Class: MagBin

URI: nmdc:MagBin

classDiagram class MagBin click MagBin href "../MagBin" MagBin : bin_name MagBin : bin_quality MagBin --> "0..1" BinQualityEnum : bin_quality click BinQualityEnum href "../BinQualityEnum" 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	1 String	Name of the metagenome-assembled genome	direct
bin_quality	0..1 BinQualityEnum	The quality of the metagenome-assembled genome based on MIMAG standards (http...	direct
completeness	0..1 Float	Estimate of the completeness of the metagenome-assembled genome, estimated by...	direct
contamination	0..1 Float	Estimate of the completeness of the metagenome-assembled genome, estimated by...	direct
gene_count	0..1 Integer	Number of genes	direct
gtdbtk_class	0..1 String	Taxonomic class assigned by GTDB-Tk	direct
gtdbtk_domain	0..1 String	Taxonomic domain assigned by GTDB-Tk	direct
gtdbtk_family	0..1 String	Taxonomic family assigned by GTDB-Tk	direct
gtdbtk_genus	0..1 String	Taxonomic genus assigned by GTDB-Tk	direct
gtdbtk_order	0..1 String	Taxonomic order assigned by GTDB-Tk	direct
gtdbtk_phylum	0..1 String	Taxonomic phylum assigned by GTDB-Tk	direct
gtdbtk_species	0..1 String	Taxonomic genus assigned by GTDB-Tk	direct
members_id	* String	Names of the contigs that make up a metagenome-assembled genome	direct
num_16s	0..1 Integer	Number of 16s sequences detected, a subunit of prokaryotic ribosomes	direct
num_23s	0..1 Integer	Number of 23 seqeuences detected, a subunit of ribosomes	direct
num_5s	0..1 Integer	Number of 5s seqeuences detected, a subunit of ribosomes	direct
num_t_rna	0..1 Integer	Number of transfer transfer RNAs	direct
number_of_contig	0..1 Integer	Number of contigs	direct
total_bases	0..1 Integer	Total number of basepairs	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
    description: Name of the metagenome-assembled genome.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: bin_name
    owner: MagBin
    domain_of:
    - MagBin
    range: string
    required: true
  bin_quality:
    name: bin_quality
    description: The quality of the metagenome-assembled genome based on MIMAG standards
      (https://doi.org/10.1038/nbt.3893).
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: bin_quality
    owner: MagBin
    domain_of:
    - MagBin
    range: BinQualityEnum
  completeness:
    name: completeness
    description: Estimate of the completeness of the metagenome-assembled genome,
      estimated by a tool like CheckM.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: completeness
    owner: MagBin
    domain_of:
    - EukEval
    - MagBin
    range: float
    minimum_value: 0
  contamination:
    name: contamination
    description: Estimate of the completeness of the metagenome-assembled genome,
      estimated by a tool like CheckM.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: contamination
    owner: MagBin
    domain_of:
    - EukEval
    - MagBin
    range: float
    minimum_value: 0
  gene_count:
    name: gene_count
    description: Number of genes.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: gene_count
    owner: MagBin
    domain_of:
    - MagBin
    range: integer
    minimum_value: 0
  gtdbtk_class:
    name: gtdbtk_class
    description: Taxonomic class assigned by GTDB-Tk.
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://doi.org/10.1093/bioinformatics/btz848
    exact_mappings:
    - NCBITaxon:class
    rank: 1000
    alias: gtdbtk_class
    owner: MagBin
    domain_of:
    - MagBin
    range: string
  gtdbtk_domain:
    name: gtdbtk_domain
    description: Taxonomic domain assigned by GTDB-Tk.
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://doi.org/10.1093/bioinformatics/btz848
    exact_mappings:
    - NCBITaxon:superkingdom
    rank: 1000
    alias: gtdbtk_domain
    owner: MagBin
    domain_of:
    - MagBin
    range: string
  gtdbtk_family:
    name: gtdbtk_family
    description: Taxonomic family assigned by GTDB-Tk.
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://doi.org/10.1093/bioinformatics/btz848
    exact_mappings:
    - NCBITaxon:family
    rank: 1000
    alias: gtdbtk_family
    owner: MagBin
    domain_of:
    - MagBin
    range: string
  gtdbtk_genus:
    name: gtdbtk_genus
    description: Taxonomic genus assigned by GTDB-Tk.
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://doi.org/10.1093/bioinformatics/btz848
    exact_mappings:
    - NCBITaxon:genus
    rank: 1000
    alias: gtdbtk_genus
    owner: MagBin
    domain_of:
    - MagBin
    range: string
  gtdbtk_order:
    name: gtdbtk_order
    description: Taxonomic order assigned by GTDB-Tk.
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://doi.org/10.1093/bioinformatics/btz848
    exact_mappings:
    - NCBITaxon:order
    rank: 1000
    alias: gtdbtk_order
    owner: MagBin
    domain_of:
    - MagBin
    range: string
  gtdbtk_phylum:
    name: gtdbtk_phylum
    description: Taxonomic phylum assigned by GTDB-Tk.
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://doi.org/10.1093/bioinformatics/btz848
    exact_mappings:
    - NCBITaxon:phylum
    rank: 1000
    alias: gtdbtk_phylum
    owner: MagBin
    domain_of:
    - MagBin
    range: string
  gtdbtk_species:
    name: gtdbtk_species
    description: Taxonomic genus assigned by GTDB-Tk.
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://doi.org/10.1093/bioinformatics/btz848
    exact_mappings:
    - NCBITaxon:species
    rank: 1000
    alias: gtdbtk_species
    owner: MagBin
    domain_of:
    - MagBin
    range: string
  members_id:
    name: members_id
    description: Names of the contigs that make up a metagenome-assembled genome.
    from_schema: https://w3id.org/nmdc/nmdc
    close_mappings:
    - GENEPIO:0100596
    rank: 1000
    alias: members_id
    owner: MagBin
    domain_of:
    - MagBin
    range: string
    multivalued: true
  num_16s:
    name: num_16s
    description: Number of 16s sequences detected, a subunit of prokaryotic ribosomes.
    from_schema: https://w3id.org/nmdc/nmdc
    broad_mappings:
    - NCIT:C105370
    rank: 1000
    alias: num_16s
    owner: MagBin
    domain_of:
    - MagBin
    range: integer
    minimum_value: 0
  num_23s:
    name: num_23s
    description: Number of 23 seqeuences detected, a subunit of ribosomes.
    from_schema: https://w3id.org/nmdc/nmdc
    broad_mappings:
    - OMIT:0013245
    rank: 1000
    alias: num_23s
    owner: MagBin
    domain_of:
    - MagBin
    range: integer
    minimum_value: 0
  num_5s:
    name: num_5s
    description: Number of 5s seqeuences detected, a subunit of ribosomes.
    from_schema: https://w3id.org/nmdc/nmdc
    broad_mappings:
    - OMIT:0013248
    rank: 1000
    alias: num_5s
    owner: MagBin
    domain_of:
    - MagBin
    range: integer
    minimum_value: 0
  num_t_rna:
    name: num_t_rna
    description: Number of transfer transfer RNAs.
    from_schema: https://w3id.org/nmdc/nmdc
    broad_mappings:
    - NCIT:C816
    rank: 1000
    alias: num_t_rna
    owner: MagBin
    domain_of:
    - MagBin
    range: integer
    minimum_value: 0
  number_of_contig:
    name: number_of_contig
    description: Number of contigs
    from_schema: https://w3id.org/nmdc/nmdc
    exact_mappings:
    - GENEPIO:0000093
    rank: 1000
    alias: number_of_contig
    owner: MagBin
    domain_of:
    - MagBin
    range: integer
    minimum_value: 0
  total_bases:
    name: total_bases
    description: Total number of basepairs.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: total_bases
    owner: MagBin
    domain_of:
    - MagBin
    range: integer
    minimum_value: 0
  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