PanTools graph database structure

Please see Fig. 23 for the PanTools graph database. Please use it as a reference for writing Cypher queries and for understanding the structure of the database.

digraph G { rankdir=LR; node [shape=box]; subgraph cluster_metadata { pangenome [label="pangenome"]; genome [label="genome"]; accession [label="accession"]; phenotype [label="phenotype"]; annotation [label="annotation"]; sequence [label="sequence"]; pangenome -> genome [label="has"]; genome -> phenotype [label="has_phenotype"]; genome -> accession [label="has"]; annotation -> genome [label="annotates"]; genome -> sequence [label="has"]; } subgraph cluster_nucleotide { label="nucleotide layer"; nucleotide [label="nucleotide"]; nucleotide -> nucleotide [label="FF"]; nucleotide -> nucleotide [label="FR"]; nucleotide -> nucleotide [label="RF"]; nucleotide -> nucleotide [label="RR"]; } sequence -> nucleotide [label="FF"]; nucleotide -> sequence [label="FF"]; nucleotide -> sequence [label="RF"]; nucleotide -> sequence [label="FR"]; nucleotide -> sequence [label="RR"]; subgraph cluster_annotation { label="annotation layer"; gene [label="gene"]; mRNA [label="mRNA"]; CDS [label="CDS"]; exon [label="exon"]; gene -> mRNA [label="is_parent_of"]; gene -> mRNA [label="codes_for"]; mRNA -> CDS [label="is_parent_of"]; CDS -> mRNA [label="contributes_to"]; mRNA -> exon [label="is_parent_of"]; mRNA -> mRNA [label="is_similar_to"]; } homology_group [label="homology_group"]; variant [label="variant"]; repeat [label="repeat"]; synteny [label="synteny"]; homology_group -> mRNA [label="has_homolog"]; mRNA -> variant [label="has_variant"]; repeat -> nucleotide [label="start"]; repeat -> nucleotide [label="stop"]; mRNA -> synteny [label="part_of"]; synteny -> synteny [label="is_syntenic_to"]; gene -> nucleotide [label="starts"]; gene -> nucleotide [label="stops"]; mRNA -> nucleotide [label="starts"]; mRNA -> nucleotide [label="stops"]; CDS -> nucleotide [label="starts"]; CDS -> nucleotide [label="stops"]; exon -> nucleotide [label="starts"]; exon -> nucleotide [label="stops"]; subgraph cluster_functions { label="functions layer"; GO [label="GO"]; pfam [label="pfam"]; interpro [label="interpro"]; tigrfam [label="tigrfam"]; GO -> GO [label="regulates"]; GO -> GO [label="negatively_regulates"]; GO -> GO [label="positively_regulates"]; GO -> GO [label="is_a"]; GO -> GO [label="part_of"]; pfam -> GO [label="is_similar_to"]; interpro -> GO [label="is_similar_to"]; tigrfam -> GO [label="is_similar_to"]; tigrfam -> GO [label="contributes_to"]; } mRNA -> GO [label="has_GO"]; mRNA -> pfam [label="has_pfam"]; mRNA -> interpro [label="has_interpro"]; mRNA -> tigrfam [label="has_tigrfam"]; }

Fig. 23 PanTools graph database schema in neo4j.