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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

label property: label

Properties:

- id: IRI for this Mondo entry (incorporates Mondo ID).

- label: Text label of disease.

- definition: Expanded text description of disease.

- doid: Disease ontology identifier (https://disease-ontology.org).

- umls: Unified Medical Language System identifier (https://www.nlm.nih.gov/research/umls/).

- efo: Experimental factor ontology identifier (https://www.ebi.ac.uk/efo/).

- icd9: International classification of diseases ICD9 code.

- icd10: International classification of diseases ICD10 code.

- mesh: Medical Subject Headings (MeSH) identifier.

Examples

query

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

data

 [{'n': {'definition': 'A primary or metastatic malignant neoplasm involving '
                       'the cervix.',
         'doid': ['4362'],
         'efo': ['NA'],
         'icd10': ['C53.9', 'C53'],
         'icd9': ['180.8', '180', '180.9'],
         'id': 'http://purl.obolibrary.org/obo/MONDO_0002974',
         'label': 'cervical cancer',
         'mesh': ['NA'],
         'umls': ['NA']}},
  {'n': {'definition': 'A hordeolum that results from obstruction and infection '
                       'of an eyelash follicle and adjacent glands of Zeis or '
                       'Moll glands. Follicle obstruction may be associated '
                       'with blepharitis.',
         'doid': ['13134'],
         'efo': ['NA'],
         'icd10': ['H00.03', 'H00.01'],
         'icd9': ['373.11'],
         'id': 'http://purl.obolibrary.org/obo/MONDO_0001642',
         'label': 'hordeolum externum',
         'mesh': ['NA'],
         'umls': ['C0019919']}},
  {'n': {'definition': 'A disease caused by infection with Alkhumra hemorrhagic '
                       'fever virus.',
         'doid': ['0050308'],
         'efo': ['NA'],
         'icd10': ['NA'],
         'icd9': ['NA'],
         'id': 'http://purl.obolibrary.org/obo/MONDO_0000310',
         'label': 'Alkhurma hemorrhagic fever',
         'mesh': ['NA'],
         'umls': ['NA']}}]

Drug

Drug data from Open Targets.

id property: label

label property: label

Properties:

- label: Label of the drug

- molecule_type: Type of the molecule, e.g. Antibody, Protein, Enzyme, etc.

- chembl_uri: ChEMBL Uniform Resource Identifier.

Examples

query

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

data

 [{'n': {'label': 'ABACAVIR', 'source': ['CPIC']}},
  {'n': {'label': 'ATAZANAVIR', 'source': ['CPIC']}},
  {'n': {'label': 'RASBURICASE', 'source': ['CPIC']}}]

Efo

Experimental Factor Ontology (EFO).

id property: id

label property: value

Properties:

- id: EFO URL and identifier.

- value: Text description (EFO term).

- type: EFO type.

Examples

query

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

data

 [{'n': {'id': 'http://www.orpha.net/ORDO/Orphanet_90342',
         'type': 'typed-literal',
         'value': 'Xeroderma pigmentosum variant'}},
  {'n': {'id': 'http://www.orpha.net/ORDO/Orphanet_910',
         'type': 'typed-literal',
         'value': 'Xeroderma pigmentosum'}},
  {'n': {'id': 'http://purl.obolibrary.org/obo/HP_0002140',
         'type': 'typed-literal',
         'value': 'Ischemic stroke'}}]

Event

Events in Reactome (representing biological processes).

id property: reactome_id

label property: name

Properties:

- name: Description of event.

- in_disease: Whether event occurs in disease (TRUE or FALSE).

- reactome_id: Reactome ID for event.

Examples

query

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

data

 [{'n': {'in_disease': 'FALSE',
         'name': 'CYP21A2 oxidises 17HPROG',
         'reactome_id': 'R-HSA-193981'}},
  {'n': {'in_disease': 'FALSE',
         'name': '11-deoxycortisol translocates to the mitochondrion',
         'reactome_id': 'R-HSA-194025'}},
  {'n': {'in_disease': 'FALSE',
         'name': 'Release of activated MAD2 from kinetochores',
         'reactome_id': 'R-HSA-141439'}}]

Gene

Gene data from BioMart (build 37). Gene druggability data comes from Finan et al (2017).

id property: ensembl_id

label property: name

Properties:

- chr: Chromosome.

- type: Gene type, e.g. protein_coding, pseudogene.

- name: HGNC name of the gene.

- source: Source of the gene.

- ensembl_id: Ensembl identifier of the gene.

- start: Start position on chromosome.

- end: End position on chromosome.

- description: Text description of gene.

- reactome_id: Identifier for gene in Reactome database.

- adme_gene: Is the protein product of the gene involved in absorption, distribution, metabolism, and excretion (ADME) of a compound. Evidence from Finan et al.(2017).

- small_mol_druggable: Is the protein product of the (Gene) targeted, or predicted to be targeted, by a small molecule. Evidence from Finan et al.(2017).

- bio_druggable: Is the protein product of the (Gene) targeted, or predicted to be targeted, by a biotherapeutic. Evidence from Finan et al.(2017).

- druggability_tier: The priority tier for the druggable (Gene), e.g. “Tier 1”, “Tier 2”, “Tier 3A”, “Tier 3B”. Evidence from Finan et al.(2017).

Examples

query

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

data

 [{'n': {'chr': '13',
         'end': 23552136,
         'ensembl_id': 'ENSG00000223116',
         'name': 'AL157931.1',
         'source': 'Clone-based (Ensembl) gene',
         'start': 23551994,
         'type': 'miRNA'}},
  {'n': {'chr': '13',
         'description': 'high mobility group AT-hook 1 pseudogene 6 '
                        '[Source:HGNC Symbol;Acc:19121]',
         'end': 23708703,
         'ensembl_id': 'ENSG00000233440',
         'name': 'HMGA1P6',
         'source': 'HGNC Symbol',
         'start': 23708313,
         'type': 'pseudogene'}},
  {'n': {'chr': '13',
         'description': 'RNA, Ro-associated Y3 pseudogene 4 [Source:HGNC '
                        'Symbol;Acc:42488]',
         'end': 23726825,
         'ensembl_id': 'ENSG00000207157',
         'name': 'RNY3P4',
         'source': 'HGNC Symbol',
         'start': 23726725,
         'type': 'misc_RNA'}}]

Tissue

Tissue specific gene expression from GTEx.

id property: tissue

label property: tissue

Properties:

- tissue: Text description of tissue type.

Examples

query

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

data

 [{'n': {'tissue': 'Adipose - Subcutaneous'}},
  {'n': {'tissue': 'Adipose - Visceral (Omentum)'}},
  {'n': {'tissue': 'Adrenal Gland'}}]

Gwas

Genome Wide Association Studies metadata from IEU OpenGWAS Database.

id property: id

label property: trait

Properties:

- note: Extra information.

- access: Access information (public or other).

- mr: Suitability of GWAS for Mendelian randomization.

- year: Year of publication/creation.

- author: First author of GWAS.

- consortium: GWAS consortium name, if applicable.

- sex: Males/Females.

- pmid: PubMed identifier, where available.

- priority: An obsolete field.

- population: Geographical origins of the samples included in the study.

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

- nsnp: Number of variants in results file.

- sample_size: Sample size of GWAS.

- trait: Description of measured trait.

- id: IEU OpenGWAS identifier.

- category: Binary disease phenotype or a non-disease phenotype.

- subcategory: Further categorisation.

- ncase: Number of cases.

- ncontrol: Number of controls.

- sd: Standard deviation of the phenotype analysed.

Examples

query

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

data

 [{'n': {'access': 'public',
         'author': 'Vosa U',
         'category': 'NA',
         'consortium': 'NA',
         'id': 'eqtl-a-ENSG00000261662',
         'mr': '1',
         'note': 'NA',
         'nsnp': '14407',
         'population': 'European',
         'priority': '0',
         'sample_size': '5502',
         'sex': 'Males and Females',
         'subcategory': 'NA',
         'trait': 'ENSG00000261662',
         'unit': 'NA',
         'year': '2018'}},
  {'n': {'access': 'public',
         'author': 'Vosa U',
         'category': 'NA',
         'consortium': 'NA',
         'id': 'eqtl-a-ENSG00000160460',
         'mr': '1',
         'note': 'NA',
         'nsnp': '18645',
         'population': 'European',
         'priority': '0',
         'sample_size': '29896',
         'sex': 'Males and Females',
         'subcategory': 'NA',
         'trait': 'ENSG00000160460',
         'unit': 'NA',
         'year': '2018'}},
  {'n': {'access': 'public',
         'author': 'Vosa U',
         'category': 'NA',
         'consortium': 'NA',
         'id': 'eqtl-a-ENSG00000205426',
         'mr': '1',
         'note': 'NA',
         'nsnp': '19133',
         'population': 'European',
         'priority': '0',
         'sample_size': '31684',
         'sex': 'Males and Females',
         'subcategory': 'NA',
         'trait': 'ENSG00000205426',
         'unit': 'NA',
         'year': '2018'}}]

Literature

PubMed literature data as available from SemMedDB.

id property: pubmed_id

label property: pubmed_id

Properties:

- pubmed_id: The PubMed identifier.

- issn: ISSN code of journal.

- dp: Date published.

- year: Year published.

- edat: Entrez Date is the date the citation was added to PubMed.

Examples

query

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

data

 [{'n': {'dp': '2001 Aug',
         'edat': '2001-8-9',
         'issn': '0741-5400',
         'pubmed_id': '11493615',
         'year': 2001}},
  {'n': {'dp': '2001 Aug',
         'edat': '2001-8-9',
         'issn': '0741-5400',
         'pubmed_id': '11493616',
         'year': 2001}},
  {'n': {'dp': '2001 Aug',
         'edat': '2001-8-9',
         'issn': '0741-5400',
         'pubmed_id': '11493617',
         'year': 2001}}]

Pathway

Biological pathway data from Reactome.

id property: reactome_id

label property: name

Properties:

- name: Name of the pathway.

- in_disease: Boolean indicating if there’s any evidence that the pathway is involved in the cause of any disease.

- reactome_id: Reactome identifier of the pathway.

Examples

query

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

data

 [{'n': {'in_disease': 'FALSE',
         'name': 'Mitotic Spindle Checkpoint',
         'reactome_id': 'R-HSA-69618'}},
  {'n': {'in_disease': 'FALSE',
         'name': 'Amplification of signal from the kinetochores',
         'reactome_id': 'R-HSA-141424'}},
  {'n': {'in_disease': 'FALSE',
         'name': 'Amplification  of signal from unattached  kinetochores via a '
                 'MAD2  inhibitory signal',
         'reactome_id': 'R-HSA-141444'}}]

Protein

Protein data from BioMart (build 37).

id property: uniprot_id

label property: uniprot_id

Properties:

- uniprot_id: UniProt Identifier.

Examples

query

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

data

 [{'n': {'uniprot_id': 'A8MZA4'}},
  {'n': {'uniprot_id': 'A6NJS3'}},
  {'n': {'uniprot_id': 'H3BUK9'}}]

SemmedTriple

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

id property: id

label property: id

Properties:

- id: The complete semantic triplet {subject}:{PREDICATE}:{object}.

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

- subject_name: The preferred name of the subject of the predication.

- subject_type: The semantic type of the subject of the predication (see https://mmtx.nlm.nih.gov/MMTx/semanticTypes.shtml).

- subject_id: The Concept Unique Identifier (CUI) of the subject of the predication.

- object_name: The preferred name of the object of the predication.

- object_type: The semantic type of the object of the predication (see https://mmtx.nlm.nih.gov/MMTx/semanticTypes.shtml).

- object_id: The Concept Unique Identifier (CUI) of the object of the predication.

- count: The total triple count.

Examples

query

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

data

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

SemmedTerm

Biomedical term from SemMedDB.

id property: id

label property: name

Properties:

- name: The preferred name of semantic term.

- count: The total term count.

- id: The Concept Unique Identifier (CUI) of the term.

- type: The semantic type of term (see https://mmtx.nlm.nih.gov/MMTx/semanticTypes.shtml).

Examples

query

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

data

 [{'n': {'count': 241, 'id': '7523', 'name': 'XS', 'type': 'gngm'}},
  {'n': {'count': 9746,
         'id': 'C0019878',
         'name': 'homocysteine',
         'type': 'aapp'}},
  {'n': {'count': 98630, 'id': 'C0017337', 'name': 'Genes', 'type': 'gngm'}}]

Variant

Genetic variant, e.g. SNPs.

id property: name

label property: name

Properties:

- name: rsID of the SNP.

Examples

query

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

data

 [{'n': {'name': 'rs553741'}},
  {'n': {'name': 'rs4652174'}},
  {'n': {'name': 'rs2292238'}}]

Meta

Metadata information of EpiGraphDB Graph.

Properties:

- build_date: Date of the database build.

- graph_version: Version of the database build.

Examples

query

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

data

 [{'n': {'build_date': {'_Date__day': 25,
                        '_Date__month': 4,
                        '_Date__ordinal': 737540,
                        '_Date__year': 2020},
         'graph_version': '0.3.0'}}]