EraGene cypher dataset

Résumé fourni par la source

EraGene Knowledge Graph This repository contains the annotations used to build the EraGene knowledge graph. The database is provided as a Neo4j dump (Version 2026.06.0), which can be easily imported into a Neo4j instance. Once imported, the database can be explored by querying it using the Cypher query language. The following sections provide instructions and examples for interacting with the database. Requeriments Download and install Neo4j for Desktop 2.2.1 or later here. Create an instance if none is available. Getting started Download the Dump File Download the database dump file (eragene.dump). Save it to a suitable location on your local machine. Prepare the Database Run Neo4j Desktop. Stop the instance if it is running (important). Identify the path where the instance is stored. Example for windows: Path = C:\Users\user\.Neo4jDesktop2\Data\dbmss\dbms-xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxxx Load the Database Run the following command to load the dump file and populate the database. {Path}/bin/neo4j-admin database load neo4j --from-path=/path/to/dump/eragene.dump --overwrite-destination=true Replace {Path} with the path to your Neo4j instance's directory. If no errors occur, the database has been successfully imported. Database Structure General Schema of Relationships Between Labels The relationships between node labels are represented in the following figure. CALL db.schema.visualization(); Node Properties The nodes that constitute the graph database are described in the following table. MATCH (n) UNWIND labels(n) AS label UNWIND keys(n) AS key RETURN label, key AS property, collect(DISTINCT valueType(n[key])) AS types ORDER BY label, property; Label Property Type Compound InChI STRING NOT NULL Compound InChIKey STRING NOT NULL Compound dg STRING NOT NULL Compound formule STRING NOT NULL Compound generic BOOLEAN NOT NULL Compound html_name STRING NOT NULL Compound id STRING NOT NULL Compound mm STRING NOT NULL Compound mw STRING NOT NULL Compound pk STRING NOT NULL Compound smile STRING NOT NULL Compound ubiquitous BOOLEAN NOT NULL Enzyme id STRING NOT NULL Enzyme name STRING NOT NULL ExternalLink db STRING NOT NULL ExternalLink external_id STRING NOT NULL ExternalLink id STRING NOT NULL ExternalLink pk INTEGER NOT NULL, STRING NOT NULL Gene id STRING NOT NULL Gene name STRING NOT NULL Gene pk STRING NOT NULL Gene sequence STRING NOT NULL Modification exclusion STRING NOT NULL Modification id STRING NOT NULL Modification modification_type STRING NOT NULL Modification pk STRING NOT NULL Modification sequence_optimized BOOLEAN NOT NULL Modification sequence_substitution STRING NOT NULL Organism id STRING NOT NULL Organism name STRING NOT NULL Plasmid genotype STRING NOT NULL Plasmid id STRING NOT NULL Plasmid name STRING NOT NULL Plasmid pk STRING NOT NULL Plasmid resistance LIST NOT NULL, LIST NOT NULL Production biomass STRING NOT NULL, FLOAT NOT NULL Production biomass_units STRING NOT NULL Production fermentation STRING NOT NULL Production heterologous BOOLEAN NOT NULL Production id STRING NOT NULL Production main BOOLEAN NOT NULL Production pk STRING NOT NULL Production production FLOAT NOT NULL Production production_type STRING NOT NULL Production production_units STRING NOT NULL Production time STRING NOT NULL Reaction dg STRING NOT NULL Reaction direction STRING NOT NULL Reaction id STRING NOT NULL Reaction pk STRING NOT NULL Reaction spontaneous BOOLEAN NOT NULL Reference cite STRING NOT NULL Reference doi STRING NOT NULL Reference id STRING NOT NULL Reference pk STRING NOT NULL Strain genotype STRING NOT NULL Strain id STRING NOT NULL Strain mutagen_derived BOOLEAN NOT NULL Strain name STRING NOT NULL Strain pk STRING NOT NULL Relationships The relationships that connect the nodes in the database are the following. MATCH (a)-[r]->(b) RETURN DISTINCT labels(a) AS source_labels, type(r) AS relationship, labels(b) AS target_labels ORDER BY relationship, source_labels, target_labels; Source Label Relationship Target Label Modification AFFECT_GENE Gene Modification AFFECT_REACTION Reaction Production CARBON_SOURCE Compound Enzyme CATALYZES Reaction Gene ENCODES Enzyme Gene EXTERNAL_DATABASE ExternalLink Gene GENE_FROM Organism Compound EXTERNAL_DATABASE ExternalLink Reaction EXTERNAL_DATABASE ExternalLink Reaction HAS_LEFT Compound Reaction HAS_RIGHT Compound Reaction SUPPORTED_BY Reference Strain HAS_MODIFICATION Modification Strain HAS_PLASMID Plasmid Strain PARENT_OF Strain Strain PRODUCES Production Strain SUPPORTED_BY Reference Plasmid INTRODUCED_BY_PLASMID Modification Plasmid SUPPORTED_BY Reference Organism SUPPORTED_BY Reference Production SUPPORTED_BY Reference Production TARGET Compound Usage Examples Metabolites in the Database MATCH (m:Compound) RETURN m.pk AS ID, m.html_name AS Name; ID Name "C7751" "dGTP" "C7823" "dADP" "C7783" "dATP" ... L-Tryptophan Production Levels Across Different Strains MATCH (s:Strain)-[:PRODUCES]->(p:Production)-[ :TARGET]->(c:Compound {html_name:"L-tryptophan"}) RETURN s.name AS Strain, p.production AS Production, p.production_units AS Units, p.fermentation AS Scale, c.html_name AS Metabolite; Strain Production Units Scale Metabolite "Escherichia coli KW006" 0.6 "g/L" "Flask" "L-tryptophan" "Escherichia coli KW007" 0.8 "g/L" "Flask" "L-tryptophan" "Escherichia coli KW008" 1.39 "g/L" "Flask" "L-tryptophan" "Escherichia coli KW010" 0.59 "g/L" "Flask" "L-tryptophan" ... Genetic Modifications Introduced into Strains to Enhance L-Tryptophan Production MATCH (tryptophan:Compound {html_name: "L-tryptophan"}) MATCH (tryptophan)<-[:TARGET]-(prod:Production {main:TRUE}) MATCH (prod)<-[:PRODUCES]-(strain:Strain) MATCH (strain)-[:HAS_MODIFICATION]->(mod:Modification {exclusion : ''}) MATCH (mod)-[:AFFECT_GENE]->(gene:Gene) RETURN DISTINCT mod.modification_type AS modification_type, gene.name AS gene_name ORDER BY gene.name, modification_type; modification_type gene_name organism "Overexpression" "TRP1" "Saccharomyces cerevisiae" "Overexpression" "TRP2" "Saccharomyces cerevisiae" "Overexpression" "aceB" "Escherichia coli" "Silencing" "ackA" "Escherichia coli"

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