JGI Secondary Metabolite Clusters Database

Secondary Metabolite Clusters (SMC) database for JGI. Contains biosynthetic gene clusters (BGCs), annotations, and secondary metabolite predictions. DATABASE: smc-db postgresql.public TABLES: 124 KEY FUNCTIONALITY: - Biosynthetic gene cluster (BGC) identification - Secondary metabolite class annotation - Gene and contig mapping - Analysis tool results - Collection and blog management

URI: https://w3id.org/jgi/smc

Name: smc

Classes

Class	Description
Activity	User activity log
AnalysisTool	Tool used for BGC analysis (antiSMASH, etc
ApiUsage	API usage tracking
BGC	Biosynthetic Gene Cluster - a genomic region encoding enzymes for secondary m...
BGCAnalysis	Analysis result for a BGC
BGCAnalysisToSecmetFile	Link between BGC analysis and secondary metabolite files
BGCAnnotation	Annotation for a BGC
BGCClass	Secondary metabolite class (NRPS, PKS, terpene, etc
BGCToBGCClass	Many-to-many link between BGCs and their classes
Blog	Blog post about secondary metabolites
Collection	Collection of BGCs or genomes
CollectionMember	Member of a collection
Comment	User comment on a BGC or other entity
Contig	Genomic contig/scaffold
Gene	Gene record

Slots

Slot	Description
action
analysis_tool_id
annotation_type
author_id
bgc_analysis_id
bgc_class_id
bgc_id
collection_id
content
contig_id
created_time
description
end	End coordinate
endpoint
entity_id
entity_type
genome_id
id	BGC identifier
item_id
item_type	Type of item (bgc, genome, etc
length
locus_tag
name
owner_id
product	Gene product annotation
published_time
response_time
result
secmet_file_path
start	Start coordinate
strand
text
timestamp
title
user_id
value
version

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