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ENIGMA Common Data Model

LinkML schema for ENIGMA (Environmental Molecular Sciences Laboratory Integrated Genomics Initiative) Common Data Model

URI: https://w3id.org/enigma/enigma-cdm

Name: enigma-cdm

Classes

Class Description
Assembly Assembly entity in the ENIGMA data model
Bin Bin entity in the ENIGMA data model
Community Community entity in the ENIGMA data model
Condition Condition entity in the ENIGMA data model
DubSeqLibrary DubSeq_Library entity in the ENIGMA data model
Gene Gene entity in the ENIGMA data model
Genome Genome entity in the ENIGMA data model
Image Image entity in the ENIGMA data model
Location Location entity in the ENIGMA data model
OTU OTU entity in the ENIGMA data model
Process Process entity in the ENIGMA data model
Protocol Protocol entity in the ENIGMA data model
Reads Reads entity in the ENIGMA data model
Sample Sample entity in the ENIGMA data model
Strain Strain entity in the ENIGMA data model
Taxon Taxon entity in the ENIGMA data model
TnSeqLibrary TnSeq_Library entity in the ENIGMA data model

Slots

Slot Description
assembly_id id field for Assembly
assembly_link link field for Assembly
assembly_n_contigs n_contigs field for Assembly
assembly_name name field for Assembly
assembly_strain strain field for Assembly
bin_assembly assembly field for Bin
bin_contigs contigs field for Bin
bin_id id field for Bin
bin_name name field for Bin
community_community_type community_type field for Community
community_condition condition field for Community
community_defined_strains defined_strains field for Community
community_description description field for Community
community_id id field for Community
community_name name field for Community
community_parent_community parent_community field for Community
community_sample sample field for Community
condition_id id field for Condition
condition_name name field for Condition
dubseq_library_genome genome field for DubSeq_Library
dubseq_library_id id field for DubSeq_Library
dubseq_library_n_fragments n_fragments field for DubSeq_Library
dubseq_library_name name field for DubSeq_Library
gene_aliases aliases field for Gene
gene_contig_number contig_number field for Gene
gene_function function field for Gene
gene_gene_id gene_id field for Gene
gene_genome genome field for Gene
gene_id id field for Gene
gene_start start field for Gene
gene_stop stop field for Gene
gene_strand strand field for Gene
genome_id id field for Genome
genome_link link field for Genome
genome_n_contigs n_contigs field for Genome
genome_n_features n_features field for Genome
genome_name name field for Genome
genome_strain strain field for Genome
image_description description field for Image
image_dimensions dimensions field for Image
image_id id field for Image
image_link link field for Image
image_MIME_type MIME type field for Image
image_name name field for Image
image_size size field for Image
location_biome biome field for Location
location_continent continent field for Location
location_country country field for Location
location_feature feature field for Location
location_id id field for Location
location_latitude latitude field for Location
location_longitude longitude field for Location
location_name name field for Location
location_region region field for Location
otu_id id field for OTU
otu_name name field for OTU
process_campaign campaign field for Process
process_date_end date_end field for Process
process_date_start date_start field for Process
process_id id field for Process
process_input_objects input_objects field for Process
process_output_objects output_objects field for Process
process_person person field for Process
process_process process field for Process
process_protocol protocol field for Process
protocol_description description field for Protocol
protocol_id id field for Protocol
protocol_link link field for Protocol
protocol_name name field for Protocol
reads_id id field for Reads
reads_link link field for Reads
reads_name name field for Reads
reads_read_count read_count field for Reads
reads_read_type read_type field for Reads
reads_sequencing_technology sequencing_technology field for Reads
sample_date date field for Sample
sample_depth depth field for Sample
sample_description description field for Sample
sample_elevation elevation field for Sample
sample_env_package env_package field for Sample
sample_id id field for Sample
sample_location location field for Sample
sample_material material field for Sample
sample_name name field for Sample
sample_time time field for Sample
sample_timezone timezone field for Sample
strain_derived_from derived_from field for Strain
strain_description description field for Strain
strain_genes_changed genes_changed field for Strain
strain_genome genome field for Strain
strain_id id field for Strain
strain_name name field for Strain
taxon_id id field for Taxon
taxon_name name field for Taxon
taxon_ncbi_taxid ncbi_taxid field for Taxon
tnseq_library_genome genome field for TnSeq_Library
tnseq_library_hit_rate_essential hit_rate_essential field for TnSeq_Library
tnseq_library_hit_rate_other hit_rate_other field for TnSeq_Library
tnseq_library_id id field for TnSeq_Library
tnseq_library_n_barcodes n_barcodes field for TnSeq_Library
tnseq_library_n_insertion_locations n_insertion_locations field for TnSeq_Library
tnseq_library_n_mapped_reads n_mapped_reads field for TnSeq_Library
tnseq_library_n_usable_barcodes n_usable_barcodes field for TnSeq_Library
tnseq_library_name name field for TnSeq_Library
tnseq_library_primers_model primers_model field for TnSeq_Library

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