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schema.json
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{
"$schema": "http://json-schema.org/draft-07/schema#",
"$schema_created": "2022-08-18T19:36:44+02:00",
"$schema_version": "2.12",
"additionalProperties": false,
"properties": {
"changelog": {
"items": {
"additionalProperties": false,
"properties": {
"comments": {
"items": {
"type": "string"
},
"type": "array"
},
"contributors": {
"items": {
"type": "string"
},
"type": "array"
},
"updated_at": {
"items": {
"type": "string",
"format": "date-time"
},
"type":"array"
},
"version": {
"pattern": "^(\\d+(\\.\\d+)*|next)$",
"type": "string"
}
},
"required": [
"comments",
"contributors",
"version"
],
"type": "object"
},
"minItems": 1,
"type": "array"
},
"cluster": {
"additionalProperties": false,
"allOf": [
{
"if": {
"properties": {
"status": {
"const": "active"
}
},
"required": [
"status"
]
},
"then": {
"properties": {
"publications": {
"minItems": 1
}
},
"required": [
"publications"
]
}
},
{
"if": {
"properties": {
"status": {
"const": "retired"
}
},
"required": [
"status"
]
},
"then": {
"properties": {
"retirement_reasons": {
"minItems": 1
}
},
"required": [
"retirement_reasons"
]
},
"else": {
"not": {
"required": [
"retirement_reasons"
]
}
}
}
],
"properties": {
"alkaloid": {
"additionalProperties": false,
"properties": {
"subclass": {
"title": "Alkaloid subclass",
"type": "string"
}
},
"title": "Alkaloid-specific parameters",
"type": "object"
},
"biosyn_class": {
"items": {
"enum": [
"Alkaloid",
"Polyketide",
"RiPP",
"NRP",
"Saccharide",
"Terpene",
"Other"
],
"type": "string"
},
"minItems": 1,
"title": "Biosynthetic class",
"type": "array"
},
"compounds": {
"items": {
"additionalProperties": false,
"properties": {
"chem_acts": {
"items": {
"$ref": "#/$defs/chemical_activity"
},
"title": "Molecular activities",
"type": "array"
},
"chem_moieties": {
"items": {
"additionalProperties": false,
"properties": {
"moiety": {
"title": "Chemical moiety",
"type": "string"
},
"subcluster": {
"items": {
"pattern": "^[^,\\- ]*$",
"type": "string"
},
"title": "Sub-cluster involved in the biosynthesis of this moiety",
"type": "array"
}
},
"required": [
"moiety"
],
"title": "Chemical moiety",
"type": "object"
},
"title": "Unusual chemical moieties in this molecule",
"type": "array"
},
"chem_struct": {
"$ref": "#/$defs/smiles",
"title": "Compound structure"
},
"chem_synonyms": {
"items": {
"type": "string"
},
"title": "Synonyms for this compound",
"type": "array"
},
"chem_targets": {
"items": {
"additionalProperties": false,
"properties": {
"publications": {
"items": {
"$ref": "#/$defs/publication"
},
"title": "Publication id",
"type": "array"
},
"target": {
"title": "Target protein, RNA, molecule, etc",
"type": "string"
}
},
"type": "object"
},
"title": "Molecular targets",
"type": "array"
},
"compound": {
"pattern": "^[a-zA-Zα-ωΑ-Ω0-9\\[\\]'()/&,. +-]+$",
"title": "Compound name (from PUBMED or NPAtlas)",
"type": "string"
},
"database_id": {
"items": {
"oneOf": [
{
"pattern": "^pubchem:(\\d+)$"
},
{
"pattern": "^chebi:(\\d+)$"
},
{
"pattern": "^chembl:CHEMBL(\\d+)$"
},
{
"pattern": "^chemspider:(\\d+)$"
},
{
"pattern": "^npatlas:NPA(\\d+)$"
},
{
"pattern": "^lotus:Q(\\d+)$"
}
],
"type": "string"
},
"title": "Database Compound IDs (PubChem/ChEBI/ChEMBL/ChemSpider/NPAtlas/LOTUS)",
"type": "array"
},
"evidence": {
"items": {
"type": "string"
},
"title": "Technique(s) used to elucidate/verify the structure",
"type": "array"
},
"mass_spec_ion_type": {
"title": "Ion type for this mass spec",
"type": "string"
},
"mol_mass": {
"title": "Exact molecular mass",
"type": "number",
"minimum": 0
},
"molecular_formula": {
"title": "Molecular formula",
"type": "string"
}
},
"title": "Chemical compound",
"type": "object"
},
"minItems": 1,
"title": "Chemical compound(s)",
"type": "array"
},
"genes": {
"additionalProperties": false,
"properties": {
"annotations": {
"items": {
"additionalProperties": false,
"properties": {
"comments": {
"title": "Comments on this gene",
"type": "string"
},
"domains": {
"items": {
"additionalProperties": false,
"properties": {
"location": {
"additionalProperties": false,
"properties": {
"begin": {
"minimum": 0,
"type": "number"
},
"end": {
"minimum": 1,
"type": "number"
}
},
"required": [
"begin",
"end"
],
"title": "Location of the domain within the gene (in AAs)",
"type": "object"
},
"name": {
"type": "string"
},
"substrates": {
"items": {
"additionalProperties": false,
"properties": {
"evidence": {
"items": {
"$ref": "#/$defs/substrate_evidence"
},
"type": "array"
},
"name": {
"type": "string"
},
"publications": {
"itmes": {
"$ref": "#/$defs/publication"
},
"type": "array"
},
"structure": {
"$ref": "#/$defs/smiles",
"title": "Monomer structure"
},
"tool": {
"$ref": "#/$defs/tool"
}
},
"required": [
"name",
"structure"
],
"type": "object"
},
"type": "array"
}
},
"required": [
"location",
"name"
],
"type": "object"
},
"type": "array"
},
"functions": {
"items": {
"additionalProperties": false,
"properties": {
"category": {
"title": "Gene function category",
"type": "string"
},
"evidence": {
"items": {
"enum": [
"Sequence-based prediction",
"Other in vivo study",
"Heterologous expression",
"Knock-out",
"Activity assay"
],
"type": "string"
},
"title": "Evidence for function",
"type": "array"
}
},
"required": [
"category",
"evidence"
],
"type": "object"
},
"title": "Gene function categories",
"type": "array"
},
"id": {
"pattern": "^[^, ]*$",
"title": "Gene ID",
"type": "string"
},
"mut_pheno": {
"title": "Knockout mutation phenotype for this gene, if known",
"type": "string"
},
"name": {
"pattern": "^[^, ]*$",
"title": "Gene name, ",
"type": "string"
},
"product": {
"title": "Gene product",
"type": "string"
},
"publications": {
"items": {
"$ref": "#/$defs/publication"
},
"title": "Publications on this gene",
"type": "array"
},
"tailoring": {
"items": {
"type": "string"
},
"title": "Tailoring reaction type",
"type": "array"
}
},
"title": "Gene",
"type": "object"
},
"required": [
"id"
],
"title": "Genes",
"type": "array"
},
"extra_genes": {
"items": {
"additionalProperties": false,
"properties": {
"id": {
"pattern": "^[^, ]*$",
"title": "Gene ID",
"type": "string"
},
"location": {
"additionalProperties": false,
"properties": {
"exons": {
"items": {
"additionalProperties": false,
"properties": {
"end": {
"minimum": 2,
"title": "End coordinate of the exon, in nt",
"type": "integer"
},
"start": {
"minimum": 1,
"title": "Start coordinate of the exon, in nt",
"type": "integer"
}
},
"required": [
"start",
"end"
],
"type": "object"
},
"minItems": 1,
"title": "Exons",
"type": "array"
},
"strand": {
"enum": [
-1,
1
],
"type": "integer"
}
},
"required": [
"exons",
"strand"
],
"title": "Gene location",
"type": "object"
},
"translation": {
"type": "string"
}
},
"required": [
"id",
"location"
],
"title": "Gene",
"type": "object"
},
"type": "array"
},
"operons": {
"items": {
"additionalProperties": false,
"properties": {
"evidence": {
"items": {
"enum": [
"Sequence-based prediction",
"RACE",
"ChIPseq",
"RNAseq"
],
"type": "string"
},
"title": "Experimental evidence for this operon",
"type": "array"
},
"genes": {
"items": {
"type": "string"
},
"minItems": 1,
"title": "Genes in operon",
"type": "array"
}
},
"required": [
"genes",
"evidence"
],
"title": "Operon",
"type": "object"
},
"title": "Operons",
"type": "array"
}
},
"title": "Genes in this gene cluster",
"type": "object"
},
"loci": {
"additionalProperties": false,
"properties": {
"accession": {
"pattern": "^([A-Za-z0-9_]{3,}\\.\\d)|(MIBIG\\.BGC\\d{7}\\.\\d)$",
"title": "GenBank nucleotide accession number",
"type": "string"
},
"completeness": {
"enum": [
"incomplete",
"complete",
"Unknown"
],
"title": "Complete gene cluster sequence?",
"type": "string"
},
"end_coord": {
"minimum": 2,
"title": "End coordinate (1-indexed, exclusive)",
"type": "integer"
},
"evidence": {
"items": {
"enum": [
"Homology-based prediction",
"Correlation of genomic and metabolomic data",
"Gene expression correlated with compound production",
"Knock-out studies",
"Enzymatic assays",
"Heterologous expression",
"In vitro expression"
],
"type": "string"
},
"title": "Evidence of involvement",
"type": "array"
},
"mixs_compliant": {
"title": "TODO: use old title",
"type": "boolean"
},
"start_coord": {
"minimum": 1,
"title": "Start coordinate (1-indexed, inclusive)",
"type": "integer"
}
},
"required": [
"completeness",
"accession"
],
"title": "Gene cluster sequence information",
"type": "object"
},
"mibig_accession": {
"title": "MIBiG accession number",
"type": "string"
},
"minimal": {
"title": "if the entry contains no experimental data",
"type": "boolean"
},
"ncbi_tax_id": {
"type": "string"
},
"nrp": {
"additionalProperties": false,
"properties": {
"cyclic": {
"title": "is the NRP cyclic (otherwise linear)",
"type": "boolean"
},
"lipid_moiety": {
"title": "Lipid moiety attached to the peptide",
"type": "string"
},
"nrps_genes": {
"items": {
"additionalProperties": false,
"properties": {
"gene_id": {
"pattern": "^[^, ]*$",
"title": "NRPS-encoding gene",
"type": "string"
},
"modules": {
"items": {
"additionalProperties": false,
"properties": {
"a_substr_spec": {
"additionalProperties": false,
"properties": {
"aa_subcluster": {
"items": {
"type": "string"
},
"title": "Genes responsible for biosynthesis of the specificity, if within this gene cluster",
"type": "array"
},
"epimerized": {
"type": "boolean"
},
"evidence": {
"items": {
"$ref": "#/$defs/substrate_evidence"
},
"title": "Evidence for A-domain specificity",
"type": "array"
},
"publications": {
"items": {
"$ref": "#/$defs/publication"
},
"type": "array"
},
"substrates": {
"items": {
"additionalProperties": false,
"allOf": [
{
"if": {
"properties": {
"proteinogenic": {
"const": true
}
},
"required": [
"proteinogenic"
]
},
"then": {
"properties": {
"name": {
"$ref": "#/$defs/proteinogenic_amino_acids"
}
},
"required": [
"name"
]
},
"else": {
"not": {
"properties": {
"name": {
"$ref": "#/$defs/proteinogenic_amino_acids"
}
},
"required": [
"name"
]
}
}
}
],
"properties": {
"name": {
"type": "string"
},
"proteinogenic": {
"type": "boolean"
},
"structure": {
"$ref": "#/$defs/smiles"
}
},
"required": [
"name",
"proteinogenic",
"structure"
],
"type": "object"
},
"type": "array"
}
},
"title": "Adenylation domain substrate specificity",
"type": "object"
},
"active": {
"type": "boolean"
},
"c_dom_subtype": {
"enum": [
"Dual",
"Starter",
"LCL",
"Unknown",
"DCL",
"Ester bond-forming",
"Heterocyclization"
],
"title": "Subtype of condensation domain in this module",
"type": "string"
},
"comments": {
"type": "string"
},
"integrated_monomers": {
"items": {
"additionalProperties": false,
"properties": {
"evidence": {
"items": {
"$ref": "#/$defs/substrate_evidence"
},
"title": "Evidence for integrated monomer",
"type": "array"
},
"name": {
"type": "string"
},
"publications": {
"items": {
"$ref": "#/$defs/publication"
},
"type": "array"
},
"structure": {
"$ref": "#/$defs/smiles",
"title": "Monomer structure"
}
},
"required": [
"name",
"structure"
],
"type": "object"
},
"type": "array"
},
"modification_domains": {
"items": {
"type": "string"
},
"title": "Scaffold-modifying domains in this module",
"type": "array"
},
"module_number": {
"pattern": "^[A-Z]*[0-9]+[A-Z]*$",
"title": "Assembly line module number",
"type": "string"
},
"non_canonical": {
"additionalProperties": false,
"properties": {
"evidence": {
"items": {
"enum": [
"Sequence-based prediction",
"Structure-based inference",
"Activity assay"
],
"type": "string"
},
"title": "Evidence for non-canonical activity",
"type": "array"
},
"iterated": {
"type": "boolean"
},
"non_elongating": {
"type": "boolean"
},
"skipped": {
"type": "boolean"
}
},
"type": "object"
}
},
"title": "NRPS Module",
"type": "object"
},
"title": "NRPS modules in this gene",
"type": "array"
}
},
"title": "NRPS gene",
"type": "object"
},
"title": "NRPS genes in cluster",
"type": "array"
},
"release_type": {
"items": {
"type": "string"
},
"title": "Release/cyclization type",
"type": "array"
},
"subclass": {
"title": "NRP subclass",
"type": "string"
},
"thioesterases": {
"items": {
"additionalProperties": false,
"properties": {
"gene": {
"pattern": "^[^, ]*$",
"title": "Thioesterase-encoding gene id",
"type": "string"
},
"thioesterase_type": {
"enum": [
"Unknown",
"Type II",
"Type I"
],
"title": "Thioesterase type",
"type": "string"
}
},
"type": "object"
},
"type": "array"
}
},
"title": "NRP-specific parameters",
"type": "object"
},
"organism_name": {
"type": "string"
},
"other": {
"additionalProperties": false,
"properties": {
"subclass": {
"title": "Other biosynthetic class",
"type": "string"
}
},
"title": "Parameters specific for other classes",
"type": "object"
},
"polyketide": {
"additionalProperties": false,
"properties": {
"cyclases": {
"items": {
"type": "string"
},
"title": "Gene(s) in cluster involved in folding and cyclization of the aromatic polyketide",
"type": "array"
},
"cyclic": {
"title": "is the polyketide cyclic (otherwise linear)",
"type": "boolean"
},
"ketide_length": {
"title": "Polyketide length",
"type": "integer",
"minimum": 0
},
"release_type": {
"items": {
"type": "string"
},
"title": "Release/cyclization type",
"type": "array"
},
"starter_unit": {
"title": "Starter unit",
"type": "string"
},
"subclasses": {
"items": {
"type": "string"
},
"title": "Polyketide subclasses",
"type": "array"
},
"synthases": {
"items": {
"additionalProperties": false,
"properties": {
"genes": {
"items": {
"pattern": "^[^, ]*$",
"type": "string"
},
"minItems": 1,
"title": "all genes forming the synthase",
"type": "array"
},
"iterative": {
"additionalProperties": false,
"properties": {
"cyclization_type": {
"title": "Iterative PKS cyclization type",
"type": "string"
},
"evidence": {
"enum": [
"Sequence-based prediction",
"Structure-based inference",
"Activity assay"
],
"title": "Evidence for iteration",
"type": "string"
},
"genes": {
"items": {
"pattern": "^[^, ]*$",
"type": "string"
},
"minItems": 1,
"title": "all genes forming the synthase",
"type": "array"
},
"nr_iterations": {
"minimum": 1,
"title": "Number of chain synthesis iterations performed by iterative PKS module",
"type": "integer"
},
"subtype": {
"enum": [
"Partially reducing",
"Non-reducing",
"Highly reducing"
],
"title": "Iterative PKS subtype",
"type": "string"
}
},
"required": [
"subtype",
"cyclization_type"
],
"type": "object"
},
"modules": {
"items": {
"additionalProperties": false,
"properties": {
"at_specificities": {
"items": {
"type": "string"
},
"title": "Acyltransferase substrate specificities",
"type": "array"
},
"comments": {
"type": "string"
},
"domains": {
"items": {
"type": "string"
},
"title": "Core PKS domains present in this module",
"type": "array"
},
"evidence": {
"enum": [
"Sequence-based prediction",
"Structure-based inference",
"Feeding study",
"Activity assay"
],
"title": "Evidence for AT/CAL specificity",
"type": "string"
},
"genes": {
"items": {
"pattern": "^[^, ]*$",
"type": "string"
},
"minItems": 1,
"title": "all genes forming the module",
"type": "array"
},
"kr_stereochem": {
"enum": [
"Unknown",
"Inactive",
"L-OH",
"D-OH"
],
"title": "KR domain stereochemistry / activity",
"type": "string"
},
"module_number": {