EpiGraphDB meta nodes

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

Disease

Disease data from Mondo Disease Ontology.

_id property: id

_name property: label

Properties:

• definition: str, required; Expanded text description of disease.

• doid: List[str], optional; Disease ontology identifier (https://disease-ontology.org).

• efo: List[str], optional; Experimental factor ontology identifier (https://www.ebi.ac.uk/efo/).

• icd10: List[str], optional; International classification of diseases ICD10 code.

• icd9: List[str], optional; International classification of diseases ICD9 code.

• id: str, required; IRI for this Mondo entry (incorporates Mondo ID).

• label: str, required; Text label of disease.

• mesh: List[str], optional; Medical Subject Headings (MeSH) identifier.

• umls: List[str], optional; Unified Medical Language System identifier (https://www.nlm.nih.gov/research/umls/).

Examples

query

MATCH (n:Disease) RETURN n SKIP 0 LIMIT 3

data

[{'n': {'_id': 'http://purl.obolibrary.org/obo/MONDO_0002974',
        '_name': 'cervical cancer',
        '_source': ['Mondo-2021-01-12'],
        'definition': 'A primary or metastatic malignant neoplasm involving '
                      'the cervix.',
        'doid': ['4362'],
        'icd10': ['C53.9', 'C53'],
        'icd9': ['180.8', '180', '180.9'],
        'id': 'http://purl.obolibrary.org/obo/MONDO_0002974',
        'label': 'cervical cancer'}},
 {'n': {'_id': 'http://purl.obolibrary.org/obo/MONDO_0000310',
        '_name': 'Alkhurma hemorrhagic fever',
        '_source': ['Mondo-2021-01-12'],
        'definition': 'A disease caused by infection with Alkhumra hemorrhagic '
                      'fever virus.',
        'doid': ['0050308'],
        'id': 'http://purl.obolibrary.org/obo/MONDO_0000310',
        'label': 'Alkhurma hemorrhagic fever'}},
 {'n': {'_id': 'http://purl.obolibrary.org/obo/MONDO_0002975',
        '_name': 'malignant breast melanoma',
        '_source': ['Mondo-2021-01-12'],
        'definition': 'A melanoma that arises usually from the breast skin and '
                      'less often from the breast glandular tissue. Primary '
                      'breast melanomas are rare.',
        'doid': ['4364'],
        'id': 'http://purl.obolibrary.org/obo/MONDO_0002975',
        'label': 'malignant breast melanoma',
        'umls': ['C0346787']}}]

Drug

Drug data from the following sources:

• Open Targets.
• CPIC.

_id property: label

_name property: label

Properties:

• chembl_uri: str, optional; Label of the drug

• label: str, required; Type of the molecule, e.g. Antibody, Protein, Enzyme, etc.

• molecule_type: str, optional; Type of the molecule, e.g. Antibody, Protein, Enzyme, etc.

Examples

query

MATCH (n:Drug) RETURN n SKIP 0 LIMIT 3

data

[{'n': {'_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': 'DANUSERTIB',
        '_name': 'DANUSERTIB',
        '_source': ['Opentargets-2020-10-19'],
        'chembl_uri': 'http://identifiers.org/chembl.compound/CHEMBL402548',
        'label': 'DANUSERTIB',
        'molecule_type': 'Small molecule'}},
 {'n': {'_id': 'ILORASERTIB',
        '_name': 'ILORASERTIB',
        '_source': ['Opentargets-2020-10-19'],
        'chembl_uri': 'http://identifiers.org/chembl.compound/CHEMBL1980297',
        'label': 'ILORASERTIB',
        'molecule_type': 'Small molecule'}}]

Efo

Experimental Factor Ontology (EFO).

_id property: id

_name property: value

Properties:

• id: str, required; EFO URL and identifier.

• type: str, required; EFO type.

• value: str, required; Text description (EFO term).

Examples

query

MATCH (n:Efo) RETURN n SKIP 0 LIMIT 3

data

[{'n': {'_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_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_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'}}]

Gene

Gene data from BioMart (build 37).

Gene druggability data comes from Finan et al (2017).

_id property: ensembl_id

_name property: name

Properties:

• adme_gene: str, optional; Is the protein product of the gene involved in absorption, distribution, metabolism, and excretion (ADME) of a compound.

  Evidence from Finan et al.(2017).

• biomart_source: str, optional; The origin of the info, e.g. miRBase, RFAM, HGNC

• bio_druggable: str, optional; Is the protein product of the (Gene) targeted, or predicted to be targeted, by a biotherapeutic.

  Evidence from Finan et al.(2017).

• chr: str, optional; Chromosome.

• description: str, optional; End position on chromosome.

• druggability_tier: str, optional; The priority tier for the druggable (Gene), e.g. "Tier 1", "Tier 2", "Tier 3A", "Tier 3B".

  Evidence from Finan et al.(2017).

• end: int, optional; End position on chromosome.

• ensembl_id: str, required; Ensembl identifier of the gene.

• name: str, required; HGNC name of the gene.

• reactome_id: str, optional; Identifier for gene in Reactome database.

• small_mol_druggable: str, optional; Is the protein product of the (Gene) targeted, or predicted to be targeted, by a small molecule.

  Evidence from Finan et al.(2017).

• start: int, optional; Start position on chromosome.

• type: str, optional; Gene type, e.g. protein_coding, pseudogene.

Examples

query

MATCH (n:Gene) RETURN n SKIP 0 LIMIT 3

data

[{'n': {'_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': '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': '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'}}]

Gwas

Genome Wide Association Studies metadata from IEU OpenGWAS Database.

_id property: id

_name property: trait

Properties:

• author: str, optional; First author of GWAS.

• build: str, optional; Genome build used for harmonisation

• category: str, optional; Binary disease phenotype or a non-disease phenotype.

• consortium: str, optional; GWAS consortium name, if applicable.

• id: str, required; IEU OpenGWAS identifier.

• mr: str, optional; Suitability of GWAS for Mendelian randomization.

• ncase: str, optional; Number of cases.

• ncontrol: str, optional; Number of controls.

• note: str, optional; Extra information.

• nsnp: str, required; Number of variants in results file.

• pmid: str, optional; PubMed identifier, where available.

• population: str, optional; Geographical origins of the samples included in the study.

• sample_size: str, optional; Sample size of GWAS.

• sd: str, optional; Standard deviation of the phenotype analysed.

• sex: str, optional; Males/Females.

• subcategory: str, optional; Further categorisation.

• trait: str, required; Description of measured trait.

• unit: str, optional; How to interpret a 1-unit change in the phenotype, e.g. log odds ratio, mmol/L, SD units.

• year: str, optional; Year of publication/creation.

Examples

query

MATCH (n:Gwas) RETURN n SKIP 0 LIMIT 3

data

[{'n': {'_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': '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': 'ieu-b-39',
        '_name': 'diastolic blood pressure',
        '_source': ['OpenGWAS-2020-10-13'],
        'author': 'Evangelou, E',
        'build': 'HG19/GRCh37',
        'category': 'Continuous',
        'consortium': 'International Consortium of Blood Pressure',
        'id': 'ieu-b-39',
        'mr': '1',
        'nsnp': '7160619',
        'pmid': '30224653.0',
        'population': 'European',
        'sample_size': '757601.0',
        'sex': 'Males and Females',
        'subcategory': 'Blood pressure',
        'trait': 'diastolic blood pressure',
        'unit': 'mm Hg',
        'year': '2018.0'}}]

Literature

PubMed literature data as available from SemMedDB.

_id property: id

_name property: id

Properties:

• doi: str, optional; DOI of publication

• dp: str, optional; Date published.

• edat: str, optional; Entrez Date is the date the citation was added to PubMed.

• issn: str, optional; ISSN code of journal.

• id: str, required; Unique identifier, e.g. PubMed ID or DOI

• title: str, optional; Title of publication if available

• year: int, optional; Year published.

Examples

query

MATCH (n:Literature) RETURN n SKIP 0 LIMIT 3

data

[{'n': {'_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': '19667075',
        '_name': '19667075',
        '_source': ['SemMedDB_VER42_2020_R'],
        'dp': '2009 Oct',
        'edat': '2009-8-12',
        'id': '19667075',
        'issn': '1098-5549',
        'year': 2009}},
 {'n': {'_id': '19667076',
        '_name': '19667076',
        '_source': ['SemMedDB_VER42_2020_R'],
        'dp': '2009 Oct',
        'edat': '2009-8-12',
        'id': '19667076',
        'issn': '1098-5549',
        'year': 2009}}]

LiteratureTerm

Biomedical term from SemMedDB.

_id property: id

_name property: name

Properties:

• id: str, required; The Concept Unique Identifier (CUI) of the term.

• name: str, required; The preferred name of semantic term.

• type: List[str], required; The semantic type of term (see https://mmtx.nlm.nih.gov/MMTx/semanticTypes.shtml).

Examples

query

MATCH (n:LiteratureTerm) RETURN n SKIP 0 LIMIT 3

data

[{'n': {'_id': 'C0406778',
        '_name': 'Dermatopathia pigmentosa reticularis',
        '_source': ['SemMedDB_VER42_2020_R'],
        'id': 'C0406778',
        'name': 'Dermatopathia pigmentosa reticularis',
        'type': ['dsyn']}},
 {'n': {'_id': 'C0758622',
        '_name': 'PKC-3 protein',
        '_source': ['SemMedDB_VER42_2020_R'],
        'id': 'C0758622',
        'name': 'PKC-3 protein',
        'type': ['aapp']}},
 {'n': {'_id': 'C0571588',
        '_name': 'Hydrocortisone allergy',
        '_source': ['SemMedDB_VER42_2020_R'],
        'id': 'C0571588',
        'name': 'Hydrocortisone allergy',
        'type': ['dsyn']}}]

LiteratureTriple

Semantic triplet (subject - predicate - object) from SemMedDB.

_id property: id

_name property: name

Properties:

• id: str, required; Unique identifier made from subject ID, predicate name and object ID

• name: str, required; The complete semantic triplet {subject}:{PREDICATE}:{object}.

• object_id: str, required; The CUI of the object of the predication

• predicate: str, required; The string representation of each predicate (for example TREATS, PROCESS_OF).

• subject_id: str, required; The CUI of the subject of the predication

Examples

query

MATCH (n:LiteratureTriple) RETURN n SKIP 0 LIMIT 3

data

[{'n': {'_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: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': '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'}}]

Pathway

Biological pathway data from Reactome.

_id property: id

_name property: name

Properties:

• url: str, optional; Reactome pathway URL

• name: str, required; Name of the pathway.

• id: str, required; Reactome pathway ID

Examples

query

MATCH (n:Pathway) RETURN n SKIP 0 LIMIT 3

data

[{'n': {'_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-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-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'}}]

Protein

Protein data from BioMart (build 37).

_id property: uniprot_id

_name property: uniprot_id

Properties:

• uniprot_id: str, required; UniProt Identifier.

• name: str, required; Protein name

Examples

query

MATCH (n:Protein) RETURN n SKIP 0 LIMIT 3

data

[{'n': {'_id': 'O43298',
        '_name': 'O43298',
        '_source': ['BioMart-2020-10-13', 'STRING-v11'],
        'name': 'O43298',
        'uniprot_id': 'O43298'}},
 {'n': {'_id': 'Q6UWM5',
        '_name': 'Q6UWM5',
        '_source': ['BioMart-2020-10-13'],
        'name': 'Q6UWM5',
        'uniprot_id': 'Q6UWM5'}},
 {'n': {'_id': 'A6NJS3',
        '_name': 'A6NJS3',
        '_source': ['BioMart-2020-10-13'],
        'name': 'A6NJS3',
        'uniprot_id': 'A6NJS3'}}]

Tissue

Tissue specific gene expression from GTEx.

_id property: id

_name property: name

Properties:

• id: str, required; Tissue name

• name: str, required; Tissue name

Examples

query

MATCH (n:Tissue) RETURN n SKIP 0 LIMIT 3

data

[{'n': {'_id': 'Adipose - Subcutaneous',
        '_name': 'Adipose - Subcutaneous',
        '_source': ['GTEx-2016-01-15_v7_RNASeQCv1.1.8'],
        'id': 'Adipose - Subcutaneous',
        'name': 'Adipose - Subcutaneous'}},
 {'n': {'_id': 'Adipose - Visceral (Omentum)',
        '_name': 'Adipose - Visceral (Omentum)',
        '_source': ['GTEx-2016-01-15_v7_RNASeQCv1.1.8'],
        'id': 'Adipose - Visceral (Omentum)',
        'name': 'Adipose - Visceral (Omentum)'}},
 {'n': {'_id': 'Adrenal Gland',
        '_name': 'Adrenal Gland',
        '_source': ['GTEx-2016-01-15_v7_RNASeQCv1.1.8'],
        'id': 'Adrenal Gland',
        'name': 'Adrenal Gland'}}]

Variant

Genetic variant, e.g. SNPs.

_id property: name

_name property: name

Properties:

• name: str, required; rsID of the SNP.

• pos: int, optional; Chromosome position

• chr: str, optional; Chromosome

• ref: str, optional; Reference allele

• alt: str, optional; Alternative allele

• build: str, optional; Genome build

Examples

query

MATCH (n:Variant) RETURN n SKIP 0 LIMIT 3

data

[{'n': {'_id': 'rs34712273',
        '_name': 'rs34712273',
        '_source': ['OpenGWAS-2020-10-13'],
        'name': 'rs34712273'}},
 {'n': {'_id': 'rs34397747',
        '_name': 'rs34397747',
        '_source': ['OpenGWAS-2020-10-13'],
        'name': 'rs34397747'}},
 {'n': {'_id': 'rs35628716',
        '_name': 'rs35628716',
        '_source': ['OpenGWAS-2020-10-13'],
        'name': 'rs35628716'}}]