Class: SemiBin

URI: img_mysql_mbin:SemiBin

classDiagram class SemiBin click SemiBin href "../SemiBin/" SemiBin : avg_coverage SemiBin : bin_add_date SemiBin : bin_class SemiBin : bin_created_by SemiBin : bin_domain SemiBin : bin_family SemiBin : bin_genus SemiBin : bin_L50 SemiBin : bin_methods SemiBin : bin_N50 SemiBin : bin_oid SemiBin : bin_order SemiBin : bin_phylum SemiBin : bin_quality SemiBin : bin_species SemiBin : completeness SemiBin : contamination SemiBin : gene_count SemiBin : gtdbtk_class SemiBin : gtdbtk_domain SemiBin : gtdbtk_family SemiBin : gtdbtk_genus SemiBin : gtdbtk_order SemiBin : gtdbtk_phylum SemiBin : gtdbtk_species SemiBin : has_datafile SemiBin : in_portal SemiBin : num_16s SemiBin : num_23s SemiBin : num_5s SemiBin : num_trna SemiBin : scaffold_count SemiBin : taxon_oid SemiBin : total_base

Slots

Name	Cardinality and Range	Inheritance
bin_oid	0..1 String	direct
taxon_oid	0..1 Integer	direct
bin_domain	0..1 String	direct
bin_phylum	0..1 String	direct
bin_class	0..1 String	direct
bin_order	0..1 String	direct
bin_family	0..1 String	direct
bin_genus	0..1 String	direct
bin_species	0..1 String	direct
completeness	0..1 Float	direct
contamination	0..1 Float	direct
total_base	0..1 Integer	direct
gene_count	0..1 Integer	direct
bin_quality	0..1 String	direct
gtdbtk_domain	0..1 String	direct
gtdbtk_phylum	0..1 String	direct
gtdbtk_class	0..1 String	direct
gtdbtk_order	0..1 String	direct
gtdbtk_family	0..1 String	direct
gtdbtk_genus	0..1 String	direct
gtdbtk_species	0..1 String	direct
bin_add_date	0..1 Datetime	direct
bin_methods	0..1 String	direct
bin_created_by	0..1 Integer	direct
num_16s	0..1 Integer	direct
num_5s	0..1 Integer	direct
num_23s	0..1 Integer	direct
num_trna	0..1 Integer	direct
scaffold_count	0..1 Integer	direct
avg_coverage	0..1 Float	direct
bin_N50	0..1 String	direct
bin_L50	0..1 String	direct
in_portal	0..1 String	direct
has_datafile	0..1 String	direct

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/jgi/img_mysql_mbin

Mappings

Mapping Type	Mapped Value
self	img_mysql_mbin:SemiBin
native	img_mysql_mbin:SemiBin

LinkML Source

Direct

name: semi_bin
from_schema: https://w3id.org/jgi/img_mysql_mbin
attributes:
  bin_oid:
    name: bin_oid
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    domain_of:
    - bin
    - bin_coverage
    - bin_scaffolds
    - semi_bin
    - semi_bin_coverage
    - semi_bin_scaffolds
    - semi_lq
    range: string
    required: false
  taxon_oid:
    name: taxon_oid
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    domain_of:
    - bin
    - ebin
    - ebin_not_loaded_metagenomes
    - img_umag_bin_tarballs_02062024
    - not_loaded_metagenomes
    - semi_bin
    - semi_bin_not_loaded
    - semi_ebin
    - semi_ebin_not_loaded
    - semi_lq
    range: integer
    required: false
  bin_domain:
    name: bin_domain
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    domain_of:
    - bin
    - semi_bin
    range: string
    required: false
  bin_phylum:
    name: bin_phylum
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    domain_of:
    - bin
    - semi_bin
    range: string
    required: false
  bin_class:
    name: bin_class
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    domain_of:
    - bin
    - semi_bin
    range: string
    required: false
  bin_order:
    name: bin_order
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    domain_of:
    - bin
    - semi_bin
    range: string
    required: false
  bin_family:
    name: bin_family
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    domain_of:
    - bin
    - semi_bin
    range: string
    required: false
  bin_genus:
    name: bin_genus
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    domain_of:
    - bin
    - semi_bin
    range: string
    required: false
  bin_species:
    name: bin_species
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    domain_of:
    - bin
    - semi_bin
    range: string
    required: false
  completeness:
    name: completeness
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    domain_of:
    - bin
    - ebin
    - semi_bin
    - semi_ebin
    range: float
    required: false
  contamination:
    name: contamination
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    domain_of:
    - bin
    - ebin
    - semi_bin
    - semi_ebin
    range: float
    required: false
  total_base:
    name: total_base
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    domain_of:
    - bin
    - semi_bin
    range: integer
    required: false
  gene_count:
    name: gene_count
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    domain_of:
    - bin
    - bin_scaffolds
    - semi_bin
    - semi_bin_scaffolds
    range: integer
    required: false
  bin_quality:
    name: bin_quality
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    domain_of:
    - bin
    - semi_bin
    range: string
    required: false
  gtdbtk_domain:
    name: gtdbtk_domain
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    domain_of:
    - bin
    - semi_bin
    range: string
    required: false
  gtdbtk_phylum:
    name: gtdbtk_phylum
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    domain_of:
    - bin
    - semi_bin
    range: string
    required: false
  gtdbtk_class:
    name: gtdbtk_class
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    domain_of:
    - bin
    - semi_bin
    range: string
    required: false
  gtdbtk_order:
    name: gtdbtk_order
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    domain_of:
    - bin
    - semi_bin
    range: string
    required: false
  gtdbtk_family:
    name: gtdbtk_family
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    domain_of:
    - bin
    - semi_bin
    range: string
    required: false
  gtdbtk_genus:
    name: gtdbtk_genus
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    domain_of:
    - bin
    - semi_bin
    range: string
    required: false
  gtdbtk_species:
    name: gtdbtk_species
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    domain_of:
    - bin
    - semi_bin
    range: string
    required: false
  bin_add_date:
    name: bin_add_date
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    domain_of:
    - bin
    - semi_bin
    range: datetime
    required: false
  bin_methods:
    name: bin_methods
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    domain_of:
    - bin
    - not_loaded_metagenomes
    - semi_bin
    - semi_bin_not_loaded
    range: string
    required: false
  bin_created_by:
    name: bin_created_by
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    domain_of:
    - bin
    - not_loaded_metagenomes
    - semi_bin
    - semi_bin_not_loaded
    range: integer
    required: false
  num_16s:
    name: num_16s
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    domain_of:
    - bin
    - semi_bin
    range: integer
    required: false
  num_5s:
    name: num_5s
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    domain_of:
    - bin
    - ebin
    - ebin_scaffolds
    - semi_bin
    - semi_ebin
    - semi_ebin_scaffolds
    range: integer
    required: false
  num_23s:
    name: num_23s
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    domain_of:
    - bin
    - semi_bin
    range: integer
    required: false
  num_trna:
    name: num_trna
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    domain_of:
    - bin
    - semi_bin
    range: integer
    required: false
  scaffold_count:
    name: scaffold_count
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    domain_of:
    - bin
    - ebin
    - semi_bin
    - semi_ebin
    range: integer
    required: false
  avg_coverage:
    name: avg_coverage
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    domain_of:
    - bin
    - bin_coverage
    - ebin
    - semi_bin
    - semi_bin_coverage
    - semi_ebin
    range: float
    required: false
  bin_N50:
    name: bin_N50
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    rank: 1000
    domain_of:
    - semi_bin
    range: string
    required: false
  bin_L50:
    name: bin_L50
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    rank: 1000
    domain_of:
    - semi_bin
    range: string
    required: false
  in_portal:
    name: in_portal
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    rank: 1000
    domain_of:
    - semi_bin
    - semi_ebin
    range: string
    required: false
  has_datafile:
    name: has_datafile
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    rank: 1000
    domain_of:
    - semi_bin
    - semi_ebin
    range: string
    required: false

Induced

name: semi_bin
from_schema: https://w3id.org/jgi/img_mysql_mbin
attributes:
  bin_oid:
    name: bin_oid
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    alias: bin_oid
    owner: semi_bin
    domain_of:
    - bin
    - bin_coverage
    - bin_scaffolds
    - semi_bin
    - semi_bin_coverage
    - semi_bin_scaffolds
    - semi_lq
    range: string
    required: false
  taxon_oid:
    name: taxon_oid
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    alias: taxon_oid
    owner: semi_bin
    domain_of:
    - bin
    - ebin
    - ebin_not_loaded_metagenomes
    - img_umag_bin_tarballs_02062024
    - not_loaded_metagenomes
    - semi_bin
    - semi_bin_not_loaded
    - semi_ebin
    - semi_ebin_not_loaded
    - semi_lq
    range: integer
    required: false
  bin_domain:
    name: bin_domain
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    alias: bin_domain
    owner: semi_bin
    domain_of:
    - bin
    - semi_bin
    range: string
    required: false
  bin_phylum:
    name: bin_phylum
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    alias: bin_phylum
    owner: semi_bin
    domain_of:
    - bin
    - semi_bin
    range: string
    required: false
  bin_class:
    name: bin_class
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    alias: bin_class
    owner: semi_bin
    domain_of:
    - bin
    - semi_bin
    range: string
    required: false
  bin_order:
    name: bin_order
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    alias: bin_order
    owner: semi_bin
    domain_of:
    - bin
    - semi_bin
    range: string
    required: false
  bin_family:
    name: bin_family
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    alias: bin_family
    owner: semi_bin
    domain_of:
    - bin
    - semi_bin
    range: string
    required: false
  bin_genus:
    name: bin_genus
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    alias: bin_genus
    owner: semi_bin
    domain_of:
    - bin
    - semi_bin
    range: string
    required: false
  bin_species:
    name: bin_species
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    alias: bin_species
    owner: semi_bin
    domain_of:
    - bin
    - semi_bin
    range: string
    required: false
  completeness:
    name: completeness
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    alias: completeness
    owner: semi_bin
    domain_of:
    - bin
    - ebin
    - semi_bin
    - semi_ebin
    range: float
    required: false
  contamination:
    name: contamination
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    alias: contamination
    owner: semi_bin
    domain_of:
    - bin
    - ebin
    - semi_bin
    - semi_ebin
    range: float
    required: false
  total_base:
    name: total_base
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    alias: total_base
    owner: semi_bin
    domain_of:
    - bin
    - semi_bin
    range: integer
    required: false
  gene_count:
    name: gene_count
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    alias: gene_count
    owner: semi_bin
    domain_of:
    - bin
    - bin_scaffolds
    - semi_bin
    - semi_bin_scaffolds
    range: integer
    required: false
  bin_quality:
    name: bin_quality
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    alias: bin_quality
    owner: semi_bin
    domain_of:
    - bin
    - semi_bin
    range: string
    required: false
  gtdbtk_domain:
    name: gtdbtk_domain
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    alias: gtdbtk_domain
    owner: semi_bin
    domain_of:
    - bin
    - semi_bin
    range: string
    required: false
  gtdbtk_phylum:
    name: gtdbtk_phylum
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    alias: gtdbtk_phylum
    owner: semi_bin
    domain_of:
    - bin
    - semi_bin
    range: string
    required: false
  gtdbtk_class:
    name: gtdbtk_class
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    alias: gtdbtk_class
    owner: semi_bin
    domain_of:
    - bin
    - semi_bin
    range: string
    required: false
  gtdbtk_order:
    name: gtdbtk_order
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    alias: gtdbtk_order
    owner: semi_bin
    domain_of:
    - bin
    - semi_bin
    range: string
    required: false
  gtdbtk_family:
    name: gtdbtk_family
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    alias: gtdbtk_family
    owner: semi_bin
    domain_of:
    - bin
    - semi_bin
    range: string
    required: false
  gtdbtk_genus:
    name: gtdbtk_genus
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    alias: gtdbtk_genus
    owner: semi_bin
    domain_of:
    - bin
    - semi_bin
    range: string
    required: false
  gtdbtk_species:
    name: gtdbtk_species
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    alias: gtdbtk_species
    owner: semi_bin
    domain_of:
    - bin
    - semi_bin
    range: string
    required: false
  bin_add_date:
    name: bin_add_date
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    alias: bin_add_date
    owner: semi_bin
    domain_of:
    - bin
    - semi_bin
    range: datetime
    required: false
  bin_methods:
    name: bin_methods
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    alias: bin_methods
    owner: semi_bin
    domain_of:
    - bin
    - not_loaded_metagenomes
    - semi_bin
    - semi_bin_not_loaded
    range: string
    required: false
  bin_created_by:
    name: bin_created_by
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    alias: bin_created_by
    owner: semi_bin
    domain_of:
    - bin
    - not_loaded_metagenomes
    - semi_bin
    - semi_bin_not_loaded
    range: integer
    required: false
  num_16s:
    name: num_16s
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    alias: num_16s
    owner: semi_bin
    domain_of:
    - bin
    - semi_bin
    range: integer
    required: false
  num_5s:
    name: num_5s
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    alias: num_5s
    owner: semi_bin
    domain_of:
    - bin
    - ebin
    - ebin_scaffolds
    - semi_bin
    - semi_ebin
    - semi_ebin_scaffolds
    range: integer
    required: false
  num_23s:
    name: num_23s
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    alias: num_23s
    owner: semi_bin
    domain_of:
    - bin
    - semi_bin
    range: integer
    required: false
  num_trna:
    name: num_trna
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    alias: num_trna
    owner: semi_bin
    domain_of:
    - bin
    - semi_bin
    range: integer
    required: false
  scaffold_count:
    name: scaffold_count
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    alias: scaffold_count
    owner: semi_bin
    domain_of:
    - bin
    - ebin
    - semi_bin
    - semi_ebin
    range: integer
    required: false
  avg_coverage:
    name: avg_coverage
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    alias: avg_coverage
    owner: semi_bin
    domain_of:
    - bin
    - bin_coverage
    - ebin
    - semi_bin
    - semi_bin_coverage
    - semi_ebin
    range: float
    required: false
  bin_N50:
    name: bin_N50
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    rank: 1000
    alias: bin_N50
    owner: semi_bin
    domain_of:
    - semi_bin
    range: string
    required: false
  bin_L50:
    name: bin_L50
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    rank: 1000
    alias: bin_L50
    owner: semi_bin
    domain_of:
    - semi_bin
    range: string
    required: false
  in_portal:
    name: in_portal
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    rank: 1000
    alias: in_portal
    owner: semi_bin
    domain_of:
    - semi_bin
    - semi_ebin
    range: string
    required: false
  has_datafile:
    name: has_datafile
    from_schema: https://w3id.org/jgi/img_mysql_mbin
    rank: 1000
    alias: has_datafile
    owner: semi_bin
    domain_of:
    - semi_bin
    - semi_ebin
    range: string
    required: false