PhageFoundry Genome Browser Database
PhageFoundry comparative genome browser databases for bacterial pathogens. Contains genome annotations, functional classifications, and regulatory information for phage therapy target organisms. AVAILABLE DATABASES: | Database | Organism | Genomes | Description | |----------|----------|---------|-------------| | phagefoundry_acinetobacter_genome_browser | A. baumannii | 891 | Nosocomial pathogen | | phagefoundry_klebsiella_genome_browser_genomedepot | K. pneumoniae | 220 | Carbapenem-resistant | | phagefoundry_paeruginosa_genome_browser | P. aeruginosa | 535 | Opportunistic pathogen | | phagefoundry_pviridiflava_genome_browser | P. viridiflava | 259 | Plant pathogen | TABLE STRUCTURE (30 tables per database): - Core: browser_genome, browser_contig, browser_gene, browser_protein - Annotations: browser_cazy_family, browser_cog_class, browser_ec_number, browser_go_term, browser_kegg_ortholog, browser_kegg_pathway - Protein links: browser_protein_* (many-to-many annotation links) - Regulation: browser_operon, browser_regulon, browser_regulon_regulators - Metadata: browser_sample, browser_sample_metadata, browser_site, browser_genome_tags PHAGEFOUNDRY PROJECT: Developing phage therapies for antibiotic-resistant bacterial infections. Genome browsers support identification of phage receptor genes and resistance mechanisms.
URI: https://w3id.org/kbase/phagefoundry_genome_browser
Name: phagefoundry_genome_browser
Classes
| Class | Description |
|---|---|
| Annotation | Generic annotation record (used by browser_annotation) |
| CAZyFamily | Carbohydrate-Active enZYme family classification |
| COGClass | COG (Clusters of Orthologous Groups) functional class |
| Contig | Genome contig/scaffold with sequence and GC content |
| ECNumber | Enzyme Commission number for enzymatic function |
| EggNOGDescription | eggNOG ortholog group functional description |
| Gene | Predicted gene with coordinates and strand |
| Genome | Bacterial genome assembly with basic statistics |
| GenomeTag | Tags/labels for genome classification or grouping |
| GOTerm | Gene Ontology term for functional annotation |
| KEGGOrtholog | KEGG Orthology (KO) identifier for pathway mapping |
| KEGGPathway | KEGG metabolic or signaling pathway |
| KEGGReaction | KEGG biochemical reaction |
| Operon | Predicted operon (co-transcribed gene cluster) |
| OrthologGroup | Ortholog group across genomes in the database |
| Protein | Protein sequence with functional annotations |
| ProteinCAZyFamily | Protein to CAZy family assignments |
| ProteinCOGClass | Protein to COG class assignments |
| ProteinECNumber | Protein to EC number assignments |
| ProteinGOTerm | Protein to GO term assignments |
| ProteinKEGGOrtholog | Protein to KEGG ortholog assignments |
| ProteinKEGGPathway | Protein to KEGG pathway assignments |
| ProteinKEGGReaction | Protein to KEGG reaction assignments |
| ProteinOrthologGroup | Protein to ortholog group assignments |
| ProteinTCFamily | Protein to Transporter Classification family assignments |
| Regulon | Regulatory network/regulon controlled by transcription factors |
| RegulonRegulator | Transcription factor/regulator in a regulon |
| Sample | Sample/isolate metadata |
| SampleMetadata | Extended sample metadata key-value pairs |
| Site | Sampling site/location information |
Slots
| Slot | Description |
|---|---|
| cazy_family_id | |
| cog_class_id | |
| contig_id | |
| contigs | Number of contigs in assembly |
| description | Genome description (often same as name) |
| ec_number_id | |
| eggnog_description_id | Link to eggNOG functional description |
| end | End coordinate |
| external_id | NCBI accession number |
| external_url | NCBI nucleotide URL |
| gbk_filepath | Path to GenBank file on server |
| gc_content | GC content (0-1) |
| gene_id | |
| genes | Total number of predicted genes |
| genome_id | |
| go_id | GO term ID (GO:NNNNNNN) |
| go_term_id | |
| id | Internal genome ID |
| json_url | Relative URL to genome JSON data |
| kegg_ortholog_id | |
| kegg_pathway_id | |
| kegg_reaction_id | |
| key | |
| ko_id | KO identifier (KXXXXX) |
| length | Protein length in amino acids |
| locus_tag | Locus tag identifier |
| name | Genome/strain name |
| ortholog_group_id | |
| pathway_id | KEGG pathway ID |
| protein_hash | MD5 hash of protein sequence |
| protein_id | |
| pub_date | Publication/upload date |
| reaction_id | |
| regulon_id | |
| sample_id | Link to sample metadata |
| sequence | Amino acid sequence |
| size | Total genome size in base pairs |
| start | Start coordinate (1-based) |
| strain_id | Strain identifier |
| strand | Strand (1 or -1) |
| tag | |
| taxon_id | Taxonomy reference |
| taxonomy_id_id | Taxonomy reference |
| tc_family_id | |
| type | Gene type (CDS, tRNA, rRNA, etc |
| 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 |
|---|---|