PhageFoundry Strain Modelling Database

PhageFoundry strain modelling database for phage-host interaction studies. Contains organisms, genomes, genes, experiments, and interaction data for understanding phage-bacteria dynamics. DATABASE STATISTICS: - 284 organisms (primarily E. coli strains) - Genome sets, sequences, and gene annotations - Experimental data with metrics and features - Protein family and interaction data TABLE STRUCTURE (18 tables): - Core: strainmodelling_organism, strainmodelling_genome, strainmodelling_sequence, strainmodelling_gene - Metadata: strainmodelling_organism_metadata, strainmodelling_genome_set, strainmodelling_genome_set_genomes - Experiments: strainmodelling_experiment, strainmodelling_experiment_metadata, strainmodelling_experiment_metric - Features: strainmodelling_feature, strainmodelling_feature_metric, strainmodelling_feature_intervals - Analysis: strainmodelling_interaction, strainmodelling_interval - Protein families: strainmodelling_protein_family, strainmodelling_protein_family_genes, strainmodelling_protein_family_features PROJECT CONTEXT: Supports computational modelling of phage-host interactions for phage therapy development. Focus on E. coli strains.

URI: https://w3id.org/kbase/phagefoundry_strain_modelling

Name: phagefoundry_strain_modelling

Classes

Class	Description
Experiment	Phage-host interaction experiment
ExperimentMetadata	Extended experiment metadata as key-value pairs
ExperimentMetric	Quantitative metrics from experiments (e
Feature	Genomic or phenotypic feature relevant to phage interaction
FeatureInterval	Genomic intervals (coordinates) for features
FeatureMetric	Quantitative metrics associated with features
Gene	Predicted gene with location and annotation
Genome	Genome assembly for an organism
GenomeSet	Collection of genomes for comparative analysis
GenomeSetGenome	Many-to-many link between genome sets and genomes
Interaction	Phage-host interaction data (infection, resistance, etc
Interval	Genomic interval (coordinate range)
Organism	Bacterial organism/strain used in phage interaction studies
OrganismMetadata	Extended metadata for organisms as key-value pairs
ProteinFamily	Protein family grouping related proteins
ProteinFamilyFeature	Features associated with protein families
ProteinFamilyGene	Genes belonging to protein families
Sequence	DNA/RNA sequence (contig, chromosome, or plasmid)

Slots

Slot	Description
description	Organism description (optional)
domain	Taxonomic domain
end
experiment_id
feature_id
feature_type	Type of feature (e
full_name	Full organism name with species
gene_id
genome_id
genome_set_id
host_id	Host organism identifier
id	Internal organism ID
interaction_type	Type of interaction (infection, resistance, etc
interval_id
key
length	Sequence length in base pairs
locus_tag
metric_name
name	Short organism/strain name
organism_id
phage_id	Phage identifier
product	Gene product/function
protein_family_id
sequence_id
size	Genome size in base pairs
start
strand	Strand (1 or -1)
value

Enumerations

Enumeration	Description

Types

Type	Description
Boolean	A binary (true or false) value
Curie	a compact URI
Date	a date (year, month and day) in an idealized calendar
DateOrDatetime	Either a date or a datetime
Datetime	The combination of a date and time
Decimal	A real number with arbitrary precision that conforms to the xsd:decimal speci...
Double	A real number that conforms to the xsd:double specification
Float	A real number that conforms to the xsd:float specification
Integer	An integer
Jsonpath	A string encoding a JSON Path
Jsonpointer	A string encoding a JSON Pointer
Ncname	Prefix part of CURIE
Nodeidentifier	A URI, CURIE or BNODE that represents a node in a model
Objectidentifier	A URI or CURIE that represents an object in the model
Sparqlpath	A string encoding a SPARQL Property Path
String	A character string
Time	A time object represents a (local) time of day, independent of any particular...
Uri	a complete URI
Uriorcurie	a URI or a CURIE

Subsets

Subset	Description