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

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="assay">
    <xs:annotation>
        <xs:documentation>
An assay for a single SNP. Contains the experimental parameters that
distinguishes this assay from assay for other SNPs designed using the same protocol
(primers, extension probe etc., depending on the experimental protocol). The assay
input and output parameters are largely platform-specific. See example assays in the
/xml-examples/ directory. IMPORTANT! the plan is for all groups to submit an assay
record for all attempted assays, not merely the ones that were successful. The
status for such failed or otherwise unsuccessful (e.g. rejected prior to design
phase because of repeats in area).. The point of this exercise is that the DCC can
calculate all sorts of useful stats (most notably overall assay conversion rate) if
we have a record of every attempted assay.
        </xs:documentation>
    </xs:annotation>
    <xs:complexType>
        <xs:sequence>
            <xs:element name="snp_assayed">
                <xs:complexType>
<!--LSID pointing to an existing SNP record that the assay was designed
from. IMPORTANT: this includes the exact version of the SNP, information
that the full SNP LSID conveys.-->
                    <xs:attribute name="lsid" type="lsidType" use="required"/>
                </xs:complexType>
            </xs:element>
            <xs:element name="protocol_used">
                <xs:complexType>
<!--LSID pointing to existing protocol record in database-->
                    <xs:attribute name="lsid" type="lsidType" use="required"/>
                </xs:complexType>
            </xs:element>
<!--One or more groups that this assay belongs to. usually at least the multiplex
pool that it was designed to work in, in tandem with other assays-->
            <xs:element minOccurs="0" ref="batch"/>
            <xs:element name="status">
                <xs:complexType>
                    <xs:choice>
                        <xs:element name="pass"/>
                        <xs:element name="fail" maxOccurs="unbounded">
                            <xs:complexType>
                                <xs:simpleContent>
                                    <xs:extension base="xs:string">
                                        <xs:attribute name="code" type="assay_failure_code"/>
                                    </xs:extension>
                                </xs:simpleContent>
                            </xs:complexType>
                        </xs:element>
                    </xs:choice>
                </xs:complexType>
            </xs:element>
<!--Section describing SNP sequence and other parameters used as input to the
assay design program. This varies between genotyping platforms-->
            <xs:element name="input_parameters">
                <xs:complexType>
                    <xs:sequence>
<!--Only one of the following platform-specific sections may appear-->
                        <xs:choice>
<!--Illumina's BeadArray platform-->
                            <xs:element name="beadarray_platform">
                                <xs:complexType>
                                    <xs:sequence>
                                        <xs:element name="seq_for_oligo_design">
                                            <xs:simpleType>
                                                <xs:restriction base="xs:string">
                                                    <xs:whiteSpace value="collapse"/>
                                                    <xs:pattern
                                                        value="([ACTGactgnMVNHRDWSBYKxX\[\]//])+"/>
                                                </xs:restriction>
                                            </xs:simpleType>
                                        </xs:element>
                                    </xs:sequence>
                                </xs:complexType>
                            </xs:element>
<!--Third Wave/UoTokyo Invader platform-->
                            <xs:element name="invader_platform">
                                <xs:complexType>
                                    <xs:sequence>
                                        <xs:element name="seq_for_probe_design" type="dnaType"/>
                                        <xs:element name="seq_for_primer_design" type="dnaType"/>
                                    </xs:sequence>
                                </xs:complexType>
                            </xs:element>
<!--Sequenom platform-->
                            <xs:element name="sequenom_platform">
                                <xs:complexType>
                                    <xs:sequence>
                                        <xs:element name="seq_for_oligo_design" type="dnaType"/>
                                    </xs:sequence>
                                </xs:complexType>
                            </xs:element>
<!--ParAllele Molecular Inversion probe platform-->
                            <xs:element name="mip_platform">
                                <xs:complexType>
                                    <xs:sequence>
                                        <xs:element name="seq_for_mip_probe_design">
                                            <xs:simpleType>
                                                <xs:restriction base="xs:string">
                                                    <xs:whiteSpace value="collapse"/>
                                                    <xs:pattern
                                                        value="([ACTGactgMmVvNnHhRrDdWwSsBbYyKkXx\[\]//])+"/>
                                                </xs:restriction>
                                            </xs:simpleType>
                                        </xs:element>
                                    </xs:sequence>
                                </xs:complexType>
                            </xs:element>
<!--WashU/UCSF FP-TDI platform-->
                            <xs:element name="fp_tdi_platform">
                                <xs:complexType>
                                    <xs:sequence>
                                        <xs:element name="seq_for_pcr_oligo_design" type="dnaType"/>
                                        <xs:element name="seq_for_extension_oligo_design"
                                            type="dnaType"/>
                                    </xs:sequence>
                                </xs:complexType>
                            </xs:element>
<!--Perlegen platform-->
                            <xs:element name="perlegen_platform">
                                <xs:complexType>
                                    <xs:sequence>
                                        <xs:element name="genome_assembly_region" minOccurs="0">
                                            <xs:simpleType>
                                                <xs:restriction base="xs:string">
                                                    <xs:whiteSpace value="collapse"/>
                                                    <xs:pattern
                                                        value=".+:Chr[1-9XY][0-9]?:[0-9]+\.\.[0-9]+"/>
                                                </xs:restriction>
                                            </xs:simpleType>
                                        </xs:element>
                                    </xs:sequence>
                                </xs:complexType>
                            </xs:element>
<!--Affymetrix Centurion platform-->
                            <xs:element name="affymetrix_mapping100k_platform">
                                <xs:complexType>
                                    <xs:sequence>
                                        <xs:element name="seq_for_oligo_design" type="dnaType"/>
                                    </xs:sequence>
                                </xs:complexType>
                            </xs:element>
<!--Baylor/ABI SNPlex platform-->
                            <xs:element name="snplex_platform">
                                <xs:complexType>
                                    <xs:sequence>
                                        <xs:element name="seq_for_oligo_design">
                                            <xs:simpleType>
                                                <xs:restriction base="xs:string">
                                                    <xs:whiteSpace value="collapse"/>
                                                    <xs:pattern
                                                        value="([ACTGactgMmVvNnHhRrDdWwSsBbYyKkXx\[\]//])+"/>
                                                </xs:restriction>
                                            </xs:simpleType>
                                        </xs:element>
                                    </xs:sequence>
                                </xs:complexType>
                            </xs:element>
                        </xs:choice>
                    </xs:sequence>
                </xs:complexType>
            </xs:element>
<!--Section describing the output from the assay design program, the
info used in the genotyping procedure. Usually some kind of oligos (primers,
probes of some kind. Varies between genotyping platforms-->
            <xs:element minOccurs="0" name="output_design">
                <xs:complexType>
                    <xs:sequence>
<!--The strand that the assay produces allele calls on: the original strand
around the SNP that the assay was designed from (forward), or its reverse
compliment (reverse)-->
                        <xs:element name="strand" type="strandType"/>
<!--Same as above; only one platform-specific output-info-->
                        <xs:choice>
                            <xs:element name="beadarray_platform">
                                <xs:complexType>
                                    <xs:sequence>
                                        <xs:element name="allele1_combined_seq" type="dnaType"/>
                                        <xs:element name="allele2_combined_seq" type="dnaType"/>
                                        <xs:element name="common_combined_seq" type="dnaType"/>
                                        <xs:element name="illumina_strand">
                                            <xs:simpleType>
                                                <xs:restriction base="xs:NMTOKEN">
                                                    <xs:enumeration value="top"/>
                                                    <xs:enumeration value="bottom"/>
                                                </xs:restriction>
                                            </xs:simpleType>
                                        </xs:element>
<!--<xs:element name="design_score">
<xs:simpleType>
<xs:restriction base="xs:float"/>
</xs:simpleType>
</xs:element>-->
                                    </xs:sequence>
                                </xs:complexType>
                            </xs:element>
                            <xs:element name="invader_platform">
                                <xs:complexType>
                                    <xs:sequence>
                                        <xs:element name="pcr_primer_forward" type="dnaType"/>
                                        <xs:element name="pcr_primer_reverse" type="dnaType"/>
                                        <xs:element name="invader_probe" type="dnaType"/>
                                        <xs:element name="allele_probe1" type="dnaType"/>
                                        <xs:element name="allele_probe2" type="dnaType"/>
                                    </xs:sequence>
                                </xs:complexType>
                            </xs:element>
                            <xs:element name="sequenom_platform">
                                <xs:complexType>
                                    <xs:sequence>
                                        <xs:element name="pcr_primer_forward" type="dnaType"/>
                                        <xs:element name="pcr_primer_reverse" type="dnaType"/>
                                        <xs:element name="extension_probe" type="dnaType"/>
                                    </xs:sequence>
                                </xs:complexType>
                            </xs:element>
                            <xs:element name="mip_platform">
                                <xs:complexType>
                                    <xs:sequence>
                                        <xs:element name="mip_probe">
                                            <xs:simpleType>
                                                <xs:restriction base="xs:string">
                                                    <xs:whiteSpace value="collapse"/>
<!--<xs:pattern value="([ACTGactgnyuMVNHRDWSBYKU\[\]//\-])+"></xs:pattern>-->
                                                </xs:restriction>
                                            </xs:simpleType>
                                        </xs:element>
                                    </xs:sequence>
                                </xs:complexType>
                            </xs:element>
                            <xs:element name="fp_tdi_platform">
                                <xs:complexType>
                                    <xs:sequence>
                                        <xs:element name="pcr_primer_forward" type="dnaType"/>
                                        <xs:element name="pcr_primer_reverse" type="dnaType"/>
                                        <xs:element name="extension_primer" type="dnaType"/>
                                    </xs:sequence>
                                </xs:complexType>
                            </xs:element>
                            <xs:element name="perlegen_platform">
                                <xs:complexType>
                                    <xs:sequence>
<!--<xs:element name="pcr_primer_forward_1" type="dnaType" minOccurs="0"/>
<xs:element name="pcr_primer_reverse_1" type="dnaType" minOccurs="0"/>
<xs:element name="pcr_primer_forward_2" type="dnaType" minOccurs="0"/>
<xs:element name="pcr_primer_reverse_2" type="dnaType" minOccurs="0"/>-->
                                        <xs:element name="pcr_amplicon" type="xs:string"
                                            minOccurs="0"/>
                                        <xs:element name="tiled_ref_probe_seq" type="dnaType"/>
                                        <xs:element name="tiled_alt_probe_seq" type="dnaType"/>
                                    </xs:sequence>
                                </xs:complexType>
                            </xs:element>
                            <xs:element name="affymetrix_mapping100k_platform">
                                <xs:complexType>
                                    <xs:sequence>
                                        <xs:element name="allele_a_probe" type="dnaType"/>
                                        <xs:element name="allele_b_probe" type="dnaType"/>
                                    </xs:sequence>
                                </xs:complexType>
                            </xs:element>
                            <xs:element name="snplex_platform">
                                <xs:complexType>
                                    <xs:sequence>
                                        <xs:element name="allele1_seq" type="dnaType"/>
                                        <xs:element name="allele2_seq" type="dnaType"/>
                                    </xs:sequence>
                                </xs:complexType>
                            </xs:element>
                        </xs:choice>
                    </xs:sequence>
                </xs:complexType>
            </xs:element>
        </xs:sequence>
<!--unique submitter-assigned LSID for this genotype-->
        <xs:attribute name="lsid" type="lsidType" use="required"/>
    </xs:complexType>
</xs:element>

Documentation

 
An assay for a single SNP. Contains the experimental parameters that
               distinguishes this assay from assay for other SNPs designed using the same protocol
               (primers, extension probe etc., depending on the experimental protocol). The assay
               input and output parameters are largely platform-specific. See example assays in the
               /xml-examples/ directory. IMPORTANT! the plan is for all groups to submit an assay
               record for all attempted assays, not merely the ones that were successful. The
               status for such failed or otherwise unsuccessful (e.g. rejected prior to design
               phase because of repeats in area).. The point of this exercise is that the DCC can
               calculate all sorts of useful stats (most notably overall assay conversion rate) if
               we have a record of every attempted assay.

Overview Namespace Document  Object  Tree Project Catalog Help
element assay
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