Class: MagBin

URI: nmdc:MagBin

classDiagram class MagBin click MagBin href "../MagBin" MagBin : bin_name MagBin : bin_quality MagBin : completeness MagBin : contamination MagBin : eukaryotic_evaluation MagBin --> "0..1" EukEval : eukaryotic_evaluation click EukEval href "../EukEval" MagBin : gene_count MagBin : gtdbtk_class MagBin : gtdbtk_domain MagBin : gtdbtk_family MagBin : gtdbtk_genus MagBin : gtdbtk_order MagBin : gtdbtk_phylum MagBin : gtdbtk_species MagBin : members_id MagBin : num_16s MagBin : num_23s MagBin : num_5s MagBin : num_t_rna MagBin : number_of_contig MagBin : total_bases MagBin : type

Slots

Name	Cardinality and Range	Description	Inheritance
bin_name	0..1 String		direct
bin_quality	0..1 String		direct
completeness	0..1 Float		direct
contamination	0..1 Float		direct
gene_count	0..1 Integer		direct
gtdbtk_class	0..1 String		direct
gtdbtk_domain	0..1 String		direct
gtdbtk_family	0..1 String		direct
gtdbtk_genus	0..1 String		direct
gtdbtk_order	0..1 String		direct
gtdbtk_phylum	0..1 String		direct
gtdbtk_species	0..1 String		direct
members_id	0..1 String		direct
num_16s	0..1 Integer		direct
num_23s	0..1 Integer		direct
num_5s	0..1 Integer		direct
num_t_rna	0..1 Integer		direct
number_of_contig	0..1 Integer		direct
total_bases	0..1 Integer		direct
type	1 Uriorcurie	the class_uri of the class that has been instantiated	direct
eukaryotic_evaluation	0..1 EukEval	Contains results from evaluating if a Metagenome-Assembled Genome is of eukar...	direct

Usages

used by	used in	type	used
MagsAnalysis	mags_list	range	MagBin

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/nmdc/nmdc

Mappings

Mapping Type	Mapped Value
self	nmdc:MagBin
native	nmdc:MagBin

LinkML Source

Direct

name: MagBin
from_schema: https://w3id.org/nmdc/nmdc
slots:
- bin_name
- bin_quality
- completeness
- contamination
- gene_count
- gtdbtk_class
- gtdbtk_domain
- gtdbtk_family
- gtdbtk_genus
- gtdbtk_order
- gtdbtk_phylum
- gtdbtk_species
- members_id
- num_16s
- num_23s
- num_5s
- num_t_rna
- number_of_contig
- total_bases
- type
- eukaryotic_evaluation
class_uri: nmdc:MagBin

Induced

name: MagBin
from_schema: https://w3id.org/nmdc/nmdc
attributes:
  bin_name:
    name: bin_name
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: bin_name
    owner: MagBin
    domain_of:
    - MagBin
    range: string
  bin_quality:
    name: bin_quality
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: bin_quality
    owner: MagBin
    domain_of:
    - MagBin
    range: string
  completeness:
    name: completeness
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: completeness
    owner: MagBin
    domain_of:
    - EukEval
    - MagBin
    range: float
  contamination:
    name: contamination
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: contamination
    owner: MagBin
    domain_of:
    - EukEval
    - MagBin
    range: float
  gene_count:
    name: gene_count
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: gene_count
    owner: MagBin
    domain_of:
    - MagBin
    range: integer
  gtdbtk_class:
    name: gtdbtk_class
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: gtdbtk_class
    owner: MagBin
    domain_of:
    - MagBin
    range: string
  gtdbtk_domain:
    name: gtdbtk_domain
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: gtdbtk_domain
    owner: MagBin
    domain_of:
    - MagBin
    range: string
  gtdbtk_family:
    name: gtdbtk_family
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: gtdbtk_family
    owner: MagBin
    domain_of:
    - MagBin
    range: string
  gtdbtk_genus:
    name: gtdbtk_genus
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: gtdbtk_genus
    owner: MagBin
    domain_of:
    - MagBin
    range: string
  gtdbtk_order:
    name: gtdbtk_order
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: gtdbtk_order
    owner: MagBin
    domain_of:
    - MagBin
    range: string
  gtdbtk_phylum:
    name: gtdbtk_phylum
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: gtdbtk_phylum
    owner: MagBin
    domain_of:
    - MagBin
    range: string
  gtdbtk_species:
    name: gtdbtk_species
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: gtdbtk_species
    owner: MagBin
    domain_of:
    - MagBin
    range: string
  members_id:
    name: members_id
    todos:
    - this slot needs some basic textual annotations and constraints
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: members_id
    owner: MagBin
    domain_of:
    - MagBin
    range: string
  num_16s:
    name: num_16s
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: num_16s
    owner: MagBin
    domain_of:
    - MagBin
    range: integer
  num_23s:
    name: num_23s
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: num_23s
    owner: MagBin
    domain_of:
    - MagBin
    range: integer
  num_5s:
    name: num_5s
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: num_5s
    owner: MagBin
    domain_of:
    - MagBin
    range: integer
  num_t_rna:
    name: num_t_rna
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: num_t_rna
    owner: MagBin
    domain_of:
    - MagBin
    range: integer
  number_of_contig:
    name: number_of_contig
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: number_of_contig
    owner: MagBin
    domain_of:
    - MagBin
    range: integer
  total_bases:
    name: total_bases
    todos:
    - this slot needs some basic textual annotations and constraints
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: total_bases
    owner: MagBin
    domain_of:
    - MagBin
    range: integer
  type:
    name: type
    description: the class_uri of the class that has been instantiated
    notes:
    - replaces legacy nmdc:type slot
    - makes it easier to read example data files
    - required for polymorphic MongoDB collections
    examples:
    - value: nmdc:Biosample
    - value: nmdc:Study
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://github.com/microbiomedata/nmdc-schema/issues/1048
    - https://github.com/microbiomedata/nmdc-schema/issues/1233
    - https://github.com/microbiomedata/nmdc-schema/issues/248
    rank: 1000
    slot_uri: rdf:type
    designates_type: true
    alias: type
    owner: MagBin
    domain_of:
    - EukEval
    - FunctionalAnnotationAggMember
    - MobilePhaseSegment
    - PortionOfSubstance
    - MagBin
    - MetaboliteIdentification
    - PeptideQuantification
    - ProteinQuantification
    - GenomeFeature
    - FunctionalAnnotation
    - AttributeValue
    - NamedThing
    - FailureCategorization
    - Protocol
    - CreditAssociation
    - Doi
    range: uriorcurie
    required: true
  eukaryotic_evaluation:
    name: eukaryotic_evaluation
    description: Contains results from evaluating if a Metagenome-Assembled Genome
      is of eukaryotic lineage.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: eukaryotic_evaluation
    owner: MagBin
    domain_of:
    - MagBin
    range: EukEval
class_uri: nmdc:MagBin