Schema annotation.xsd


schema location:  C:\Dev\omnigene\resources\das\annotation.xsd
targetNamespace:  http://www.biodas.org/names/annotation
 
Elements  Complex types 
Chromosome  Chromosome 
Code  Contig 
Contig  DataSource 
Feature  Feature 
Location  Location 
Segment  Segment 
TileLocation  TileLocation 
Type  Type 


schema location:  C:\Dev\omnigene\resources\das\lscore.xsd
targetNamespace:  http://www.i3c.org/names/core
 
Elements  Simple types 
lsid  lsid 


element Chromosome
diagram
namespace http://www.biodas.org/names/annotation
type tns:Chromosome
children View Assembly Features tns:Code Tiling
attributes
Name  Type  Use  Default  Fixed  Annotation
ls:lsid  lsid        
tns:length  integer        
number  string  optional      
documentation 
The chromosome identifier, for example, "1", "2", "X".
annotation
documentation 
The chromosome contains sub-assemblies of DNA such as contigs or BACs.

element Code
diagram
namespace http://www.biodas.org/names/annotation
type string
used by
complexType Segment
annotation
documentation 
Code string representing a molecular sequence

element Contig
diagram
namespace http://www.biodas.org/names/annotation
type tns:Contig
children View Assembly Features tns:Code Tiling
used by
element Segment/Assembly
attributes
Name  Type  Use  Default  Fixed  Annotation
ls:lsid  lsid        
tns:length  integer        

element Feature
diagram
namespace http://www.biodas.org/names/annotation
type tns:Feature
children tns:Type Features
used by
elements Feature/Features Segment/Features
attributes
Name  Type  Use  Default  Fixed  Annotation
ls:lsid  lsid        

element Location
diagram
namespace http://www.biodas.org/names/annotation
type tns:Location
attributes
Name  Type  Use  Default  Fixed  Annotation
tns:start  integer  required      
documentation 
the start position in the container 
coordinate system.
tns:length  integer    1    
tns:orientation  string  optional      
documentation 
indicates the orientation within the 
sequence

element Segment
diagram
namespace http://www.biodas.org/names/annotation
type tns:Segment
children View Assembly Features tns:Code Tiling
attributes
Name  Type  Use  Default  Fixed  Annotation
ls:lsid  lsid        
tns:length  integer        
annotation
documentation 
A Segment is any physical sequence such as a Chromosome, Contig, or BAC.

element TileLocation
diagram
namespace http://www.biodas.org/names/annotation
type tns:TileLocation
used by
element Segment/Tiling
attributes
Name  Type  Use  Default  Fixed  Annotation
tns:start  integer  required      
documentation 
the start position in the container 
coordinate system.
tns:length  integer    1    
tns:orientation  string  optional      
documentation 
indicates the orientation within the 
sequence
substart  integer        
documentation 
The start point of the sub-segment that aligns with a point on its parent.  The parent start point is specified with the "start" attribute.
annotation
documentation 
Locates a segment within a parent segment.

element Type
diagram
namespace http://www.biodas.org/names/annotation
type tns:Type
used by
complexType Feature
attributes
Name  Type  Use  Default  Fixed  Annotation
system  string        
id  ls:lsid        

complexType Chromosome
diagram
namespace http://www.biodas.org/names/annotation
type extension of tns:Segment
children View Assembly Features tns:Code Tiling
used by
element Chromosome
attributes
Name  Type  Use  Default  Fixed  Annotation
ls:lsid  lsid        
tns:length  integer        
number  string  optional      
documentation 
The chromosome identifier, for example, "1", "2", "X".

complexType Contig
diagram
namespace http://www.biodas.org/names/annotation
type extension of tns:Segment
children View Assembly Features tns:Code Tiling
used by
element Contig
attributes
Name  Type  Use  Default  Fixed  Annotation
ls:lsid  lsid        
tns:length  integer        

complexType DataSource
diagram
namespace http://www.biodas.org/names/annotation
children description
attributes
Name  Type  Use  Default  Fixed  Annotation
lsid  ls:lsid        

element DataSource/description
diagram
type string

complexType Feature
diagram
namespace http://www.biodas.org/names/annotation
children tns:Type Features
used by
element Feature
attributes
Name  Type  Use  Default  Fixed  Annotation
ls:lsid  lsid        

element Feature/Features
diagram
children tns:Feature

complexType Location
diagram
namespace http://www.biodas.org/names/annotation
used by
elements Location Segment/View
complexType TileLocation
attributes
Name  Type  Use  Default  Fixed  Annotation
tns:start  integer  required      
documentation 
the start position in the container 
coordinate system.
tns:length  integer    1    
tns:orientation  string  optional      
documentation 
indicates the orientation within the 
sequence
annotation
documentation 
A contiguous region of 
sequence.

complexType Segment
diagram
namespace http://www.biodas.org/names/annotation
children View Assembly Features tns:Code Tiling
used by
element Segment
complexTypes Chromosome Contig
attributes
Name  Type  Use  Default  Fixed  Annotation
ls:lsid  lsid        
tns:length  integer        

element Segment/View
diagram
type extension of tns:Location
attributes
Name  Type  Use  Default  Fixed  Annotation
tns:start  integer  required      
documentation 
the start position in the container 
coordinate system.
tns:length  integer    1    
tns:orientation  string  optional      
documentation 
indicates the orientation within the 
sequence
annotation
documentation 
A View is a way to divide the features of large segments among multiple documents.  The View specifies the range in which features appear.

element Segment/Assembly
diagram
children tns:Contig
annotation
documentation 
an assembly or ordering of segments that tile the parent segment.  Use the TileLocation to provide a position for the segments within the parent.

element Segment/Features
diagram
children tns:Feature

element Segment/Tiling
diagram
children tns:TileLocation

complexType TileLocation
diagram
namespace http://www.biodas.org/names/annotation
type extension of tns:Location
used by
element TileLocation
attributes
Name  Type  Use  Default  Fixed  Annotation
tns:start  integer  required      
documentation 
the start position in the container 
coordinate system.
tns:length  integer    1    
tns:orientation  string  optional      
documentation 
indicates the orientation within the 
sequence
substart  integer        
documentation 
The start point of the sub-segment that aligns with a point on its parent.  The parent start point is specified with the "start" attribute.

complexType Type
diagram
namespace http://www.biodas.org/names/annotation
used by
element Type
attributes
Name  Type  Use  Default  Fixed  Annotation
system  string        
id  ls:lsid        

element ls:lsid
diagram
namespace http://www.i3c.org/names/core
attributes
Name  Type  Use  Default  Fixed  Annotation
value  lsid  required      
annotation
documentation 
Element can be used as a reference to an object named by the LSID

simpleType ls:lsid
namespace http://www.i3c.org/names/core
type restriction of string
used by
attributes Type/@id DataSource/@lsid ls:lsid/@value
facets
pattern urn:lsid:[\c/]+:[\c/]+:[\c]+(:[\c]+)?
annotation
documentation 
A Life Sciences Identifier (LSID) is a URN that uniquely names an object.  The syntax is
urn:lsid:<authority>:<namespace>:<value>:<version>
where authority is the name of the organization that has defined an entity, namespace is a namespace within the authority for the Id, value is an 
alpha-numeric sequence that uniquely identifies an object to its authority, and version is a version number for an Id.  <authority> and
<namespace> can have hierarchical path elements separated by "/".


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