ENIGMA CoRAL Groundwater Microbiome Database

ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies) CoRAL (Collaborative Research for Applied Learning) groundwater microbiome data. Contains samples, taxonomic data, and environmental metadata from groundwater monitoring wells. PROJECT CONTEXT: ENIGMA is a DOE Scientific Focus Area studying microbial communities in contaminated groundwater environments, particularly at the Oak Ridge Field Research Center (ORFRC) in Tennessee. DATABASE STRUCTURE: - sdt_sample: Environmental samples with location and depth - sdt_location: Sampling sites/wells - sdt_taxon: Taxonomic identifications (linked to NCBI taxonomy) - sdt_asv: Amplicon sequence variants from 16S sequencing - sdt_condition: Experimental conditions - sdt_strain: Cultured isolates - ddt_brick: Data bricks (array data storage) - sys_: System/ontology tables ONTOLOGY INTEGRATION: Uses ENVO (Environment Ontology) and MIxS (Minimum Information about any Sequence) terms for standardized sample description.

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

Name: enigma_coral

Classes

Class	Description
ASV	Amplicon Sequence Variant from 16S rRNA gene sequencing
Condition	Experimental or environmental condition metadata
DataBrick	Data brick for array/matrix data storage (ddt_brick* tables)
Location	Sampling location (groundwater monitoring well)
NDArray	N-dimensional array metadata and type definitions
OntologyTerm	System ontology term (ENVO, MIxS, etc
Process	Data processing workflow or analysis process
Sample	Environmental sample from groundwater monitoring wells
Strain	Cultured microbial strain/isolate
Taxon	Taxonomic identification linked to NCBI taxonomy
TypeDefinition	System type definitions for data bricks

Slots

Slot	Description
brick_id	Data brick identifier
date	Sampling date (YYYY-MM-DD)
depth_meter	Sample depth in meters below ground surface
elevation_meter	Elevation in meters (above sea level)
env_package_sys_oterm_id	MIxS environmental package term ID
env_package_sys_oterm_name	MIxS environmental package name
material_sys_oterm_id	ENVO ontology term ID for sample material type
material_sys_oterm_name	Human-readable material type name
ncbi_taxid	NCBI Taxonomy ID with NCBITaxon prefix
ndarray_id	Array identifier
sdt_asv_id	ASV identifier
sdt_condition_id	Condition identifier
sdt_location_name	Sampling location/well identifier
sdt_sample_description	Free-text sample description
sdt_sample_id	Unique sample identifier
sdt_sample_name	Human-readable sample name (well-date format)
sdt_strain_id	Strain identifier
sdt_taxon_id	Internal taxon identifier
sdt_taxon_name	Taxonomic name (any rank)
sys_oterm_id	Ontology term ID (CURIE format)
sys_process_id	Process identifier
time	Sampling time (HH:MM format)
timezone	Timezone offset
typedef_id	Type definition identifier

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