NucleicAcidSequenceFeature

: Public Class

Created:	10/17/2008 1:09:17 AM
Modified:	3/26/2015 6:04:07 PM

Project:
Author:
Version:	1.0
Phase:	1.0
Status:
Complexity:	Easy
Difficulty:
Priority:
Multiplicity:
Advanced:
UUID:	{7A7836F5-F09E-48e8-8E69-30841FCB4796}
Appears In:	UML-Based Comprehensive BRIDG Model Diagram, View EX: Experiment, View MB: Molecular Biology

DEFINITION: An annotation assigned to a defined nucleic acid physical location. EXAMPLE(S): promoter region, protein binding domains OTHER NAME(S): NOTE(S):

Attributes
Associations To
Associations From
Tagged Values
Other Links

Attribute

Public CD
typeCode

Details:

Alias:
Initial:
Stereotype:
Ordered:
Range:	Range:0 to 1
Transient:	False
Derived:	False
IsID:	False

Map:LSDAM=NucleicAcidSequenceFeature.typeCode

Notes:

DEFINITION:#lt;br /#gt;#lt;/p#gt;#lt;p#gt;A coded value specifying the category of the nucleic acid sequence feature. #lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;EXAMPLE(S):#lt;br /#gt;#lt;/p#gt;#lt;p#gt;DNA methylation#lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;OTHER NAME(S):#lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;NOTE(S):#lt;br /#gt;#lt;/p#gt;#lt;p#gt;[Glycosylation Site:C16643, C37901; Binding Site:C13671]#lt;br /#gt;#lt;/p#gt;

Public ST
orientation

Details:

Alias:
Initial:
Stereotype:
Ordered:
Range:	Range:0 to 1
Transient:	False
Derived:	False
IsID:	False

Map:LSDAM=NucleicAcidSequenceFeature.orientation

Notes:

DEFINITION:#lt;br /#gt;#lt;/p#gt;#lt;p#gt;The orientation of the feature relative to the sequence upon which it is annotated. #lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;EXAMPLE(S):#lt;br /#gt;#lt;/p#gt;#lt;p#gt;"forward", "for", "F", "+", "reverse", "rev", "R", "-"#lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;OTHER NAME(S):#lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;NOTE(S):#lt;br /#gt;#lt;/p#gt;#lt;p#gt;Features that are annotated on the same strand as the underlying sequence are usually indicated by "forward", "for", "F", or "+". Features that are on the opposite strand (the reverse-complement of the underlying sequence) are usually indicated by "reverse", "rev", "R", or "-".#lt;br /#gt;#lt;/p#gt;

Element	Source Role	Target Role
NucleicAcidPhysicalLocation Class	Name: includedNucleicAcidSequenceFeature	Name: includingNucleicAcidPhysicalLocation
Details: DESCRIPTION:<br /></p><p>Each NucleicAcidSequenceFeature always is included in one or more NucleicAcidPhysicalLocation. Each NucleicAcidPhysicalLocation might include one or more NucleicAcidSequenceFeature. <br /></p><p><br /></p><p>DEFINITION:<br /></p><p><br /></p><p>EXAMPLE(S):<br /></p><p><br /></p><p>OTHER NAME(S):<br /></p><p><br /></p><p>NOTE(S):<br /></p>

Element	Source Role	Target Role
MolecularSequenceAnnotation Class	Name: reportingMolecularSequenceAnnotation	Name: reportedNucleicAcidSequenceFeature
Details: DESCRIPTION:<br /></p><p>Each MolecularSequenceAnnotation might report one or more NucleicAcidSequenceFeature. Each NucleicAcidSequenceFeature might be reported by one or more MolecularSequenceAnnotation.<br /></p><p><br /></p><p>DEFINITION:<br /></p><p><br /></p><p>EXAMPLE(S):<br /></p><p><br /></p><p>OTHER NAME(S):<br /></p><p><br /></p><p>NOTE(S):<br /></p>
Biomarker Class	Name: basingBiomarker	Name: basedNucleicAcidSequenceFeature
Details: DESCRIPTION:<br /></p><p>Each Biomarker might be based on one or more NucleicAcidSequenceFeature. Each NucleicAcidSequenceFeature might be the basis of one or more Biomarker.<br /></p><p><br /></p><p>DEFINITION:<br /></p><p><br /></p><p>EXAMPLE(S):<br /></p><p><br /></p><p>OTHER NAME(S):<br /></p><p><br /></p><p>NOTE(S):<br /></p>

Tag	Value
Map:LSDAM	NucleicAcidSequenceFeature
Details:
Map:LSDAMv2.2.3Plus	NucleicAcidSequenceFeature
Details:

Object	Type	Connection	Direction	Notes
Intron	Class	Generalization	From	DESCRIPTION: Each Intron always specializes one NucleicAcidSequenceFeature. Each NucleicAcidSequenceFeature might be specialized by one Intron. DEFINITION: EXAMPLE(S): OTHER NAME(S): NOTE(S):
GeneticVariation	Class	Generalization	From	DESCRIPTION: Each GeneticVariation always specializes one NucleicAcidSequenceFeature. Each NucleicAcidSequenceFeature might be specialized by one GeneticVariation. DEFINITION: EXAMPLE(S): OTHER NAME(S): NOTE(S):
Gene	Class	Generalization	From	DESCRIPTION: Each Gene always specializes one NucleicAcidSequenceFeature. Each NucleicAcidSequenceFeature might be specialized by one Gene. DEFINITION: EXAMPLE(S): OTHER NAME(S): NOTE(S):
Exon	Class	Generalization	From	DESCRIPTION: Each Exon always specializes one NucleicAcidSequenceFeature. Each NucleicAcidSequenceFeature might be specialized by one Exon. DEFINITION: EXAMPLE(S): OTHER NAME(S): NOTE(S):