Class: EukEval

This class contains information pertaining to evaluating if a Metagenome-Assembled Genome (MAG) is eukaryotic.

classDiagram class EukEval click EukEval href "../EukEval" EukEval : completeness EukEval : contamination EukEval : ncbi_lineage EukEval : ncbi_lineage_tax_ids EukEval : type

Slots

Name	Cardinality and Range	Description	Inheritance
type	1 Uriorcurie	the class_uri of the class that has been instantiated	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
ncbi_lineage_tax_ids	0..1 String	Dash-delimited ordered list of NCBI taxonomy identifiers (TaxId)	direct
ncbi_lineage	0..1 String	Comma delimited ordered list of NCBI taxonomy names	direct

Usages

used by	used in	type	used
MagBin	eukaryotic_evaluation	range	EukEval

Comments

A tool like eukCC (https://doi.org/10.1186/s13059-020-02155-4) would generate information for this class.

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: EukEval
description: This class contains information pertaining to evaluating if a Metagenome-Assembled
  Genome (MAG) is eukaryotic.
comments:
- A tool like eukCC (https://doi.org/10.1186/s13059-020-02155-4) would generate information
  for this class.
from_schema: https://w3id.org/nmdc/nmdc
slots:
- type
- completeness
- contamination
- ncbi_lineage_tax_ids
- ncbi_lineage
class_uri: nmdc:EukEval

Induced

name: EukEval
description: This class contains information pertaining to evaluating if a Metagenome-Assembled
  Genome (MAG) is eukaryotic.
comments:
- A tool like eukCC (https://doi.org/10.1186/s13059-020-02155-4) would generate information
  for this class.
from_schema: https://w3id.org/nmdc/nmdc
attributes:
  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: EukEval
    domain_of:
    - EukEval
    - FunctionalAnnotationAggMember
    - PeptideQuantification
    - ProteinQuantification
    - MobilePhaseSegment
    - PortionOfSubstance
    - MagBin
    - MetaboliteIdentification
    - GenomeFeature
    - FunctionalAnnotation
    - AttributeValue
    - NamedThing
    - OntologyRelation
    - FailureCategorization
    - Protocol
    - CreditAssociation
    - Doi
    range: uriorcurie
    required: true
  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: EukEval
    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: EukEval
    domain_of:
    - EukEval
    - MagBin
    range: float
    minimum_value: 0
  ncbi_lineage_tax_ids:
    name: ncbi_lineage_tax_ids
    description: Dash-delimited ordered list of NCBI taxonomy identifiers (TaxId)
    comments:
    - Example 1-131567-2759-2611352-33682-191814-2603949
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: ncbi_lineage_tax_ids
    owner: EukEval
    domain_of:
    - EukEval
    range: string
    pattern: ^\d+(-\d+)*$
  ncbi_lineage:
    name: ncbi_lineage
    description: Comma delimited ordered list of NCBI taxonomy names.
    comments:
    - Example root,cellular organisms,Eukaryota,Discoba,Euglenozoa,Diplonemea,Diplonemidae
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: ncbi_lineage
    owner: EukEval
    domain_of:
    - EukEval
    range: string
class_uri: nmdc:EukEval