Class: EukEval
This class contains information pertaining to evaluating if a Metagenome-Assembled Genome (MAG) is eukaryotic.
URI: nmdc:EukEval
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 |
direct | |
contamination | 0..1 Float |
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
- MobilePhaseSegment
- PortionOfSubstance
- MagBin
- MetaboliteIdentification
- PeptideQuantification
- ProteinQuantification
- GenomeFeature
- FunctionalAnnotation
- AttributeValue
- NamedThing
- FailureCategorization
- Protocol
- CreditAssociation
- Doi
range: uriorcurie
required: true
completeness:
name: completeness
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: completeness
owner: EukEval
domain_of:
- EukEval
- MagBin
range: float
contamination:
name: contamination
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: contamination
owner: EukEval
domain_of:
- EukEval
- MagBin
range: float
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