Class: GenomeFeature
A feature localized to an interval along a genome
URI: nmdc:GenomeFeature
classDiagram
class GenomeFeature
click GenomeFeature href "../GenomeFeature"
GenomeFeature : encodes
GenomeFeature --> "0..1" GeneProduct : encodes
click GeneProduct href "../GeneProduct"
GenomeFeature : end
GenomeFeature : feature_category
GenomeFeature --> "0..1" ControlledIdentifiedTermValue : feature_category
click ControlledIdentifiedTermValue href "../ControlledIdentifiedTermValue"
GenomeFeature : feature_type
GenomeFeature : phase
GenomeFeature : seqid
GenomeFeature : start
GenomeFeature : strand
GenomeFeature : type
Slots
Name | Cardinality and Range | Description | Inheritance |
---|---|---|---|
encodes | 0..1 GeneProduct |
The gene product encoded by this feature | direct |
end | 1 Integer |
The end of the feature in positive 1-based integer coordinates | direct |
feature_type | 0..1 String |
TODO: Yuri to write | direct |
phase | 0..1 Integer |
The phase for a coding sequence entity | direct |
seqid | 1 String |
The ID of the landmark used to establish the coordinate system for the curren... | direct |
start | 1 Integer |
The start of the feature in positive 1-based integer coordinates | direct |
strand | 0..1 String |
The strand on which a feature is located | direct |
type | 1 Uriorcurie |
the class_uri of the class that has been instantiated | direct |
feature_category | 0..1 ControlledIdentifiedTermValue |
A Sequence Ontology term that describes the category of a feature | direct |
Usages
used by | used in | type | used |
---|---|---|---|
Database | genome_feature_set | range | GenomeFeature |
Comments
- corresponds to an entry in GFF3
See Also
Identifier and Mapping Information
Schema Source
- from schema: https://w3id.org/nmdc/nmdc
Mappings
Mapping Type | Mapped Value |
---|---|
self | nmdc:GenomeFeature |
native | nmdc:GenomeFeature |
LinkML Source
Direct
name: GenomeFeature
description: A feature localized to an interval along a genome
comments:
- corresponds to an entry in GFF3
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md
slots:
- encodes
- end
- feature_type
- phase
- seqid
- start
- strand
- type
- feature_category
slot_usage:
seqid:
name: seqid
domain_of:
- GenomeFeature
required: true
start:
name: start
domain_of:
- GenomeFeature
required: true
end:
name: end
domain_of:
- GenomeFeature
required: true
class_uri: nmdc:GenomeFeature
Induced
name: GenomeFeature
description: A feature localized to an interval along a genome
comments:
- corresponds to an entry in GFF3
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md
slot_usage:
seqid:
name: seqid
domain_of:
- GenomeFeature
required: true
start:
name: start
domain_of:
- GenomeFeature
required: true
end:
name: end
domain_of:
- GenomeFeature
required: true
attributes:
encodes:
name: encodes
description: The gene product encoded by this feature. Typically this is used
for a CDS feature or gene feature which will encode a protein. It can also be
used by a nc transcript ot gene feature that encoded a ncRNA
todos:
- If we revert Reaction back into the schema, that would be a reasonable domain
for this slot
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: encodes
owner: GenomeFeature
domain_of:
- GenomeFeature
range: GeneProduct
end:
name: end
description: The end of the feature in positive 1-based integer coordinates
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
is_a: gff_coordinate
alias: end
owner: GenomeFeature
domain_of:
- GenomeFeature
range: integer
required: true
minimum_value: 1
feature_type:
name: feature_type
description: 'TODO: Yuri to write'
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: feature_type
owner: GenomeFeature
domain_of:
- GenomeFeature
range: string
phase:
name: phase
description: The phase for a coding sequence entity. For example, phase of a CDS
as represented in a GFF3 with a value of 0, 1 or 2.
from_schema: https://w3id.org/nmdc/nmdc
exact_mappings:
- biolink:phase
rank: 1000
alias: phase
owner: GenomeFeature
domain_of:
- GenomeFeature
range: integer
minimum_value: 0
maximum_value: 2
seqid:
name: seqid
description: The ID of the landmark used to establish the coordinate system for
the current feature.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: seqid
owner: GenomeFeature
domain_of:
- GenomeFeature
range: string
required: true
start:
name: start
description: The start of the feature in positive 1-based integer coordinates
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
is_a: gff_coordinate
alias: start
owner: GenomeFeature
domain_of:
- GenomeFeature
range: integer
required: true
minimum_value: 1
strand:
name: strand
description: The strand on which a feature is located. Has a value of '+' (sense
strand or forward strand) or '-' (anti-sense strand or reverse strand).
todos:
- set the range to an enum?
from_schema: https://w3id.org/nmdc/nmdc
exact_mappings:
- biolink:strand
rank: 1000
alias: strand
owner: GenomeFeature
domain_of:
- GenomeFeature
range: string
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: GenomeFeature
domain_of:
- EukEval
- FunctionalAnnotationAggMember
- MobilePhaseSegment
- PortionOfSubstance
- MagBin
- MetaboliteIdentification
- PeptideQuantification
- ProteinQuantification
- GenomeFeature
- FunctionalAnnotation
- AttributeValue
- NamedThing
- FailureCategorization
- Protocol
- CreditAssociation
- Doi
range: uriorcurie
required: true
feature_category:
name: feature_category
description: A Sequence Ontology term that describes the category of a feature
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: feature_category
owner: GenomeFeature
domain_of:
- GenomeFeature
- FunctionalAnnotation
range: ControlledIdentifiedTermValue
class_uri: nmdc:GenomeFeature