Schema genoex_1_2.xsd


schema location:  http://www.ncbi.nlm.nih.gov/SNP/geno/genoex_1_2.xsd
targetNamespace:  http://www.ncbi.nlm.nih.gov/SNP/geno
 
Elements 
FlagDesc 
GenoExchange 
Individual 
Pedigree 
Population 
SnpInfo 


element FlagDesc
diagram
namespace http://www.ncbi.nlm.nih.gov/SNP/geno
used by
element GenoExchange
attributes
Name  Type  Use  Default  Fixed  Annotation
flag  xs:ID        
documentation 
Allele flag
desc  xs:string  required      
documentation 
Allele flag description
annotation
documentation 
List of allele flag descriptions.

element GenoExchange
diagram
namespace http://www.ncbi.nlm.nih.gov/SNP/geno
children Population Individual Pedigree SnpInfo FlagDesc
attributes
Name  Type  Use  Default  Fixed  Annotation
dbSNPBuildNo  xs:string        
annotation
documentation 
Structure used for the exchange of dbSNP genotype information

element Individual
diagram
namespace http://www.ncbi.nlm.nih.gov/SNP/geno
children SourceInfo SubmitInfo
used by
element GenoExchange
attributes
Name  Type  Use  Default  Fixed  Annotation
indId  xs:int  required      
documentation 
Individual Identifier
taxId  xs:int        
documentation 
Entrez taxonomy identifier
sex  xs:string        
documentation 
Sex of the individual
strain  xs:string        
documentation 
Strain, used when individual is from an organism with inbred strains.
indGroup  xs:string        
documentation 
Ethnic or subspecies grouping
annotation
documentation 
a cluster of samples from subjects or inbred strains thought to have the same  genomic composition

element Individual/SourceInfo
diagram
namespace http://www.ncbi.nlm.nih.gov/SNP/geno
attributes
Name  Type  Use  Default  Fixed  Annotation
source  xs:string        
documentation 
Defines the numbering space for this individual
sourceType  xs:string        
documentation 
Repository, Currator, Submitter, NCBI
ncbiPedId  xs:int        
pedId  xs:string        
documentation 
Pedigree iidentifier in source's identifier space
indId  xs:string        
documentation 
individual identifier in source's identifier space.  Note; This identifier is unique to one individual in the NCBI source.
maId  xs:string        
documentation 
Mother's identifier in source's identifier space.
paId  xs:string        
documentation 
Father's identifier in source's identifier space.
srcIndGroup  xs:string        
documentation 
Submitters ethnic or subspecies grouping
annotation
documentation 
source information pertaining to a molecular sample that can be clustered to an individual

element Individual/SubmitInfo
diagram
namespace http://www.ncbi.nlm.nih.gov/SNP/geno
attributes
Name  Type  Use  Default  Fixed  Annotation
popId  xs:int        
documentation 
Pedigree iidentifier in source's identifier space
submittedIndId  xs:string        
documentation 
individual identifier in source's identifier space.  Note; This identifier is unique to one individual in the NCBI source.
subIndGroup  xs:string        
documentation 
Submitters ethnic or subspecies grouping
annotation
documentation 
submission information pertaining to a molecular sample that can be clustered to an individual

element Pedigree
diagram
namespace http://www.ncbi.nlm.nih.gov/SNP/geno
used by
element GenoExchange
attributes
Name  Type  Use  Default  Fixed  Annotation
ncbiPedId          
documentation 
dbSNP unique pedigree identifier
authority  xs:string        
documentation 
Authority Name  for this pedigree
authorityPedId  xs:string        
documentation 
Pedigree Identifier in the Authoritity's numbering system
annotation
documentation 
 A Pedigree contained in this GenoExchange

element Population
diagram
namespace http://www.ncbi.nlm.nih.gov/SNP/geno
children popClass
used by
element GenoExchange
attributes
Name  Type  Use  Default  Fixed  Annotation
popId  xs:int  required      
documentation 
dbSNP Population Identifier
handle  xs:string  required      
documentation 
dbSNP Submitter's handle
locPopId  xs:string  required      
documentation 
Submitter's Population Identifier
annotation
documentation 
A Population contained in this GenoExchange

element Population/popClass
diagram
namespace http://www.ncbi.nlm.nih.gov/SNP/geno
attributes
Name  Type  Use  Default  Fixed  Annotation
self  xs:string  required      
documentation 
Population class value
annotation
documentation 
Population Class

element SnpInfo
diagram
namespace http://www.ncbi.nlm.nih.gov/SNP/geno
children SnpLoc SsInfo GTypeFreq
used by
element GenoExchange
attributes
Name  Type  Use  Default  Fixed  Annotation
rsId  xs:int  required      
documentation 
Reference snp identifier; Note; This identifier groups ssId to a single variation.
annotation
documentation 
A  clustered Genomic Variation contained in this GenoExchange

element SnpInfo/SnpLoc
diagram
namespace http://www.ncbi.nlm.nih.gov/SNP/geno
attributes
Name  Type  Use  Default  Fixed  Annotation
genomicAssembly  xs:string        
documentation 
NCBI genome Assembly --> defined as a concatenation of build identifier and contig label. SNPContigLoc.build_id:ContigInfo.contig_label from dbSNP database.
locusId  xs:string        
documentation 
Gene identifier used by entrez gene.
chrom  xs:string        
documentation 
Chromosome
start  xs:string        
documentation 
Start location in chomosome coordinates
end  xs:string        
documentation 
End location in chomosome coordinates
locType  xs:int        
documentation 
SNPContigLoc.loc_type
rsOrientToChrom  xs:string        
documentation 
Orientation of rs in chromosome coordinates
annotation
documentation 
Location information of rs cluster

element SnpInfo/SsInfo
diagram
namespace http://www.ncbi.nlm.nih.gov/SNP/geno
children ByPop
attributes
Name  Type  Use  Default  Fixed  Annotation
ssId  xs:int  required      
documentation 
dbSNP submitted snp Identifier
locSnpId  xs:string        
documentation 
Submitter's snp identifier
ssOrientToRs  xs:string        
documentation 
Orientation of this ss to it's rs cluster
annotation
documentation 
Submitted SNP information

element SnpInfo/SsInfo/ByPop
diagram
namespace http://www.ncbi.nlm.nih.gov/SNP/geno
children AlleleFreq GTypeFreq GTypeByInd
attributes
Name  Type  Use  Default  Fixed  Annotation
popId  xs:int  required      
documentation 
Population identifier
subHet  xs:double        
documentation 
Submitted heterozygosity
estHet  xs:double        
documentation 
Estimated heterzygosity either observed from genotypes or estimated from allele frequencies.
hwProb  xs:double        
documentation 
Hardy-Weinberg probability upper bound
hwChi2  xs:double        
documentation 
Hardy-Weinberg chi squared value
hwDf  xs:double        
documentation 
Hardy-Weinberg degrees of freedom
sampleSize  xs:int        
documentation 
Number of chomosomes
annotation
documentation 
Population

element SnpInfo/SsInfo/ByPop/AlleleFreq
diagram
namespace http://www.ncbi.nlm.nih.gov/SNP/geno
attributes
Name  Type  Use  Default  Fixed  Annotation
allele  xs:string  required      
documentation 
snp allele
freq  xs:double        
documentation 
Allele frequency
annotation
documentation 
Allele frequencies

element SnpInfo/SsInfo/ByPop/GTypeFreq
diagram
namespace http://www.ncbi.nlm.nih.gov/SNP/geno
attributes
Name  Type  Use  Default  Fixed  Annotation
gtype  xs:string  required      
documentation 
Genotype
freq  xs:double        
documentation 
Genotype frequency
annotation
documentation 
Genotype frequency Information

element SnpInfo/SsInfo/ByPop/GTypeByInd
diagram
namespace http://www.ncbi.nlm.nih.gov/SNP/geno
attributes
Name  Type  Use  Default  Fixed  Annotation
gtype  xs:string  required      
documentation 
Genotype in SS orientation
indId  xs:int        
documentation 
individual Identifier--> Key to Individual element
flag  xs:IDREF        
documentation 
genotype flag --> key to FlagDesc
annotation
documentation 
Genotype by Individual

element SnpInfo/GTypeFreq
diagram
namespace http://www.ncbi.nlm.nih.gov/SNP/geno
attributes
Name  Type  Use  Default  Fixed  Annotation
gtype  xs:string  required      
documentation 
Genotype
freq  xs:double        
documentation 
Genotype Frequency
annotation
documentation 
Genotype frequency Information pertaining to rs cluster


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