
Link between
(LiteratureTerm)object and(LiteratureTerm)for MedRxiv SemRep triples.
Path: (LiteratureTerm)-[MEDRXIV_PREDICATE]->(LiteratureTerm)
Properties:
count:int, required; Number of triples that have this link.
predicate:str, required; The string representation of each predicate (for example TREATS, PROCESS_OF).
Examples
query
MATCH (n)-[r: MEDRXIV_PREDICATE]-(m) RETURN n, r, m SKIP 0 LIMIT 3
data
[{'m': {'_id': 'C1416998',
'_name': 'MAN2C1 gene',
'_source': ['SemMedDB_VER42_2020_R', 'medRxiv-2020-10-06'],
'id': 'C1416998',
'name': 'MAN2C1 gene',
'type': ['gngm']},
'n': {'_id': 'C3826857',
'_name': 'Expression Quantitative Trait Locus',
'_source': ['SemMedDB_VER42_2020_R',
'bioRxiv-2020-10-06',
'medRxiv-2020-10-06'],
'id': 'C3826857',
'name': 'Expression Quantitative Trait Locus',
'type': ['gngm']},
'r': {'_source': ['medRxiv-2020-10-06'],
'count': 1,
'predicate': 'INTERACTS_WITH'}},
{'m': {'_id': 'C0023810',
'_name': 'Lipopolysaccharides',
'_source': ['SemMedDB_VER42_2020_R',
'bioRxiv-2020-10-06',
'medRxiv-2020-10-06'],
'id': 'C0023810',
'name': 'Lipopolysaccharides',
'type': ['orch']},
'n': {'_id': 'C1422064',
'_name': 'ACE2 gene',
'_source': ['SemMedDB_VER42_2020_R',
'bioRxiv-2020-10-06',
'medRxiv-2020-10-06'],
'id': 'C1422064',
'name': 'ACE2 gene',
'type': ['gngm']},
'r': {'_source': ['medRxiv-2020-10-06'],
'count': 1,
'predicate': 'STIMULATES'}},
{'m': {'_id': 'C0023810',
'_name': 'Lipopolysaccharides',
'_source': ['SemMedDB_VER42_2020_R',
'bioRxiv-2020-10-06',
'medRxiv-2020-10-06'],
'id': 'C0023810',
'name': 'Lipopolysaccharides',
'type': ['orch']},
'n': {'_id': 'C0079189',
'_name': 'cytokine',
'_source': ['SemMedDB_VER42_2020_R',
'bioRxiv-2020-10-06',
'medRxiv-2020-10-06'],
'id': 'C0079189',
'name': 'cytokine',
'type': ['aapp', 'gngm']},
'r': {'_source': ['medRxiv-2020-10-06'],
'count': 1,
'predicate': 'STIMULATES'}}]
MEDRXIV_SUB
Link between
(LiteratureTriple)subject and(LiteratureTerm)for MedRxiv SemRep triples.
Path: (LiteratureTriple)-[MEDRXIV_SUB]->(LiteratureTerm)
Examples
query
MATCH (n)-[r: MEDRXIV_SUB]-(m) RETURN n, r, m SKIP 0 LIMIT 3
data
[{'m': {'_id': 'C0042210:TREATS:C0012634',
'_name': 'Vaccines TREATS Disease',
'_source': ['SemMedDB_VER42_2020_R',
'bioRxiv-2020-10-06',
'medRxiv-2020-10-06'],
'id': 'C0042210:TREATS:C0012634',
'name': 'Vaccines TREATS Disease',
'object_id': 'C0012634',
'predicate': 'TREATS',
'subject_id': 'C0042210'},
'n': {'_id': 'C0042210',
'_name': 'Vaccines',
'_source': ['SemMedDB_VER42_2020_R',
'bioRxiv-2020-10-06',
'medRxiv-2020-10-06'],
'id': 'C0042210',
'name': 'Vaccines',
'type': ['aapp', 'gngm', 'phsu']},
'r': {'_source': ['medRxiv-2020-10-06']}},
{'m': {'_id': 'C0455829:PREDISPOSES:C0020538',
'_name': 'Waist Circumference PREDISPOSES Hypertensive disease',
'_source': ['SemMedDB_VER42_2020_R', 'medRxiv-2020-10-06'],
'id': 'C0455829:PREDISPOSES:C0020538',
'name': 'Waist Circumference PREDISPOSES Hypertensive disease',
'object_id': 'C0020538',
'predicate': 'PREDISPOSES',
'subject_id': 'C0455829'},
'n': {'_id': 'C0455829',
'_name': 'Waist Circumference',
'_source': ['SemMedDB_VER42_2020_R', 'medRxiv-2020-10-06'],
'id': 'C0455829',
'name': 'Waist Circumference',
'type': ['clna']},
'r': {'_source': ['medRxiv-2020-10-06']}},
{'m': {'_id': 'C0017337:COEXISTS_WITH:C0043047',
'_name': 'Genes COEXISTS_WITH water',
'_source': ['SemMedDB_VER42_2020_R',
'bioRxiv-2020-10-06',
'medRxiv-2020-10-06'],
'id': 'C0017337:COEXISTS_WITH:C0043047',
'name': 'Genes COEXISTS_WITH water',
'object_id': 'C0043047',
'predicate': 'COEXISTS_WITH',
'subject_id': 'C0017337'},
'n': {'_id': 'C0017337',
'_name': 'Genes',
'_source': ['SemMedDB_VER42_2020_R',
'bioRxiv-2020-10-06',
'medRxiv-2020-10-06'],
'id': 'C0017337',
'name': 'Genes',
'type': ['aapp', 'gngm']},
'r': {'_source': ['medRxiv-2020-10-06']}}]
MEDRXIV_TO_LIT
Link between
(LiteratureTriple)object and(Literature)for MedRxiv SemRep triples.
Path: (LiteratureTriple)-[MEDRXIV_TO_LIT]->(Literature)
Examples
query
MATCH (n)-[r: MEDRXIV_TO_LIT]-(m) RETURN n, r, m SKIP 0 LIMIT 3
data
[{'m': {'_id': '10.1101/2020.10.02.20204784',
'_name': '10.1101/2020.10.02.20204784',
'_source': ['medRxiv-2020-10-06'],
'doi': '10.1101/2020.10.02.20204784',
'id': '10.1101/2020.10.02.20204784',
'issn': 'medrxiv',
'title': 'Microbial population shift and metabolic characterization of '
'silver diamine fluoride treatment failure on dental caries',
'year': 2020},
'n': {'_id': 'C0074538:DISRUPTS:C0011334',
'_name': 'silver diamine fluoride DISRUPTS Dental caries',
'_source': ['SemMedDB_VER42_2020_R', 'medRxiv-2020-10-06'],
'id': 'C0074538:DISRUPTS:C0011334',
'name': 'silver diamine fluoride DISRUPTS Dental caries',
'object_id': 'C0011334',
'predicate': 'DISRUPTS',
'subject_id': 'C0074538'},
'r': {'_source': ['medRxiv-2020-10-06']}},
{'m': {'_id': '10.1101/2020.09.16.20195677',
'_name': '10.1101/2020.09.16.20195677',
'_source': ['medRxiv-2020-10-06'],
'doi': '10.1101/2020.09.16.20195677',
'id': '10.1101/2020.09.16.20195677',
'issn': 'medrxiv',
'title': 'Evaluation of Serum Zinc Concentration in Vitiligo, A '
'Case-Control Study',
'year': 2020},
'n': {'_id': 'C0043481:TREATS(INFER):C0042900',
'_name': 'Zinc TREATS(INFER) Vitiligo',
'_source': ['medRxiv-2020-10-06'],
'id': 'C0043481:TREATS(INFER):C0042900',
'name': 'Zinc TREATS(INFER) Vitiligo',
'object_id': 'C0042900',
'predicate': 'TREATS(INFER)',
'subject_id': 'C0043481'},
'r': {'_source': ['medRxiv-2020-10-06']}},
{'m': {'_id': '10.1101/2020.09.16.20195677',
'_name': '10.1101/2020.09.16.20195677',
'_source': ['medRxiv-2020-10-06'],
'doi': '10.1101/2020.09.16.20195677',
'id': '10.1101/2020.09.16.20195677',
'issn': 'medrxiv',
'title': 'Evaluation of Serum Zinc Concentration in Vitiligo, A '
'Case-Control Study',
'year': 2020},
'n': {'_id': 'C0042900:COEXISTS_WITH:C1274648',
'_name': 'Vitiligo COEXISTS_WITH Segmental vitiligo',
'_source': ['SemMedDB_VER42_2020_R', 'medRxiv-2020-10-06'],
'id': 'C0042900:COEXISTS_WITH:C1274648',
'name': 'Vitiligo COEXISTS_WITH Segmental vitiligo',
'object_id': 'C1274648',
'predicate': 'COEXISTS_WITH',
'subject_id': 'C0042900'},
'r': {'_source': ['medRxiv-2020-10-06']}}]
METAMAP_LITE
Mapping between Gwas and SemmedTerm via MetaMap Lite.
Path: (Gwas)-[METAMAP_LITE]->(LiteratureTerm)
Properties:
mesh:str, optional; MeSH tree ID
mmi_score:float, required; 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': {'_id': 'ieu-b-43',
'_name': 'frontotemporal dementia (TDP subtype)',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Van Deerlin,V',
'build': 'HG19/GRCh37',
'category': 'Binary',
'id': 'ieu-b-43',
'mr': '1',
'ncase': '515.0',
'ncontrol': '2509.0',
'nsnp': '494577',
'pmid': '20154673.0',
'population': 'European',
'sample_size': '3024.0',
'sex': 'Males and Females',
'subcategory': 'Psychiatric / neurological',
'trait': 'frontotemporal dementia (TDP subtype)',
'unit': 'log odds ratio',
'year': '2010.0'},
'n': {'_id': 'C0236642',
'_name': 'Pick Disease of the Brain',
'_source': ['SemMedDB_VER42_2020_R',
'bioRxiv-2020-10-06',
'medRxiv-2020-10-06'],
'id': 'C0236642',
'name': 'Pick Disease of the Brain',
'type': ['dsyn']},
'r': {'_source': ['MetaMapLite-2018AA'],
'mesh': 'C10.228.140.380.266.299;C10.574.950.300.299;C18.452.845.800.300.299;F03.615.400.380.299',
'mmi_score': 10.19}},
{'m': {'_id': 'ieu-b-43',
'_name': 'frontotemporal dementia (TDP subtype)',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Van Deerlin,V',
'build': 'HG19/GRCh37',
'category': 'Binary',
'id': 'ieu-b-43',
'mr': '1',
'ncase': '515.0',
'ncontrol': '2509.0',
'nsnp': '494577',
'pmid': '20154673.0',
'population': 'European',
'sample_size': '3024.0',
'sex': 'Males and Females',
'subcategory': 'Psychiatric / neurological',
'trait': 'frontotemporal dementia (TDP subtype)',
'unit': 'log odds ratio',
'year': '2010.0'},
'n': {'_id': 'C0338451',
'_name': 'Frontotemporal dementia',
'_source': ['bioRxiv-2020-10-06'],
'id': 'C0338451',
'name': 'Frontotemporal dementia',
'type': ['dsyn']},
'r': {'_source': ['MetaMapLite-2018AA'],
'mesh': 'C10.228.140.380.266.299;C10.574.950.300.299;C18.452.845.800.300.299;F03.615.400.380.299',
'mmi_score': 10.19}},
{'m': {'_id': 'ieu-b-40',
'_name': 'body mass index',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Yengo, L',
'build': 'HG19/GRCh37',
'category': 'Continuous',
'consortium': 'GIANT',
'id': 'ieu-b-40',
'mr': '1',
'nsnp': '2336260',
'pmid': '30124842.0',
'population': 'European',
'sample_size': '681275.0',
'sex': 'Males and Females',
'subcategory': 'Anthropometric',
'trait': 'body mass index',
'unit': 'SD',
'year': '2018.0'},
'n': {'_id': 'C0005893',
'_name': 'Body mass index',
'_source': ['SemMedDB_VER42_2020_R'],
'id': 'C0005893',
'name': 'Body mass index',
'type': ['clna']},
'r': {'_source': ['MetaMapLite-2018AA'],
'mesh': 'E01.370.600.115.100.125;E05.041.124.125;G07.100.100.125;N06.850.505.200.100.175',
'mmi_score': 9.27}}]
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': {'_id': 'http://purl.obolibrary.org/obo/MONDO_0002971',
'_name': 'amelanotic melanoma',
'_source': ['Mondo-2021-01-12'],
'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'],
'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',
'_name': 'amelanotic melanoma',
'_source': ['EpiGraphDB v0.3'],
'id': 'http://www.ebi.ac.uk/efo/EFO_1001937',
'type': 'typed-literal',
'value': 'amelanotic melanoma'},
'r': {'_source': 'Mondo'}},
{'m': {'_id': 'http://purl.obolibrary.org/obo/MONDO_0000309',
'_name': 'aniseikonia',
'_source': ['Mondo-2021-01-12'],
'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']},
'n': {'_id': 'http://www.ebi.ac.uk/efo/EFO_1001266',
'_name': 'Aniseikonia',
'_source': ['EpiGraphDB v0.3'],
'id': 'http://www.ebi.ac.uk/efo/EFO_1001266',
'type': 'typed-literal',
'value': 'Aniseikonia'},
'r': {'_source': 'Mondo'}},
{'m': {'_id': 'http://purl.obolibrary.org/obo/MONDO_0002987',
'_name': 'spongiotic dermatitis',
'_source': ['Mondo-2021-01-12'],
'definition': 'A chronic inflammatory skin condition characterized by '
'itchiness and a rash in the chest and abdominal areas. '
'It affects males more than females and is usually '
'contracted at a relatively young age. It is thought to '
'be caused by an allergic reaction to food, insect '
'bites, or medication.',
'doid': ['4406'],
'efo': ['1000768'],
'icd9': ['692.9'],
'id': 'http://purl.obolibrary.org/obo/MONDO_0002987',
'label': 'spongiotic dermatitis',
'umls': ['C0262984']},
'n': {'_id': 'http://www.ebi.ac.uk/efo/EFO_1000768',
'_name': 'spongiotic dermatitis',
'_source': ['EpiGraphDB v0.3'],
'id': 'http://www.ebi.ac.uk/efo/EFO_1000768',
'type': 'typed-literal',
'value': 'spongiotic dermatitis'},
'r': {'_source': 'Mondo'}}]
MONDO_MAP_UMLS
Mapping between a
(Disease)term and an(LiteratureTerm)term, based on Mondo.
Path: (Disease)-[MONDO_MAP_UMLS]->(Efo)
Examples
query
MATCH (n)-[r: MONDO_MAP_UMLS]-(m) RETURN n, r, m SKIP 0 LIMIT 3
data
[{'m': {'_id': 'http://purl.obolibrary.org/obo/MONDO_0002977',
'_name': 'autoimmune disease of the nervous system',
'_source': ['Mondo-2021-01-12'],
'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'],
'id': 'http://purl.obolibrary.org/obo/MONDO_0002977',
'label': 'autoimmune disease of the nervous system',
'mesh': ['D020274'],
'umls': ['C0751872', 'C0751871']},
'n': {'_id': 'C0751871',
'_name': 'Autoimmune Diseases of the Nervous System',
'_source': ['SemMedDB_VER42_2020_R'],
'id': 'C0751871',
'name': 'Autoimmune Diseases of the Nervous System',
'type': ['dsyn']},
'r': {'_source': 'Mondo'}},
{'m': {'_id': 'http://purl.obolibrary.org/obo/MONDO_0002977',
'_name': 'autoimmune disease of the nervous system',
'_source': ['Mondo-2021-01-12'],
'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'],
'id': 'http://purl.obolibrary.org/obo/MONDO_0002977',
'label': 'autoimmune disease of the nervous system',
'mesh': ['D020274'],
'umls': ['C0751872', 'C0751871']},
'n': {'_id': 'C0751872',
'_name': 'Immune Disorders, Nervous System',
'_source': ['SemMedDB_VER42_2020_R'],
'id': 'C0751872',
'name': 'Immune Disorders, Nervous System',
'type': ['dsyn']},
'r': {'_source': 'Mondo'}},
{'m': {'_id': 'http://purl.obolibrary.org/obo/MONDO_0000313',
'_name': 'hypophosphatemia (disease)',
'_source': ['Mondo-2021-01-12'],
'definition': 'Lower than normal levels of phosphates in the '
'circulating blood.',
'doid': ['0050336'],
'id': 'http://purl.obolibrary.org/obo/MONDO_0000313',
'label': 'hypophosphatemia (disease)',
'mesh': ['D017674'],
'umls': ['C0085682']},
'n': {'_id': 'C0085682',
'_name': 'Hypophosphatemia',
'_source': ['SemMedDB_VER42_2020_R'],
'id': 'C0085682',
'name': 'Hypophosphatemia',
'type': ['dsyn']},
'r': {'_source': 'Mondo'}}]
MR_EVE_MR
Pairwise Mendelian randomization evidence between phenotypic traits.
Results from MR-EvE (Hemani et al., 2017).
Path: (Gwas)-[MR_EVE_MR]->(Gwas)
Properties:
b:float, required; Effect size.
ci_low:float, optional; Lower bound of the confidence interval.
ci_upp:float, optional; Upper bound of the confidence interval.
method:str, required; MR method, e.g. FE IVW etc.
moescore:float, required; Mix of Experts score.
nsnp:int, required; Number of SNPs.
pval:float, optional; P-value.
se:float, optional; Standard error.
-
selection:str, required; Instrument selection.- DF: directionality filtering
- HF: heterogeneity filtering
- Tophits: no filtering
- DF + HF: both types of filtering
Examples
query
MATCH (n)-[r: MR_EVE_MR]-(m) RETURN n, r, m SKIP 0 LIMIT 3
data
[{'m': {'_id': 'prot-a-1171',
'_name': 'Polypeptide N-acetylgalactosaminyltransferase 2',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Sun BB',
'build': 'HG19/GRCh37',
'category': 'Immune system',
'id': 'prot-a-1171',
'mr': '1',
'nsnp': '10534735',
'pmid': '29875488.0',
'population': 'European',
'sample_size': '3301.0',
'sex': 'Males and Females',
'subcategory': 'Protein',
'trait': 'Polypeptide N-acetylgalactosaminyltransferase 2',
'year': '2018.0'},
'n': {'_id': 'ukb-d-XIII_MUSCULOSKELET',
'_name': 'Diseases of the musculoskeletal system and connective tissue',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Neale lab',
'build': 'HG19/GRCh37',
'category': 'Binary',
'id': 'ukb-d-XIII_MUSCULOSKELET',
'mr': '1',
'ncase': '77099.0',
'ncontrol': '284095.0',
'nsnp': '13586589',
'population': 'European',
'sample_size': '361194.0',
'sex': 'Males and Females',
'trait': 'Diseases of the musculoskeletal system and connective tissue',
'year': '2018.0'},
'r': {'_source': ['MR-EvE-2021-03-10'],
'b': -0.851781600575194,
'ci_low': -2.60590765161164,
'ci_upp': 0.9023444504612571,
'method': 'FE IVW',
'moescore': 1.0,
'nsnp': 2,
'pval': 0.341223071383756,
'se': 0.8949622709369641,
'selection': 'DF'}},
{'m': {'_id': 'prot-a-1171',
'_name': 'Polypeptide N-acetylgalactosaminyltransferase 2',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Sun BB',
'build': 'HG19/GRCh37',
'category': 'Immune system',
'id': 'prot-a-1171',
'mr': '1',
'nsnp': '10534735',
'pmid': '29875488.0',
'population': 'European',
'sample_size': '3301.0',
'sex': 'Males and Females',
'subcategory': 'Protein',
'trait': 'Polypeptide N-acetylgalactosaminyltransferase 2',
'year': '2018.0'},
'n': {'_id': 'ukb-d-XI_DIGESTIVE',
'_name': 'Diseases of the digestive system',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Neale lab',
'build': 'HG19/GRCh37',
'category': 'Binary',
'id': 'ukb-d-XI_DIGESTIVE',
'mr': '1',
'ncase': '115893.0',
'ncontrol': '245301.0',
'nsnp': '13586589',
'population': 'European',
'sample_size': '361194.0',
'sex': 'Males and Females',
'trait': 'Diseases of the digestive system',
'year': '2018.0'},
'r': {'_source': ['MR-EvE-2021-03-10'],
'b': -0.390501443117296,
'ci_low': -1.66129768094485,
'ci_upp': 0.8802947947102601,
'method': 'FE IVW',
'moescore': 1.0,
'nsnp': 2,
'pval': 0.546983754393494,
'se': 0.6483654274630389,
'selection': 'DF'}},
{'m': {'_id': 'prot-a-1171',
'_name': 'Polypeptide N-acetylgalactosaminyltransferase 2',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Sun BB',
'build': 'HG19/GRCh37',
'category': 'Immune system',
'id': 'prot-a-1171',
'mr': '1',
'nsnp': '10534735',
'pmid': '29875488.0',
'population': 'European',
'sample_size': '3301.0',
'sex': 'Males and Females',
'subcategory': 'Protein',
'trait': 'Polypeptide N-acetylgalactosaminyltransferase 2',
'year': '2018.0'},
'n': {'_id': 'ukb-d-RHEUMA_NOS',
'_name': 'Other/unspecified rheumatoid arthritis',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Neale lab',
'build': 'HG19/GRCh37',
'category': 'Binary',
'id': 'ukb-d-RHEUMA_NOS',
'mr': '1',
'ncase': '1281.0',
'ncontrol': '359913.0',
'nsnp': '9704049',
'population': 'European',
'sample_size': '361194.0',
'sex': 'Males and Females',
'trait': 'Other/unspecified rheumatoid arthritis',
'year': '2018.0'},
'r': {'_source': ['MR-EvE-2021-03-10'],
'b': -7.75099861369731,
'ci_low': -20.3100138614487,
'ci_upp': 4.80801663405407,
'method': 'FE IVW',
'moescore': 1.0,
'nsnp': 2,
'pval': 0.226414920225498,
'se': 6.407660840689481,
'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:float, required; Correlation coefficient.
Examples
query
MATCH (n)-[r: OBS_COR]-(m) RETURN n, r, m SKIP 0 LIMIT 3
data
[{'m': {'_id': 'ukb-b-5011',
'_name': 'Thickness of butter/margarine spread on bread rolls: medium',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Ben Elsworth',
'build': 'HG19/GRCh37',
'category': 'Binary',
'consortium': 'MRC-IEU',
'id': 'ukb-b-5011',
'mr': '1',
'ncase': '2403.0',
'ncontrol': '62546.0',
'note': '20101#2: Output from GWAS pipeline using Phesant derived '
'variables from UKBiobank',
'nsnp': '9851867',
'population': 'European',
'sample_size': '64949.0',
'sex': 'Males and Females',
'trait': 'Thickness of butter/margarine spread on bread rolls: medium',
'unit': 'SD',
'year': '2018.0'},
'n': {'_id': 'ukb-b-5536',
'_name': 'Vitamin and/or mineral supplement use: Magnesium',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Ben Elsworth',
'build': 'HG19/GRCh37',
'category': 'Binary',
'consortium': 'MRC-IEU',
'id': 'ukb-b-5536',
'mr': '1',
'ncase': '1043.0',
'ncontrol': '63906.0',
'note': '20084#483: Output from GWAS pipeline using Phesant derived '
'variables from UKBiobank',
'nsnp': '9851867',
'population': 'European',
'sample_size': '64949.0',
'sex': 'Males and Females',
'trait': 'Vitamin and/or mineral supplement use: Magnesium',
'unit': 'SD',
'year': '2018.0'},
'r': {'_source': ['MRC-IEU UK Biobank - '
'https://www.ukbiobank.ac.uk/tag/15825/'],
'cor': 0.8969316953882069}},
{'m': {'_id': 'ukb-b-5011',
'_name': 'Thickness of butter/margarine spread on bread rolls: medium',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Ben Elsworth',
'build': 'HG19/GRCh37',
'category': 'Binary',
'consortium': 'MRC-IEU',
'id': 'ukb-b-5011',
'mr': '1',
'ncase': '2403.0',
'ncontrol': '62546.0',
'note': '20101#2: Output from GWAS pipeline using Phesant derived '
'variables from UKBiobank',
'nsnp': '9851867',
'population': 'European',
'sample_size': '64949.0',
'sex': 'Males and Females',
'trait': 'Thickness of butter/margarine spread on bread rolls: medium',
'unit': 'SD',
'year': '2018.0'},
'n': {'_id': 'ukb-b-309',
'_name': 'Types of spread used on bread/crackers: Low fat dairy spread '
'on bread/crackers',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Ben Elsworth',
'build': 'HG19/GRCh37',
'category': 'Binary',
'consortium': 'MRC-IEU',
'id': 'ukb-b-309',
'mr': '1',
'ncase': '1515.0',
'ncontrol': '63434.0',
'note': '20087#178: Output from GWAS pipeline using Phesant derived '
'variables from UKBiobank',
'nsnp': '9851867',
'population': 'European',
'sample_size': '64949.0',
'sex': 'Males and Females',
'trait': 'Types of spread used on bread/crackers: Low fat dairy spread '
'on bread/crackers',
'unit': 'SD',
'year': '2018.0'},
'r': {'_source': ['MRC-IEU UK Biobank - '
'https://www.ukbiobank.ac.uk/tag/15825/'],
'cor': 0.8871589099092092}},
{'m': {'_id': 'ukb-b-5011',
'_name': 'Thickness of butter/margarine spread on bread rolls: medium',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Ben Elsworth',
'build': 'HG19/GRCh37',
'category': 'Binary',
'consortium': 'MRC-IEU',
'id': 'ukb-b-5011',
'mr': '1',
'ncase': '2403.0',
'ncontrol': '62546.0',
'note': '20101#2: Output from GWAS pipeline using Phesant derived '
'variables from UKBiobank',
'nsnp': '9851867',
'population': 'European',
'sample_size': '64949.0',
'sex': 'Males and Females',
'trait': 'Thickness of butter/margarine spread on bread rolls: medium',
'unit': 'SD',
'year': '2018.0'},
'n': {'_id': 'ukb-b-4843',
'_name': 'Types of spreads/sauces consumed: Other sauce',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Ben Elsworth',
'build': 'HG19/GRCh37',
'category': 'Binary',
'consortium': 'MRC-IEU',
'id': 'ukb-b-4843',
'mr': '1',
'ncase': '2930.0',
'ncontrol': '62019.0',
'note': '20088#350: Output from GWAS pipeline using Phesant derived '
'variables from UKBiobank',
'nsnp': '9851867',
'population': 'European',
'sample_size': '64949.0',
'sex': 'Males and Females',
'trait': 'Types of spreads/sauces consumed: Other sauce',
'unit': 'SD',
'year': '2018.0'},
'r': {'_source': ['MRC-IEU UK Biobank - '
'https://www.ukbiobank.ac.uk/tag/15825/'],
'cor': 0.8464327430861379}}]
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': {'_id': 'DANUSERTIB',
'_name': 'DANUSERTIB',
'_source': ['Opentargets-2020-10-19'],
'chembl_uri': 'http://identifiers.org/chembl.compound/CHEMBL402548',
'label': 'DANUSERTIB',
'molecule_type': 'Small molecule'},
'n': {'_id': 'http://purl.obolibrary.org/obo/MONDO_0009693',
'_name': 'plasma cell myeloma',
'_source': ['Mondo-2021-01-12'],
'definition': 'A bone marrow-based plasma cell neoplasm characterized '
'by a serum monoclonal protein and skeletal destruction '
'with osteolytic lesions, pathological fractures, bone '
'pain, hypercalcemia, and anemia. Clinical variants '
'include non-secretory myeloma, smoldering myeloma, '
'indolent myeloma, and plasma cell leukemia. (WHO, 2001)',
'doid': ['9538'],
'efo': ['0001378'],
'icd10': ['C90.0', 'C90.00'],
'icd9': ['203.0'],
'id': 'http://purl.obolibrary.org/obo/MONDO_0009693',
'label': 'plasma cell myeloma',
'mesh': ['D009101'],
'umls': ['C0026764']},
'r': {'_source': ['Opentargets-2020-08-24']}},
{'m': {'_id': 'DANUSERTIB',
'_name': 'DANUSERTIB',
'_source': ['Opentargets-2020-10-19'],
'chembl_uri': 'http://identifiers.org/chembl.compound/CHEMBL402548',
'label': 'DANUSERTIB',
'molecule_type': 'Small molecule'},
'n': {'_id': 'http://purl.obolibrary.org/obo/MONDO_0005059',
'_name': 'leukemia (disease)',
'_source': ['Mondo-2021-01-12'],
'definition': 'A malignant (clonal) hematologic disorder, involving '
'hematopoietic stem cells and characterized by the '
'presence of primitive or atypical myeloid or lymphoid '
'cells in the bone marrow and the blood. Leukemias are '
'classified as acute or chronic based on the degree of '
'cellular differentiation and the predominant cell type '
'present. Leukemia is usually associated with anemia, '
'fever, hemorrhagic episodes, and splenomegaly. Common '
'leukemias include acute myeloid leukemia, chronic '
'myelogenous leukemia, acute lymphoblastic or precursor '
'lymphoblastic leukemia, and chronic lymphocytic '
'leukemia. Treatment is vital to patient survival; '
'untreated, the natural course of acute leukemias is '
'normally measured in weeks or months, while that of '
'chronic leukemias is more often measured in months or '
'years.',
'doid': ['1240'],
'efo': ['0000565'],
'icd10': ['C95', 'C95.9', 'C95.90'],
'icd9': ['208',
'207',
'208.90',
'208.9',
'208.8',
'207.80',
'207.8',
'208.80'],
'id': 'http://purl.obolibrary.org/obo/MONDO_0005059',
'label': 'leukemia (disease)',
'mesh': ['D007938'],
'umls': ['C0023418']},
'r': {'_source': ['Opentargets-2020-08-24']}},
{'m': {'_id': 'ILORASERTIB',
'_name': 'ILORASERTIB',
'_source': ['Opentargets-2020-10-19'],
'chembl_uri': 'http://identifiers.org/chembl.compound/CHEMBL1980297',
'label': 'ILORASERTIB',
'molecule_type': 'Small molecule'},
'n': {'_id': 'http://purl.obolibrary.org/obo/MONDO_0004992',
'_name': 'cancer',
'_source': ['Mondo-2021-01-12'],
'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',
'umls': ['C0006826']},
'r': {'_source': ['Opentargets-2020-08-24']}}]
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:
action_type:str, required; Type of the mechanism, e.g. inhibitor, etc.
phase:str, required; Phase of the target drug.
Examples
query
MATCH (n)-[r: OPENTARGETS_DRUG_TO_TARGET]-(m) RETURN n, r, m SKIP 0 LIMIT 3
data
[{'m': {'_id': 'APABETALONE',
'_name': 'APABETALONE',
'_source': ['Opentargets-2020-10-19'],
'chembl_uri': 'http://identifiers.org/chembl.compound/CHEMBL2393130',
'label': 'APABETALONE',
'molecule_type': 'Small molecule'},
'n': {'_id': 'ENSG00000169925',
'_name': 'BRD3',
'_source': ['BioMart-2020-10-13', 'Finan_et_al'],
'adme_gene': 'N',
'bio_druggable': 'N',
'biomart_source': 'HGNC Symbol',
'chr': '9',
'description': 'bromodomain containing 3 [Source:HGNC Symbol;Acc:1104]',
'druggability_tier': 'Tier 2',
'end': 136933657,
'ensembl_id': 'ENSG00000169925',
'name': 'BRD3',
'small_mol_druggable': 'Y',
'start': 136895427,
'type': 'protein_coding'},
'r': {'_source': ['Opentargets-2020-10-19'],
'action_type': 'INHIBITOR',
'phase': '3'}},
{'m': {'_id': 'APABETALONE',
'_name': 'APABETALONE',
'_source': ['Opentargets-2020-10-19'],
'chembl_uri': 'http://identifiers.org/chembl.compound/CHEMBL2393130',
'label': 'APABETALONE',
'molecule_type': 'Small molecule'},
'n': {'_id': 'ENSG00000204256',
'_name': 'BRD2',
'_source': ['BioMart-2020-10-13', 'Finan_et_al'],
'adme_gene': 'N',
'bio_druggable': 'N',
'biomart_source': 'HGNC Symbol',
'chr': '6',
'description': 'bromodomain containing 2 [Source:HGNC Symbol;Acc:1103]',
'druggability_tier': 'Tier 2',
'end': 32949282,
'ensembl_id': 'ENSG00000204256',
'name': 'BRD2',
'small_mol_druggable': 'Y',
'start': 32936437,
'type': 'protein_coding'},
'r': {'_source': ['Opentargets-2020-10-19'],
'action_type': 'INHIBITOR',
'phase': '3'}},
{'m': {'_id': 'APABETALONE',
'_name': 'APABETALONE',
'_source': ['Opentargets-2020-10-19'],
'chembl_uri': 'http://identifiers.org/chembl.compound/CHEMBL2393130',
'label': 'APABETALONE',
'molecule_type': 'Small molecule'},
'n': {'_id': 'ENSG00000137948',
'_name': 'BRDT',
'_source': ['BioMart-2020-10-13', 'Finan_et_al'],
'adme_gene': 'N',
'bio_druggable': 'N',
'biomart_source': 'HGNC Symbol',
'chr': '1',
'description': 'bromodomain, testis-specific [Source:HGNC '
'Symbol;Acc:1105]',
'druggability_tier': 'Tier 2',
'end': 92479983,
'ensembl_id': 'ENSG00000137948',
'name': 'BRDT',
'small_mol_druggable': 'Y',
'start': 92414928,
'type': 'protein_coding'},
'r': {'_source': ['Opentargets-2020-10-19'],
'action_type': 'INHIBITOR',
'phase': '3'}}]
PATHWAY_CHILD_OF
Parent/child relationship of pathways.
Path: (Pathway)-[PATHWAY_CHILD_OF]->(Pathway)
Examples
query
MATCH (n)-[r: PATHWAY_CHILD_OF]-(m) RETURN n, r, m SKIP 0 LIMIT 3
data
[{'m': {'_id': 'R-HSA-164843',
'_name': '2-LTR circle formation',
'_source': ['Reactome-2020-10-13'],
'id': 'R-HSA-164843',
'name': '2-LTR circle formation',
'url': 'https://reactome.org/PathwayBrowser/#/R-HSA-164843'},
'n': {'_id': 'R-HSA-162592',
'_name': 'Integration of provirus',
'_source': ['Reactome-2020-10-13'],
'id': 'R-HSA-162592',
'name': 'Integration of provirus',
'url': 'https://reactome.org/PathwayBrowser/#/R-HSA-162592'},
'r': {'_source': ['Reactome-2020-09-10']}},
{'m': {'_id': 'R-HSA-73843',
'_name': '5-Phosphoribose 1-diphosphate biosynthesis',
'_source': ['Reactome-2020-10-13'],
'id': 'R-HSA-73843',
'name': '5-Phosphoribose 1-diphosphate biosynthesis',
'url': 'https://reactome.org/PathwayBrowser/#/R-HSA-73843'},
'n': {'_id': 'R-HSA-71336',
'_name': 'Pentose phosphate pathway',
'_source': ['Reactome-2020-10-13'],
'id': 'R-HSA-71336',
'name': 'Pentose phosphate pathway',
'url': 'https://reactome.org/PathwayBrowser/#/R-HSA-71336'},
'r': {'_source': ['Reactome-2020-09-10']}},
{'m': {'_id': 'R-HSA-1971475',
'_name': 'A tetrasaccharide linker sequence is required for GAG '
'synthesis',
'_source': ['Reactome-2020-10-13'],
'id': 'R-HSA-1971475',
'name': 'A tetrasaccharide linker sequence is required for GAG '
'synthesis',
'url': 'https://reactome.org/PathwayBrowser/#/R-HSA-1971475'},
'n': {'_id': 'R-HSA-1793185',
'_name': 'Chondroitin sulfate/dermatan sulfate metabolism',
'_source': ['Reactome-2020-10-13'],
'id': 'R-HSA-1793185',
'name': 'Chondroitin sulfate/dermatan sulfate metabolism',
'url': 'https://reactome.org/PathwayBrowser/#/R-HSA-1793185'},
'r': {'_source': ['Reactome-2020-09-10']}}]
PROTEIN_IN_PATHWAY
A protein is part of the pathway annotation in the lowest level pathway hierarchy.
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': {'_id': 'R-HSA-164843',
'_name': '2-LTR circle formation',
'_source': ['Reactome-2020-10-13'],
'id': 'R-HSA-164843',
'name': '2-LTR circle formation',
'url': 'https://reactome.org/PathwayBrowser/#/R-HSA-164843'},
'n': {'_id': 'Q13426',
'_name': 'Q13426',
'_source': ['BioMart-2020-10-13', 'Reactome-2020-10-13', 'STRING-v11'],
'name': 'Q13426',
'uniprot_id': 'Q13426'},
'r': {'_source': ['Reactome-2020-09-10']}},
{'m': {'_id': 'R-HSA-164843',
'_name': '2-LTR circle formation',
'_source': ['Reactome-2020-10-13'],
'id': 'R-HSA-164843',
'name': '2-LTR circle formation',
'url': 'https://reactome.org/PathwayBrowser/#/R-HSA-164843'},
'n': {'_id': 'P69726',
'_name': 'P69726',
'_source': ['Reactome-2020-10-13'],
'name': 'P69726',
'uniprot_id': 'P69726'},
'r': {'_source': ['Reactome-2020-09-10']}},
{'m': {'_id': 'R-HSA-164843',
'_name': '2-LTR circle formation',
'_source': ['Reactome-2020-10-13'],
'id': 'R-HSA-164843',
'name': '2-LTR circle formation',
'url': 'https://reactome.org/PathwayBrowser/#/R-HSA-164843'},
'n': {'_id': 'P69723',
'_name': 'P69723',
'_source': ['Reactome-2020-10-13'],
'name': 'P69723',
'uniprot_id': 'P69723'},
'r': {'_source': ['Reactome-2020-09-10']}}]
PRS
Pairwise polygenic risk scores between GWAS.
Results from PRS Atlas ( Richardson et al., 2019 ).
Path: (Gwas)-[PRS]->(Gwas)
Properties:
beta:float, required; Effect size.
model:str, required; Name of the model used, e.g. lm, glm, etc.
n:int, required; Sample size.
nsnps:int, required; Number of SNPs.
p:float, required; P-value.
r2:float, required; R2 metric.
se:float, required; Standard error.
Examples
query
MATCH (n)-[r: PRS]-(m) RETURN n, r, m SKIP 0 LIMIT 3
data
[{'m': {'_id': 'ukb-b-9433',
'_name': 'Age started oral contraceptive pill',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Ben Elsworth',
'build': 'HG19/GRCh37',
'category': 'Continuous',
'consortium': 'MRC-IEU',
'id': 'ukb-b-9433',
'mr': '1',
'note': '2794: Output from GWAS pipeline using Phesant derived '
'variables from UKBiobank',
'nsnp': '9851867',
'population': 'European',
'sample_size': '198213.0',
'sex': 'Males and Females',
'trait': 'Age started oral contraceptive pill',
'unit': 'SD',
'year': '2018.0'},
'n': {'_id': 'ieu-a-803',
'_name': 'PGC cross-disorder traits',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Smoller JW',
'build': 'HG19/GRCh37',
'category': 'Disease',
'id': 'ieu-a-803',
'mr': '1',
'ncase': '33332.0',
'ncontrol': '27888.0',
'note': 'PGC (psychiatric genomics consortium)',
'nsnp': '1249700',
'pmid': '23453885.0',
'population': 'European',
'sample_size': '61220.0',
'sex': 'Males and Females',
'subcategory': 'Psychiatric / neurological',
'trait': 'PGC cross-disorder traits',
'year': '2013.0'},
'r': {'_source': ['PRS-ATLAS'],
'beta': 0.002062185,
'model': 'lm',
'n': 143342,
'nsnps': 83,
'p': 0.332558651,
'r2': 1.36e-05,
'se': 0.00212821}},
{'m': {'_id': 'ukb-b-9433',
'_name': 'Age started oral contraceptive pill',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Ben Elsworth',
'build': 'HG19/GRCh37',
'category': 'Continuous',
'consortium': 'MRC-IEU',
'id': 'ukb-b-9433',
'mr': '1',
'note': '2794: Output from GWAS pipeline using Phesant derived '
'variables from UKBiobank',
'nsnp': '9851867',
'population': 'European',
'sample_size': '198213.0',
'sex': 'Males and Females',
'trait': 'Age started oral contraceptive pill',
'unit': 'SD',
'year': '2018.0'},
'n': {'_id': 'ieu-a-1005',
'_name': 'Percent emphysema',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Manichaikul A',
'build': 'HG19/GRCh37',
'category': 'Risk factor',
'id': 'ieu-a-1005',
'mr': '1',
'nsnp': '2968584',
'pmid': '24383474.0',
'population': 'Mixed',
'sample_size': '7667.0',
'sd': '0.708',
'sex': 'Males and Females',
'subcategory': 'Lung disease',
'trait': 'Percent emphysema',
'year': '2014.0'},
'r': {'_source': ['PRS-ATLAS'],
'beta': 0.000193919,
'model': 'lm',
'n': 143342,
'nsnps': 53,
'p': 0.927543023,
'r2': 4.8e-06,
'se': 0.002132467}},
{'m': {'_id': 'ukb-b-9433',
'_name': 'Age started oral contraceptive pill',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Ben Elsworth',
'build': 'HG19/GRCh37',
'category': 'Continuous',
'consortium': 'MRC-IEU',
'id': 'ukb-b-9433',
'mr': '1',
'note': '2794: Output from GWAS pipeline using Phesant derived '
'variables from UKBiobank',
'nsnp': '9851867',
'population': 'European',
'sample_size': '198213.0',
'sex': 'Males and Females',
'trait': 'Age started oral contraceptive pill',
'unit': 'SD',
'year': '2018.0'},
'n': {'_id': 'ieu-a-818',
'_name': "Parkinson's disease",
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Pankratz',
'build': 'HG19/GRCh37',
'category': 'Disease',
'id': 'ieu-a-818',
'mr': '1',
'ncase': '816.0',
'ncontrol': '856.0',
'note': "Familial Parkinson's disease; effect allele frequencies are "
'missing',
'nsnp': '318553',
'pmid': '21829596.0',
'population': 'European',
'sample_size': '1672.0',
'sex': 'Males and Females',
'subcategory': 'Psychiatric / neurological',
'trait': "Parkinson's disease",
'year': '2011.0'},
'r': {'_source': ['PRS-ATLAS'],
'beta': 0.003211184,
'model': 'lm',
'n': 143342,
'nsnps': 6,
'p': 0.12943688,
'r2': 4.07e-06,
'se': 0.002117727}}]
TERM_TO_GENE
Connection from semantic term
(LiteratureTerm)to(Gene)nodes where terms are genes.
Path: (LiteratureTerm)-[TERM_TO_GENE]->(Gene)
Examples
query
MATCH (n)-[r: TERM_TO_GENE]-(m) RETURN n, r, m SKIP 0 LIMIT 3
data
[{'m': {'_id': 'ENSG00000109519',
'_name': 'GRPEL1',
'_source': ['BioMart-2020-10-13'],
'biomart_source': 'HGNC Symbol',
'chr': '4',
'description': 'GrpE-like 1, mitochondrial (E. coli) [Source:HGNC '
'Symbol;Acc:19696]',
'end': 7069924,
'ensembl_id': 'ENSG00000109519',
'name': 'GRPEL1',
'start': 7060633,
'type': 'protein_coding'},
'n': {'_id': '80273',
'_name': 'GRPEL1',
'_source': ['SemMedDB_VER42_2020_R'],
'id': '80273',
'name': 'GRPEL1',
'type': ['aapp', 'gngm']},
'r': {'_source': 'LiteratureTerm'}},
{'m': {'_id': 'ENSG00000167434',
'_name': 'CA4',
'_source': ['BioMart-2020-10-13', 'Finan_et_al'],
'adme_gene': 'N',
'bio_druggable': 'Y',
'biomart_source': 'HGNC Symbol',
'chr': '17',
'description': 'carbonic anhydrase IV [Source:HGNC Symbol;Acc:1375]',
'druggability_tier': 'Tier 1',
'end': 58248260,
'ensembl_id': 'ENSG00000167434',
'name': 'CA4',
'small_mol_druggable': 'Y',
'start': 58227297,
'type': 'protein_coding'},
'n': {'_id': '762',
'_name': 'CA4',
'_source': ['SemMedDB_VER42_2020_R'],
'id': '762',
'name': 'CA4',
'type': ['aapp', 'gngm']},
'r': {'_source': 'LiteratureTerm'}},
{'m': {'_id': 'ENSG00000109182',
'_name': 'CWH43',
'_source': ['BioMart-2020-10-13'],
'biomart_source': 'HGNC Symbol',
'chr': '4',
'description': 'cell wall biogenesis 43 C-terminal homolog (S. '
'cerevisiae) [Source:HGNC Symbol;Acc:26133]',
'end': 49064098,
'ensembl_id': 'ENSG00000109182',
'name': 'CWH43',
'start': 48988264,
'type': 'protein_coding'},
'n': {'_id': '80157',
'_name': 'CWH43',
'_source': ['SemMedDB_VER42_2020_R'],
'id': '80157',
'name': 'CWH43',
'type': ['gngm']},
'r': {'_source': 'LiteratureTerm'}}]
SEMMEDDB_OBJ
Link between
(LiteratureTriple)object and(LiteratureTerm)for SemMedDB.
Path: (LiteratureTriple)-[SEMMEDDB_OBJ]->(LiteratureTerm)
Examples
query
MATCH (n)-[r: SEMMEDDB_OBJ]-(m) RETURN n, r, m SKIP 0 LIMIT 3
data
[{'m': {'_id': '51237:INTERACTS_WITH:C0669516',
'_name': 'pituitary adenylate cyclase activating '
'polypeptide|ADCYAP1|MZB1 INTERACTS_WITH superoxide dismutase '
'1|SOD1',
'_source': ['SemMedDB_VER42_2020_R'],
'id': '51237:INTERACTS_WITH:C0669516',
'name': 'pituitary adenylate cyclase activating '
'polypeptide|ADCYAP1|MZB1 INTERACTS_WITH superoxide dismutase '
'1|SOD1',
'object_id': 'C0669516',
'predicate': 'INTERACTS_WITH',
'subject_id': '51237'},
'n': {'_id': 'C0669516',
'_name': 'superoxide dismutase 1',
'_source': ['SemMedDB_VER42_2020_R'],
'id': 'C0669516',
'name': 'superoxide dismutase 1',
'type': ['aapp', 'gngm', 'enzy']},
'r': {'_source': ['SemMedDB_VER42_2020_R']}},
{'m': {'_id': '51237:INTERACTS_WITH:6647',
'_name': 'pituitary adenylate cyclase activating '
'polypeptide|ADCYAP1|MZB1 INTERACTS_WITH superoxide dismutase '
'1|SOD1',
'_source': ['SemMedDB_VER42_2020_R'],
'id': '51237:INTERACTS_WITH:6647',
'name': 'pituitary adenylate cyclase activating '
'polypeptide|ADCYAP1|MZB1 INTERACTS_WITH superoxide dismutase '
'1|SOD1',
'object_id': '6647',
'predicate': 'INTERACTS_WITH',
'subject_id': '51237'},
'n': {'_id': '6647',
'_name': 'SOD1',
'_source': ['SemMedDB_VER42_2020_R'],
'id': '6647',
'name': 'SOD1',
'type': ['aapp', 'gngm', 'phsu', 'enzy']},
'r': {'_source': ['SemMedDB_VER42_2020_R']}},
{'m': {'_id': 'C0214743:INHIBITS:3497',
'_name': 'Interleukin-13 INHIBITS IGHE',
'_source': ['SemMedDB_VER42_2020_R'],
'id': 'C0214743:INHIBITS:3497',
'name': 'Interleukin-13 INHIBITS IGHE',
'object_id': '3497',
'predicate': 'INHIBITS',
'subject_id': 'C0214743'},
'n': {'_id': '3497',
'_name': 'IGHE',
'_source': ['SemMedDB_VER42_2020_R', 'medRxiv-2020-10-06'],
'id': '3497',
'name': 'IGHE',
'type': ['aapp', 'gngm', 'phsu']},
'r': {'_source': ['SemMedDB_VER42_2020_R']}}]
SEMMEDDB_PREDICATE
Predicate relationship between two
(LiteratureTerm)nodes.
Path: (LiteratureTerm)-[SEMMEDDB_PREDICATE]->(LiteratureTerm)
Properties:
count:int, required; Number of triples.
predicate:str, required; The string representation of each predicate (for example TREATS, PROCESS_OF).
Examples
query
MATCH (n)-[r: SEMMEDDB_PREDICATE]-(m) RETURN n, r, m SKIP 0 LIMIT 3
data
[{'m': {'_id': 'C0406778',
'_name': 'Dermatopathia pigmentosa reticularis',
'_source': ['SemMedDB_VER42_2020_R'],
'id': 'C0406778',
'name': 'Dermatopathia pigmentosa reticularis',
'type': ['dsyn']},
'n': {'_id': '3861',
'_name': 'KRT14',
'_source': ['SemMedDB_VER42_2020_R'],
'id': '3861',
'name': 'KRT14',
'type': ['aapp', 'gngm']},
'r': {'_source': ['SemMedDB_VER42_2020_R'],
'count': 1,
'predicate': 'CAUSES'}},
{'m': {'_id': 'C0758622',
'_name': 'PKC-3 protein',
'_source': ['SemMedDB_VER42_2020_R'],
'id': 'C0758622',
'name': 'PKC-3 protein',
'type': ['aapp']},
'n': {'_id': '8650',
'_name': 'NUMB',
'_source': ['SemMedDB_VER42_2020_R'],
'id': '8650',
'name': 'NUMB',
'type': ['aapp', 'gngm']},
'r': {'_source': ['SemMedDB_VER42_2020_R'],
'count': 1,
'predicate': 'INTERACTS_WITH'}},
{'m': {'_id': 'C0571588',
'_name': 'Hydrocortisone allergy',
'_source': ['SemMedDB_VER42_2020_R'],
'id': 'C0571588',
'name': 'Hydrocortisone allergy',
'type': ['dsyn']},
'n': {'_id': 'C0076748',
'_name': 'tixocortol pivalate',
'_source': ['SemMedDB_VER42_2020_R'],
'id': 'C0076748',
'name': 'tixocortol pivalate',
'type': ['phsu']},
'r': {'_source': ['SemMedDB_VER42_2020_R'],
'count': 1,
'predicate': 'PREDISPOSES'}}]
SEMMEDDB_SUB
Link between
(LiteratureTriple)suject and(LiteratureTerm)for SemMedDB.
Path: (LiteratureTriple)-[SEMMEDDB_SUB]->(LiteratureTerm)
Examples
query
MATCH (n)-[r: SEMMEDDB_SUB]-(m) RETURN n, r, m SKIP 0 LIMIT 3
data
[{'m': {'_id': '51237:INTERACTS_WITH:C0669516',
'_name': 'pituitary adenylate cyclase activating '
'polypeptide|ADCYAP1|MZB1 INTERACTS_WITH superoxide dismutase '
'1|SOD1',
'_source': ['SemMedDB_VER42_2020_R'],
'id': '51237:INTERACTS_WITH:C0669516',
'name': 'pituitary adenylate cyclase activating '
'polypeptide|ADCYAP1|MZB1 INTERACTS_WITH superoxide dismutase '
'1|SOD1',
'object_id': 'C0669516',
'predicate': 'INTERACTS_WITH',
'subject_id': '51237'},
'n': {'_id': '51237',
'_name': 'MZB1',
'_source': ['SemMedDB_VER42_2020_R'],
'id': '51237',
'name': 'MZB1',
'type': ['aapp', 'gngm']},
'r': {'_source': ['SemMedDB_VER42_2020_R']}},
{'m': {'_id': '51237:INTERACTS_WITH:6647',
'_name': 'pituitary adenylate cyclase activating '
'polypeptide|ADCYAP1|MZB1 INTERACTS_WITH superoxide dismutase '
'1|SOD1',
'_source': ['SemMedDB_VER42_2020_R'],
'id': '51237:INTERACTS_WITH:6647',
'name': 'pituitary adenylate cyclase activating '
'polypeptide|ADCYAP1|MZB1 INTERACTS_WITH superoxide dismutase '
'1|SOD1',
'object_id': '6647',
'predicate': 'INTERACTS_WITH',
'subject_id': '51237'},
'n': {'_id': '51237',
'_name': 'MZB1',
'_source': ['SemMedDB_VER42_2020_R'],
'id': '51237',
'name': 'MZB1',
'type': ['aapp', 'gngm']},
'r': {'_source': ['SemMedDB_VER42_2020_R']}},
{'m': {'_id': 'C0214743:INHIBITS:3497',
'_name': 'Interleukin-13 INHIBITS IGHE',
'_source': ['SemMedDB_VER42_2020_R'],
'id': 'C0214743:INHIBITS:3497',
'name': 'Interleukin-13 INHIBITS IGHE',
'object_id': '3497',
'predicate': 'INHIBITS',
'subject_id': 'C0214743'},
'n': {'_id': 'C0214743',
'_name': 'Interleukin-13',
'_source': ['SemMedDB_VER42_2020_R', 'bioRxiv-2020-10-06'],
'id': 'C0214743',
'name': 'Interleukin-13',
'type': ['aapp', 'gngm']},
'r': {'_source': ['SemMedDB_VER42_2020_R']}}]
SEMMEDDB_TO_LIT
Relationship between the
(LiteratureTriple)and(Literature)nodes.
Path: (LiteratureTriple)-[SEMMEDDB_TO_LIT]->(Literature)
Examples
query
MATCH (n)-[r: SEMMEDDB_TO_LIT]-(m) RETURN n, r, m SKIP 0 LIMIT 3
data
[{'m': {'_id': '19667072',
'_name': '19667072',
'_source': ['SemMedDB_VER42_2020_R'],
'dp': '2009 Nov',
'edat': '2009-8-12',
'id': '19667072',
'issn': '1098-5549',
'year': 2009},
'n': {'_id': 'C0010531:INTERACTS_WITH:C0242210',
'_name': 'Cyclic AMP-Dependent Protein Kinases INTERACTS_WITH Binding '
'Protein',
'_source': ['SemMedDB_VER42_2020_R'],
'id': 'C0010531:INTERACTS_WITH:C0242210',
'name': 'Cyclic AMP-Dependent Protein Kinases INTERACTS_WITH Binding '
'Protein',
'object_id': 'C0242210',
'predicate': 'INTERACTS_WITH',
'subject_id': 'C0010531'},
'r': {'_source': ['SemMedDB_VER42_2020_R']}},
{'m': {'_id': '19667075',
'_name': '19667075',
'_source': ['SemMedDB_VER42_2020_R'],
'dp': '2009 Oct',
'edat': '2009-8-12',
'id': '19667075',
'issn': '1098-5549',
'year': 2009},
'n': {'_id': '2071:INHIBITS:C0017337',
'_name': 'ERCC3 gene|ERCC3 INHIBITS Genes',
'_source': ['SemMedDB_VER42_2020_R'],
'id': '2071:INHIBITS:C0017337',
'name': 'ERCC3 gene|ERCC3 INHIBITS Genes',
'object_id': 'C0017337',
'predicate': 'INHIBITS',
'subject_id': '2071'},
'r': {'_source': ['SemMedDB_VER42_2020_R']}},
{'m': {'_id': '19667075',
'_name': '19667075',
'_source': ['SemMedDB_VER42_2020_R'],
'dp': '2009 Oct',
'edat': '2009-8-12',
'id': '19667075',
'issn': '1098-5549',
'year': 2009},
'n': {'_id': 'C1333357:INHIBITS:C0017337',
'_name': 'ERCC3 gene|ERCC3 INHIBITS Genes',
'_source': ['SemMedDB_VER42_2020_R'],
'id': 'C1333357:INHIBITS:C0017337',
'name': 'ERCC3 gene|ERCC3 INHIBITS Genes',
'object_id': 'C0017337',
'predicate': 'INHIBITS',
'subject_id': 'C1333357'},
'r': {'_source': ['SemMedDB_VER42_2020_R']}}]
STRING_INTERACT_WITH
(Protein)-(Protein)interactions from STRING (https://string-db.org).
Path: (Protein)-[STRING_INTERACT_WITH]->(Protein)
Properties:
score:float, required; A value from 0 (low) to 1 (high) that indicates the confidence in the interaction to be true, as annotated by STRING.
Examples
query
MATCH (n)-[r: STRING_INTERACT_WITH]-(m) RETURN n, r, m SKIP 0 LIMIT 3
data
[{'m': {'_id': 'O43298',
'_name': 'O43298',
'_source': ['BioMart-2020-10-13', 'STRING-v11'],
'name': 'O43298',
'uniprot_id': 'O43298'},
'n': {'_id': 'Q9H7P6',
'_name': 'Q9H7P6',
'_source': ['BioMart-2020-10-13', 'Reactome-2020-10-13', 'STRING-v11'],
'name': 'Q9H7P6',
'uniprot_id': 'Q9H7P6'},
'r': {'_source': ['STRING-v11'], 'score': 809.0}},
{'m': {'_id': 'O43298',
'_name': 'O43298',
'_source': ['BioMart-2020-10-13', 'STRING-v11'],
'name': 'O43298',
'uniprot_id': 'O43298'},
'n': {'_id': 'Q13421',
'_name': 'Q13421',
'_source': ['BioMart-2020-10-13', 'Reactome-2020-10-13', 'STRING-v11'],
'name': 'Q13421',
'uniprot_id': 'Q13421'},
'r': {'_source': ['STRING-v11'], 'score': 813.0}},
{'m': {'_id': 'O43298',
'_name': 'O43298',
'_source': ['BioMart-2020-10-13', 'STRING-v11'],
'name': 'O43298',
'uniprot_id': 'O43298'},
'n': {'_id': 'Q9H7P6',
'_name': 'Q9H7P6',
'_source': ['BioMart-2020-10-13', 'Reactome-2020-10-13', 'STRING-v11'],
'name': 'Q9H7P6',
'uniprot_id': 'Q9H7P6'},
'r': {'_source': ['STRING-v11'], 'score': 809.0}}]
OPENGWAS_TOPHITS
The default tophits for each GWAS, obtained from the MRC IEU OpenGWAS platform (https://gwas.mrcieu.ac.uk/).
Path: (Gwas)-[OPENGWAS_TOPHITS]->(Variant)
Properties:
beta:float, required; Effect size.
pval:float, required; P-Value.
Examples
query
MATCH (n)-[r: OPENGWAS_TOPHITS]-(m) RETURN n, r, m SKIP 0 LIMIT 3
data
[{'m': {'_id': 'rs34712273',
'_name': 'rs34712273',
'_source': ['OpenGWAS-2020-10-13'],
'name': 'rs34712273'},
'n': {'_id': 'ukb-d-30630_irnt',
'_name': 'Apoliprotein A',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Neale lab',
'build': 'HG19/GRCh37',
'category': 'Metabolites',
'id': 'ukb-d-30630_irnt',
'mr': '1',
'nsnp': '13585234',
'population': 'European',
'sex': 'Males and Females',
'trait': 'Apoliprotein A',
'year': '2018.0'},
'r': {'_source': ['OpenGWAS-2020-10-13'],
'beta': -0.015872,
'pval': 1.6062000000000002e-11}},
{'m': {'_id': 'rs34712273',
'_name': 'rs34712273',
'_source': ['OpenGWAS-2020-10-13'],
'name': 'rs34712273'},
'n': {'_id': 'ukb-d-30630_raw',
'_name': 'Apoliprotein A',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Neale lab',
'build': 'HG19/GRCh37',
'category': 'Metabolites',
'id': 'ukb-d-30630_raw',
'mr': '1',
'nsnp': '13585234',
'population': 'European',
'sex': 'Males and Females',
'trait': 'Apoliprotein A',
'year': '2018.0'},
'r': {'_source': ['OpenGWAS-2020-10-13'],
'beta': -0.004418899999999999,
'pval': 4.6216800000000006e-12}},
{'m': {'_id': 'rs34397747',
'_name': 'rs34397747',
'_source': ['OpenGWAS-2020-10-13'],
'name': 'rs34397747'},
'n': {'_id': 'ukb-d-30630_irnt',
'_name': 'Apoliprotein A',
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Neale lab',
'build': 'HG19/GRCh37',
'category': 'Metabolites',
'id': 'ukb-d-30630_irnt',
'mr': '1',
'nsnp': '13585234',
'population': 'European',
'sex': 'Males and Females',
'trait': 'Apoliprotein A',
'year': '2018.0'},
'r': {'_source': ['OpenGWAS-2020-10-13'],
'beta': -0.039638,
'pval': 3.1989e-21}}]
VARIANT_TO_GENE
Relationships between
(Variant)and(Gene), obtained via Ensembl VEP v37.
Path: (Variant)-[VARIANT_TO_GENE]->(Gene)
Properties:
allele:str, required; The variant allele used to calculate the consequence.
amino_acids:str, required; Only given if the variant affects the protein-coding sequence.
cdna_position:str, required; Relative position of base pair in cDNA sequence.
cds_position:str, required; Relative position of base pair in coding sequence.
codons:str, required; The alternative codons with the variant base in upper case.
consequence:str, required; Consequence type of this variant (see https://www.ensembl.org/info/genome/variation/prediction/predicted_data.html#consequences).
existing_variation:str, required; Known identifier of existing variant.
extra:str, required; 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).
feature:str, required; Ensembl stable ID of feature.
feature_type:str, required; Type of feature. Currently one of Transcript, RegulatoryFeature, MotifFeature.
location:str, required; In standard coordinate format (chr:start or chr:start-end).
protein_position:str, required; Relative position of amino acid in protein.
Examples
query
MATCH (n)-[r: VARIANT_TO_GENE]-(m) RETURN n, r, m SKIP 0 LIMIT 3
data
[{'m': {'_id': 'rs34397747',
'_name': 'rs34397747',
'_source': ['OpenGWAS-2020-10-13'],
'name': 'rs34397747'},
'n': {'_id': 'ENSG00000266138',
'_name': 'RN7SL501P',
'_source': ['BioMart-2020-10-13'],
'biomart_source': 'HGNC Symbol',
'chr': '1',
'description': 'RNA, 7SL, cytoplasmic 501, pseudogene [Source:HGNC '
'Symbol;Acc:46517]',
'end': 27090393,
'ensembl_id': 'ENSG00000266138',
'name': 'RN7SL501P',
'start': 27090115,
'type': 'misc_RNA'},
'r': {'_source': ['Ensembl-VEP-v37'],
'allele': 'C',
'amino_acids': '-',
'cdna_position': '-',
'cds_position': '-',
'codons': '-',
'consequence': 'downstream_gene_variant',
'existing_variation': '-',
'extra': 'IMPACT=MODIFIER;DISTANCE=1929;STRAND=1',
'feature': 'ENST00000578818',
'feature_type': 'Transcript',
'location': '1:27092322',
'protein_position': '-'}},
{'m': {'_id': 'rs34397747',
'_name': 'rs34397747',
'_source': ['OpenGWAS-2020-10-13'],
'name': 'rs34397747'},
'n': {'_id': 'ENSG00000117713',
'_name': 'ARID1A',
'_source': ['BioMart-2020-10-13'],
'biomart_source': 'HGNC Symbol',
'chr': '1',
'description': 'AT rich interactive domain 1A (SWI-like) [Source:HGNC '
'Symbol;Acc:11110]',
'end': 27108595,
'ensembl_id': 'ENSG00000117713',
'name': 'ARID1A',
'start': 27022524,
'type': 'protein_coding'},
'r': {'_source': ['Ensembl-VEP-v37'],
'allele': 'C',
'amino_acids': '-',
'cdna_position': '-',
'cds_position': '-',
'codons': '-',
'consequence': 'intron_variant',
'existing_variation': '-',
'extra': 'IMPACT=MODIFIER;STRAND=1',
'feature': 'ENST00000324856',
'feature_type': 'Transcript',
'location': '1:27092322',
'protein_position': '-'}},
{'m': {'_id': 'rs35628716',
'_name': 'rs35628716',
'_source': ['OpenGWAS-2020-10-13'],
'name': 'rs35628716'},
'n': {'_id': 'ENSG00000117505',
'_name': 'DR1',
'_source': ['BioMart-2020-10-13'],
'biomart_source': 'HGNC Symbol',
'chr': '1',
'description': 'down-regulator of transcription 1, TBP-binding '
'(negative cofactor 2) [Source:HGNC Symbol;Acc:3017]',
'end': 93835055,
'ensembl_id': 'ENSG00000117505',
'name': 'DR1',
'start': 93811445,
'type': 'protein_coding'},
'r': {'_source': ['Ensembl-VEP-v37'],
'allele': 'T',
'amino_acids': '-',
'cdna_position': '-',
'cds_position': '-',
'codons': '-',
'consequence': 'downstream_gene_variant',
'existing_variation': '-',
'extra': 'IMPACT=MODIFIER;DISTANCE=4553;STRAND=1',
'feature': 'ENST00000370272',
'feature_type': 'Transcript',
'location': '1:93839608',
'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:float, required; Effect size.
mr_method:str, required; underlying Mendelian randomization method, e.g. IVW, Egger, etc.
p:float, required; P-Value.
qtl_type:str, required; pQTL, or eQTL.
se:float, required; Standard error.
Examples
query
MATCH (n)-[r: XQTL_MULTI_SNP_MR]-(m) RETURN n, r, m SKIP 0 LIMIT 3
data
[{'m': {'_id': 'ieu-a-297',
'_name': "Alzheimer's disease",
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Lambert',
'build': 'HG19/GRCh37',
'category': 'Disease',
'id': 'ieu-a-297',
'mr': '1',
'ncase': '17008.0',
'ncontrol': '37154.0',
'note': 'Effect allele frequencies are missing; forward(+) strand',
'nsnp': '7055882',
'pmid': '24162737.0',
'population': 'European',
'sample_size': '54162.0',
'sex': 'Males and Females',
'subcategory': 'Psychiatric / neurological',
'trait': "Alzheimer's disease",
'year': '2013.0'},
'n': {'_id': 'ENSG00000239736',
'_name': 'CEACAMP3',
'_source': ['BioMart-2020-10-13'],
'biomart_source': 'HGNC Symbol',
'chr': '19',
'description': 'carcinoembryonic antigen-related cell adhesion '
'molecule pseudogene 3 [Source:HGNC Symbol;Acc:1825]',
'end': 42112339,
'ensembl_id': 'ENSG00000239736',
'name': 'CEACAMP3',
'start': 42106090,
'type': 'pseudogene'},
'r': {'_source': ['xQTL'],
'beta': -0.000367347863147393,
'mr_method': 'IVW',
'p': 0.9881522276028252,
'qtl_type': 'eQTL',
'se': 0.0247380188527883}},
{'m': {'_id': 'ieu-a-297',
'_name': "Alzheimer's disease",
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Lambert',
'build': 'HG19/GRCh37',
'category': 'Disease',
'id': 'ieu-a-297',
'mr': '1',
'ncase': '17008.0',
'ncontrol': '37154.0',
'note': 'Effect allele frequencies are missing; forward(+) strand',
'nsnp': '7055882',
'pmid': '24162737.0',
'population': 'European',
'sample_size': '54162.0',
'sex': 'Males and Females',
'subcategory': 'Psychiatric / neurological',
'trait': "Alzheimer's disease",
'year': '2013.0'},
'n': {'_id': 'ENSG00000184517',
'_name': 'ZFP1',
'_source': ['BioMart-2020-10-13'],
'biomart_source': 'HGNC Symbol',
'chr': '16',
'description': 'ZFP1 zinc finger protein [Source:HGNC '
'Symbol;Acc:23328]',
'end': 75206134,
'ensembl_id': 'ENSG00000184517',
'name': 'ZFP1',
'start': 75182390,
'type': 'protein_coding'},
'r': {'_source': ['xQTL'],
'beta': 0.00185604352678048,
'mr_method': 'Egger',
'p': 0.988066404188022,
'qtl_type': 'eQTL',
'se': 0.0990024821536597}},
{'m': {'_id': 'ieu-a-297',
'_name': "Alzheimer's disease",
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Lambert',
'build': 'HG19/GRCh37',
'category': 'Disease',
'id': 'ieu-a-297',
'mr': '1',
'ncase': '17008.0',
'ncontrol': '37154.0',
'note': 'Effect allele frequencies are missing; forward(+) strand',
'nsnp': '7055882',
'pmid': '24162737.0',
'population': 'European',
'sample_size': '54162.0',
'sex': 'Males and Females',
'subcategory': 'Psychiatric / neurological',
'trait': "Alzheimer's disease",
'year': '2013.0'},
'n': {'_id': 'ENSG00000125877',
'_name': 'ITPA',
'_source': ['BioMart-2020-10-13'],
'biomart_source': 'HGNC Symbol',
'chr': '20',
'description': 'inosine triphosphatase (nucleoside triphosphate '
'pyrophosphatase) [Source:HGNC Symbol;Acc:6176]',
'end': 3204516,
'ensembl_id': 'ENSG00000125877',
'name': 'ITPA',
'start': 3189514,
'type': 'protein_coding'},
'r': {'_source': ['xQTL'],
'beta': -0.00144540599959653,
'mr_method': 'IVW',
'p': 0.9878357330917308,
'qtl_type': 'eQTL',
'se': 0.0948041063517875}}]
XQTL_SINGLE_SNP_MR_GENE_GWAS
Association of exposure gene and outcome phenotype of xQTL (Zheng et al. 2020), single SNP MR methods.
Path: (Gene)-[XQTL_SINGLE_SNP_MR_GENE_GWAS]->(Gwas)
Properties:
beta:float, required; Effect size.
p:float, required; P-Value.
qtl_type:str, required; pQTL, or eQTL.
rsid:str, required; SNP rsID.
se:float, required; Standard error.
Examples
query
MATCH (n)-[r: XQTL_SINGLE_SNP_MR_GENE_GWAS]-(m) RETURN n, r, m SKIP 0 LIMIT 3
data
[{'m': {'_id': 'ieu-a-297',
'_name': "Alzheimer's disease",
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Lambert',
'build': 'HG19/GRCh37',
'category': 'Disease',
'id': 'ieu-a-297',
'mr': '1',
'ncase': '17008.0',
'ncontrol': '37154.0',
'note': 'Effect allele frequencies are missing; forward(+) strand',
'nsnp': '7055882',
'pmid': '24162737.0',
'population': 'European',
'sample_size': '54162.0',
'sex': 'Males and Females',
'subcategory': 'Psychiatric / neurological',
'trait': "Alzheimer's disease",
'year': '2013.0'},
'n': {'_id': 'ENSG00000185436',
'_name': 'IFNLR1',
'_source': ['BioMart-2020-10-13'],
'biomart_source': 'HGNC Symbol',
'chr': '1',
'description': 'interferon, lambda receptor 1 [Source:HGNC '
'Symbol;Acc:18584]',
'end': 24514449,
'ensembl_id': 'ENSG00000185436',
'name': 'IFNLR1',
'start': 24480647,
'type': 'protein_coding'},
'r': {'_source': ['xQTL'],
'beta': 0.020901639,
'p': 0.859924253,
'qtl_type': 'pQTL',
'rsid': 'rs12046369',
'se': 0.118442623}},
{'m': {'_id': 'ieu-a-297',
'_name': "Alzheimer's disease",
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Lambert',
'build': 'HG19/GRCh37',
'category': 'Disease',
'id': 'ieu-a-297',
'mr': '1',
'ncase': '17008.0',
'ncontrol': '37154.0',
'note': 'Effect allele frequencies are missing; forward(+) strand',
'nsnp': '7055882',
'pmid': '24162737.0',
'population': 'European',
'sample_size': '54162.0',
'sex': 'Males and Females',
'subcategory': 'Psychiatric / neurological',
'trait': "Alzheimer's disease",
'year': '2013.0'},
'n': {'_id': 'ENSG00000176022',
'_name': 'B3GALT6',
'_source': ['BioMart-2020-10-13'],
'biomart_source': 'HGNC Symbol',
'chr': '1',
'description': 'UDP-Gal:betaGal beta 1,3-galactosyltransferase '
'polypeptide 6 [Source:HGNC Symbol;Acc:17978]',
'end': 1170421,
'ensembl_id': 'ENSG00000176022',
'name': 'B3GALT6',
'start': 1167629,
'type': 'protein_coding'},
'r': {'_source': ['xQTL'],
'beta': -0.018081181,
'p': 0.8590872079999999,
'qtl_type': 'pQTL',
'rsid': 'rs3766186',
'se': 0.101845018}},
{'m': {'_id': 'ieu-a-297',
'_name': "Alzheimer's disease",
'_source': ['OpenGWAS-2020-10-13'],
'author': 'Lambert',
'build': 'HG19/GRCh37',
'category': 'Disease',
'id': 'ieu-a-297',
'mr': '1',
'ncase': '17008.0',
'ncontrol': '37154.0',
'note': 'Effect allele frequencies are missing; forward(+) strand',
'nsnp': '7055882',
'pmid': '24162737.0',
'population': 'European',
'sample_size': '54162.0',
'sex': 'Males and Females',
'subcategory': 'Psychiatric / neurological',
'trait': "Alzheimer's disease",
'year': '2013.0'},
'n': {'_id': 'ENSG00000167755',
'_name': 'KLK6',
'_source': ['BioMart-2020-10-13', 'Finan_et_al'],
'adme_gene': 'N',
'bio_druggable': 'Y',
'biomart_source': 'HGNC Symbol',
'chr': '19',
'description': 'kallikrein-related peptidase 6 [Source:HGNC '
'Symbol;Acc:6367]',
'druggability_tier': 'Tier 3A',
'end': 51472929,
'ensembl_id': 'ENSG00000167755',
'name': 'KLK6',
'small_mol_druggable': 'N',
'start': 51461887,
'type': 'protein_coding'},
'r': {'_source': ['xQTL'],
'beta': 0.013,
'p': 0.854043058,
'qtl_type': 'pQTL',
'rsid': 'rs11667946',
'se': 0.070666667}}]
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': {'_id': 'rs13402475',
'_name': 'rs13402475',
'_source': ['OpenGWAS-2020-10-13', 'xQTL'],
'name': 'rs13402475'},
'n': {'_id': 'ENSG00000221867',
'_name': 'MAGEA3',
'_source': ['BioMart-2020-10-13', 'Finan_et_al'],
'adme_gene': 'N',
'bio_druggable': 'Y',
'biomart_source': 'HGNC Symbol',
'chr': 'X',
'description': 'melanoma antigen family A, 3 [Source:HGNC '
'Symbol;Acc:6801]',
'druggability_tier': 'Tier 1',
'end': 151938240,
'ensembl_id': 'ENSG00000221867',
'name': 'MAGEA3',
'small_mol_druggable': 'N',
'start': 151934652,
'type': 'protein_coding'},
'r': {'_source': ['xQTL']}},
{'m': {'_id': 'rs13402475',
'_name': 'rs13402475',
'_source': ['OpenGWAS-2020-10-13', 'xQTL'],
'name': 'rs13402475'},
'n': {'_id': 'ENSG00000073670',
'_name': 'ADAM11',
'_source': ['BioMart-2020-10-13'],
'biomart_source': 'HGNC Symbol',
'chr': '17',
'description': 'ADAM metallopeptidase domain 11 [Source:HGNC '
'Symbol;Acc:189]',
'end': 42859214,
'ensembl_id': 'ENSG00000073670',
'name': 'ADAM11',
'start': 42836399,
'type': 'protein_coding'},
'r': {'_source': ['xQTL']}},
{'m': {'_id': 'rs2519093',
'_name': 'rs2519093',
'_source': ['OpenGWAS-2020-10-13', 'xQTL', 'MR-EvE-2019-02-21'],
'alt': 'T',
'build': 'b37',
'chr': '9',
'name': 'rs2519093',
'pos': 136141870,
'ref': 'C'},
'n': {'_id': 'ENSG00000171155',
'_name': 'C1GALT1C1',
'_source': ['BioMart-2020-10-13'],
'biomart_source': 'HGNC Symbol',
'chr': 'X',
'description': 'C1GALT1-specific chaperone 1 [Source:HGNC '
'Symbol;Acc:24338]',
'end': 119764005,
'ensembl_id': 'ENSG00000171155',
'name': 'C1GALT1C1',
'start': 119759648,
'type': 'protein_coding'},
'r': {'_source': ['xQTL']}}]
GENE_TO_DISEASE
Gene-disease relationships from ClinVar database (https://ftp.ncbi.nlm.nih.gov/pub/clinvar/gene_condition_source_id). The sources of information for the gene-disease relationship include OMIM, GeneReviews, and a limited amount of curation by NCBI staff.
Path: (Gene)-[GENE_TO_DISEASE]->(Disease)
Properties:
gene_relationship_type:str, required; 'Associated gene': gene reported to be causative for this disorder. Includes monogenic disorders. 'Related gene': any gene that may contribute to a disorder. Includes broader concepts, for example, ABCA4 is reported as an associated gene for Retinitis pigmentosa 19, but as a related gene for Retinitis pigmentosa.
last_updated:str, optional; Last time this record was modified by NCBI staff in the ClinVar database (prior to the date it was imported into EpiGraphDB)
Examples
query
MATCH (n)-[r: GENE_TO_DISEASE]-(m) RETURN n, r, m SKIP 0 LIMIT 3
data
[{'m': {'_id': 'http://purl.obolibrary.org/obo/MONDO_0014959',
'_name': 'mitochondrial DNA depletion syndrome 12a (cardiomyopathic '
'type), autosomal dominant',
'_source': ['Mondo-2021-01-12'],
'definition': 'NA',
'id': 'http://purl.obolibrary.org/obo/MONDO_0014959',
'label': 'mitochondrial DNA depletion syndrome 12a (cardiomyopathic '
'type), autosomal dominant',
'umls': ['C4310676']},
'n': {'_id': 'ENSG00000151729',
'_name': 'SLC25A4',
'_source': ['BioMart-2020-10-13'],
'biomart_source': 'HGNC Symbol',
'chr': '4',
'description': 'solute carrier family 25 (mitochondrial carrier; '
'adenine nucleotide translocator), member 4 '
'[Source:HGNC Symbol;Acc:10990]',
'end': 186071536,
'ensembl_id': 'ENSG00000151729',
'name': 'SLC25A4',
'start': 186064395,
'type': 'protein_coding'},
'r': {'_source': ['Clinvar-2021-01-12'],
'gene_relationship_type': 'Associated gene',
'last_updated': '2017-06-20'}},
{'m': {'_id': 'http://purl.obolibrary.org/obo/MONDO_0014958',
'_name': 'Harel-Yoon syndrome',
'_source': ['Mondo-2021-01-12'],
'definition': 'NA',
'id': 'http://purl.obolibrary.org/obo/MONDO_0014958',
'label': 'Harel-Yoon syndrome',
'umls': ['C4310677']},
'n': {'_id': 'ENSG00000197785',
'_name': 'ATAD3A',
'_source': ['BioMart-2020-10-13'],
'biomart_source': 'HGNC Symbol',
'chr': '1',
'description': 'ATPase family, AAA domain containing 3A [Source:HGNC '
'Symbol;Acc:25567]',
'end': 1470067,
'ensembl_id': 'ENSG00000197785',
'name': 'ATAD3A',
'start': 1447531,
'type': 'protein_coding'},
'r': {'_source': ['Clinvar-2021-01-12'],
'gene_relationship_type': 'Associated gene',
'last_updated': '2017-06-20'}},
{'m': {'_id': 'http://purl.obolibrary.org/obo/MONDO_0014957',
'_name': 'language delay and attention deficit-hyperactivity '
'disorder/cognitive impairment with or without cardiac '
'arrhythmia',
'_source': ['Mondo-2021-01-12'],
'definition': 'NA',
'id': 'http://purl.obolibrary.org/obo/MONDO_0014957',
'label': 'language delay and attention deficit-hyperactivity '
'disorder/cognitive impairment with or without cardiac '
'arrhythmia',
'umls': ['C4310678']},
'n': {'_id': 'ENSG00000069966',
'_name': 'GNB5',
'_source': ['BioMart-2020-10-13'],
'biomart_source': 'HGNC Symbol',
'chr': '15',
'description': 'guanine nucleotide binding protein (G protein), beta 5 '
'[Source:HGNC Symbol;Acc:4401]',
'end': 52483566,
'ensembl_id': 'ENSG00000069966',
'name': 'GNB5',
'start': 52413117,
'type': 'protein_coding'},
'r': {'_source': ['Clinvar-2021-01-12'],
'gene_relationship_type': 'Associated gene',
'last_updated': '2017-06-20'}}]