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nodes_and_relationships.md

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Nodes and Relationships in CovidGraph

Format of this document

  • Nodes are declared as :Nodelabel (starting with ":" colon followed by a capital letter)
  • Realtationships are declared as :RELATIONSHIP_NAME (all capital letters)
  • Properties are declared as propertyName (starting with small letter)
  • Graph patterns are presented in Cypher query language style -- Example 1: node1 connected to node2 via relationship, (node1:Nodelabel)-[relationship:RELATIONSHIP_TYPE]->(node2:Nodelabel) -- Example 2: node connected to itself (node1)-[r:RELATIONSHIP]->(node1)

Node labels in CovidGraph

Literature information

  • :PubMedArticle represents a scientific article in the PubMed database.
    • ArticleTitle
    • PMID
    • PublicationType
  • :ArticleId of a PubMedArticle
    • ArticleId.ID
  • :Abstract of a PubMedArticle
  • :AbstractText stores text of an :Abstract as String
    • text
  • :Author of one or many PubMedArticle
    • ForeName
    • Initials
    • LastName
  • :Affiliation Affiliation of an authors
    • Affiliation
  • :Contribution is the link between combination of author, PubMedArticle and the author's affiliations
  • :Journal that published one or many PubMedArticle
    • Title
    • ISOAbbreviation
  • :DZDPubMedArticle Second label on PubMedArticle which for DZD article
    • ArticleTitle
    • PMID
    • PublicationType
  • :DZDAuthor Second label on Author for DZD scientists
    • ForeName
    • Initials
    • LastName
  • :DZDAuthorNotationsHub standardized names for DZDAuthor connecting all author spellings
    • ForeName
    • Initials
    • LastName
  • :DZDAcademy academy of the DZD, self explanary
    • AcademyName
  • :DZDInstitute institutes of the DZD, self explanary
    • InstituteName
  • :DZDAffiliation affiliations of the DZD, self explanary
    • Affiliation
  • :DZDContribution Second label on :Contribution
  • :MeshQualifier stores MeSH-Term
    • text
  • :MeshDescriptor stores MeSH-Term
    • text
  • :MeshHeading connects MeshQualifier and MeshDescriptor
  • :MeshHeadingList list of MeSH headings
  • :Keyword stores keyword of a PubMedArticle
    • Keyword
  • :KeywordList
  • :Date of a PubMedArticle
    • Day
    • Month
    • Year
  • :MedlineJournalInfo stores the iso abbreviation of a Journal
    • MedlineTA
  • :Reference of a PubMedArticle
    • Citation
  • :ChemicalList list of chemicals in a PubMedArticle
  • :ReferenceList list of references of a PubMedArticle
  • :ISSN of a PubMedArticle
  • :JournalIssue of a scientific journal
    • Issue
    • Volume
  • :Identifier from source: ORCID, ISNI, GRID and RINGGOLD
    • ID
    • Source
  • :GrantList list of grants of a PubMedArticle
  • :Grant of a PubMedArticle
  • :PersonalNameSubjectList self explanary
  • :PersonalNameSubject PubMedArticles that are Autobiographies
  • :Investigator PI of a PubMedArticle
  • :GeneralNote not yet investigated
  • :Chemical used in a PubMedArticle

Molecular entities information

  • :Gene from Ensembl holds information of a gene in sid and name
    • source
    • sid
    • name
    • taxid
  • :Transcript are RNAs from coding genes, from source=RefSeq
    • source
    • sid
    • taxid
  • :Protein from source=Uniprot, RefSeq, Swissprot stores protein information
    • source
    • sid
    • taxid
  • :Lipid from source=SwissLipid
  • :Metabolite from source=HNGC
    • name
    • definition
    • sid
    • taxid
    • source
  • :Pathway molecular pathway from source=Reactome
    • name
    • sid
    • taxid
    • source
    • org Organism
  • :SNP SingleNucleotidePolymorphism/gene varition from source=GWAS which is associated with a :Trait and a :Gene
    • snp_id
    • taxid
  • :Study associated with a :Trait and a :SNP
    • title
    • pubmedId
    • reported_genes
  • :Association between :Trait, a :SNP and :Study
  • :SNP_Interaction of two or more :SNPs
    • snp_id
    • taxid
  • :Trait nameis a feature or phenotype or disease which is connected to a gene variation :SNP
    • name
  • :Phenotype which is connected to a :Gene
    • name
  • :GtexSample specific sample of a :GtexTissue with raw data
  • :GtexTissue human tissue
    • name
  • :GtexDetailedTissue sub tissue of :GtexTissue and connected :Gene
    • name
  • :MgiDescription mouse gene description from source=MGI
  • :GeneSymbolList self explanatory

Ontology information

  • :Term with name holds a term and is connected to its :Ontology
    • name
    • definition
    • sid
  • :Disease currently empty
  • :Ontology with name, connected to :Term and source=Obo FoundryCurrently from Disease Ontology, GeneOntology, Mouse Phenotype Ontology
    • sid
  • :OntologySubset self explanatory
  • :SynonymTerm

Technical information

  • :_FulltextLookUpDone_Label_property Second label for node label. Combination of label and property was looked up on the fulltext index in abstracts
  • :_FulltextLookUpDone_Protein_name
  • :_FulltextLookUpDone_Protein_sid
  • :OmitInMatch second label for genes, and proteins that are omitted for text search
  • :OmitSpecialChar second label for genes and proteins because of special characters in name
  • :OmitLengthOne second label for genes and proteins because the name is only one character
  • :OmitWord second label for genes and proteins, because the name is an English word
  • :_PipelineLogNode technical information to one pipeline module
  • :_PubMedXmlLoadingLog technical information for data integration of one XML file from PubMed
  • :_PipelineLogRun technical information of the central pipeline run
  • :ProteinSearch intermediate label for proteins that need preprocessing steps before search
  • :Word list of words that are omitted in text search