Overview Namespace Document  Object  Tree Project Catalog Help
element snp
Jump: DOCUMENTATION | SOURCE FRAMES    NO FRAMES   
Play the video

element {http://www.hapmap.org}snp

Abstractfalse (This can be used in an instance)
Nillablefalse (Instance values cannot use xsi:nil)
Target Namespacehttp://www.hapmap.org
Declared Namespacesxmlns:xs=http://www.w3.org/2001/XMLSchema
xmlns=http://www.hapmap.org

Source
<xs:element name="snp">
    <xs:annotation>
        <xs:documentation>
 A single nucleotide polymorphism object. These are unique SNP clusters mapping
to the human genome assembly, corresponding to dbSNP rs# records which are
submitted to the DCC by the dbSNP group. The XML is based largely on the dbSNP
reference SNP records, except significant bits of dbSNP's model were not used since
they are not directly relevant to this project (e.g. dbSNP internal tracking) and/or are
redundant and can be fetched on demand if need be. Main child elements and attributes:

-lsid: The Life Science Identifier assigned to the SNP by NCBI's dbSNP, the authority
on the reference SNP records selected for genotyping. See LSID details page /docs/lsid_details.html
for more on LSIDs and their role in the project. Note that refSNP records have version
numbers corresponding to dbSNP builds; these will be tracked in the DCC database.
-snp_class: The category or class assigned to the SNP based on analysis done by the
dbSNP group. See SNP categories page /docs/snp_categories.html for details on each
category. The class signifies how desirable it is to genotype this particular SNP as opposed
to a SNP in another category (e.g. a group would much rather genotype a 'verified' SNP than
a 'bac-overlap' one). Note that only the 'highest' category is assigned to a SNP, even though
it may fall in more than one category.
-sequence: 5' and 3' sequences flanking the variation and the variation itself. The flank
sequences have standard IUPAC ambiguity codes embedded in them to signify the presence
of neighbor SNPs, if any. These SNPs, plus any others whose presence cannot easily be
indicated in the sequence, appear in the neighbor_snps list (see below).
-genomic_locations: one or more set of coordinates on the NCBI reference genome assembly.
The notation for each set follows closely the NCBI attributes for a SNP in their FTP dataset
releases in terms of the kind of locations that can appear ('exact', 'range' etc.), strandedness etc.
-neighbor_snps: a list of LSIDs that point to other SNP records that appear in either flank for the
current SNP record. These can be either SNPs selected for the HapMap project or other SNPs
(category 'non-validated'). The purpose of the neighbor list is to enable groups to design assays
from the SNPs while taking into account other SNPs that may reside in the flanks (i.e. the 'neighbors').
        </xs:documentation>
    </xs:annotation>
    <xs:complexType>
        <xs:sequence>
<!--HapMap category, as determine by dbSNP group. See website for detailed
description of each one of those. Note that a SNP may belong to one or more categories-->
            <xs:element name="snp_class" minOccurs="0">
                <xs:complexType>
                    <xs:all>
                        <xs:element name="validated" minOccurs="0">
                            <xs:complexType/>
                        </xs:element>
                        <xs:element name="two-hit" minOccurs="0">
                            <xs:complexType/>
                        </xs:element>
                        <xs:element name="jsnp-verified" minOccurs="0">
                            <xs:complexType/>
                        </xs:element>
                        <xs:element name="perlegen-verified" minOccurs="0">
                            <xs:complexType/>
                        </xs:element>
                        <xs:element name="illumina-verified" minOccurs="0">
                            <xs:complexType/>
                        </xs:element>
                        <xs:element name="bac-overlap" minOccurs="0">
                            <xs:complexType/>
                        </xs:element>
                        <xs:element name="tsc-overlap" minOccurs="0">
                            <xs:complexType/>
                        </xs:element>
                        <xs:element name="non-validated" minOccurs="0">
                            <xs:complexType/>
                        </xs:element>
                        <xs:element name="cSNP" minOccurs="0">
                            <xs:complexType/>
                        </xs:element>
                        <xs:element name="hapmap" minOccurs="0">
                            <xs:complexType/>
                        </xs:element>
                        <xs:element name="bcm-sequence" minOccurs="0">
                            <xs:complexType/>
                        </xs:element>
                    </xs:all>
                </xs:complexType>
            </xs:element>
            <xs:element name="groups_allocated_to" minOccurs="0" maxOccurs="unbounded">
                <xs:complexType>
                    <xs:sequence>
                        <xs:element name="group" minOccurs="1" maxOccurs="unbounded">
                            <xs:complexType>
<!--LSID pointing to the genotyping group(s) that this SNP has been
allocated to for genotyping-->
                                <xs:attribute name="lsid" type="lsidType" use="required"/>
                            </xs:complexType>
                        </xs:element>
                    </xs:sequence>
                </xs:complexType>
            </xs:element>
            <xs:element name="sequence">
                <xs:complexType>
                    <xs:sequence>
<!--5' flanking sequence for the SNP,, from the genome assembly, with IUPAC codes-->
                        <xs:element name="flank_5" type="dnaType"/>
                        <xs:element name="variation">
                            <xs:complexType>
                                <xs:sequence>
<!--In addition to the most common 'real' SNP allele datafields, here
may alternatively appear the other kinds of dbSNP variation types such
as microsatellites etc.-->
                                    <xs:choice>
<!--One or more alleles observed for this reference SNP cluster-->
                                        <xs:element name="allele" minOccurs="1" maxOccurs="unbounded">
                                            <xs:complexType>
                                                <xs:attribute name="base" type="dnaType"
                                                    use="optional"/>
                                                <xs:attribute name="name" type="xs:string"
                                                    use="optional"/>
                                            </xs:complexType>
                                        </xs:element>
                                        <xs:element name="heterozygous">
                                            <xs:complexType/>
                                        </xs:element>
                                        <xs:element name="repeat_element" type="dnaType"/>
                                        <xs:element name="microsatellite">
                                            <xs:simpleType>
                                                <xs:restriction base="xs:string">
                                                    <xs:pattern
                                                        value="\([ACTGactgnMVNHRDWSBYK]+\)[0-9/]+"/>
                                                </xs:restriction>
                                            </xs:simpleType>
                                        </xs:element>
                                    </xs:choice>
                                </xs:sequence>
                                <xs:attribute name="mixed" type="xs:boolean"/>
                            </xs:complexType>
                        </xs:element>
<!--3' flanking sequence for the SNP, from the genome assembly, with IUPAC codes-->
                        <xs:element name="flank_3" type="dnaType"/>
<!--the kind of sequence provided for the SNP flanks, from the genome
assembly, as provided by dbSNP (full-length, contig-end, fragment-end)-->
                        <xs:element name="length_class">
                            <xs:complexType>
                                <xs:attribute name="value" type="flankclassType" use="required"/>
                            </xs:complexType>
                        </xs:element>
                    </xs:sequence>
                </xs:complexType>
            </xs:element>
<!--See element_groups.xsd for details on this element group-->
            <xs:group ref="genomic_locationGroup" minOccurs="0"/>
            <xs:element name="neighbour_snps" minOccurs="0">
                <xs:complexType>
                    <xs:sequence>
                        <xs:element name="neighbour_snp" maxOccurs="unbounded">
                            <xs:complexType>
<!--One LSID for each refSNP that is embedded in the flanks for this SNP
record. These can be either regular SNPs (usually) or microsatellites or other
kinds of variation in dbSNP. Note that this is only a list, so if you need locations
for those, you'll need to look them elsewhere in this file or a database that these
data have been imported into-->
                                <xs:attribute name="lsid" type="lsidType" use="required"/>
                            </xs:complexType>
                        </xs:element>
                    </xs:sequence>
                </xs:complexType>
            </xs:element>
        </xs:sequence>
<!--dbSNP-assigned LSID for this SNP-->
        <xs:attribute name="lsid" type="lsidType" use="required"/>
    </xs:complexType>
</xs:element>

Documentation

 
      A single nucleotide polymorphism object. These are unique SNP clusters mapping
      to the human genome assembly, corresponding to dbSNP rs# records which are
      submitted to the DCC by the dbSNP group.  The XML is based largely on the dbSNP
      reference SNP records, except significant bits of dbSNP's model were not used since
      they are not directly relevant to this project (e.g. dbSNP internal tracking) and/or are
      redundant and can be fetched on demand if need be. Main child elements and attributes:
-lsid: The Life Science Identifier assigned to the SNP by NCBI's dbSNP, the authority
on the reference SNP records selected for genotyping. See LSID details page /docs/lsid_details.html
 for more on LSIDs and their role in the project. Note that refSNP records have version
 numbers corresponding to dbSNP builds; these will be tracked in the DCC database.
-snp_class: The category or class assigned to the SNP based on analysis done by the
dbSNP group. See SNP categories page /docs/snp_categories.html for details on each
category. The class signifies how desirable it is to genotype this particular SNP as opposed
to a SNP in another category (e.g. a group would much rather genotype a 'verified' SNP than
a 'bac-overlap' one). Note that only the 'highest' category is assigned to a SNP, even though
it may fall in more than one category.
-sequence: 5' and 3' sequences flanking the variation and the variation itself. The flank
sequences have standard IUPAC ambiguity codes embedded in them to signify the presence
of neighbor SNPs, if any. These SNPs, plus any others whose presence cannot easily be
indicated in the sequence, appear in the neighbor_snps list (see below).
-genomic_locations: one or more set of coordinates on the NCBI reference genome assembly.
The notation for each set follows closely the NCBI attributes for a SNP in their FTP dataset
releases in terms of the kind of locations that can appear ('exact', 'range' etc.), strandedness etc.
-neighbor_snps: a list of LSIDs that point to other SNP records that appear in either flank for the
current SNP record. These can be either SNPs selected for the HapMap project or other SNPs
(category 'non-validated'). The purpose of the neighbor list is to enable groups to design assays
from the SNPs while taking into account other SNPs that may reside in the flanks (i.e. the 'neighbors').

Overview Namespace Document  Object  Tree Project Catalog Help
element snp
Jump: DOCUMENTATION | SOURCE FRAMES    NO FRAMES   
Stylus Studio XML Schema Library Home
Site Map | Privacy Policy | Terms of Use | Trademarks
Stylus Scoop XML Newsletter:
W3C Member
Stylus Studio®, a product from DataDirect Technologies, is a registered trademark of Progress Software Corporation, in the U.S. and other countries. © 2004-2006 All Rights Reserved.