Schema mzXML_idx_2.1.xsd


schema location:  http://sashimi.sourceforge.net/schema_revision/mzXML_2.1/mzXML_idx_2.1.xsd
targetNamespace:  http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
 
Elements 
mzXML 


schema location:  http://sashimi.sourceforge.net/schema_revision/mzXML_2.1/mzXML_2.1.xsd
targetNamespace:  http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
 
Elements  Simple types 
msRun  strictBase64Type 
operator 
scan 
software 


schema location:  http://sashimi.sourceforge.net/schema_revision/mzXML_2.1/separations/separation_technique_1.0.xsd
targetNamespace:  http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
 
Elements  Complex types 
separationTechnique  separationTechniqueType 


schema location:  http://sashimi.sourceforge.net/schema_revision/mzXML_2.1/general_types_1.0.xsd
targetNamespace:  http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
 
Complex types 
namevalueType 
ontologyEntryType 


element mzXML
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
children msRun index indexOffset sha1
annotation
documentation 
Comment describing your root element
source 
<xs:element name="mzXML">
  <xs:annotation>
    <xs:documentation>Comment describing your root element</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:sequence>
      <xs:element ref="msRun"/>
      <xs:element name="index" minOccurs="0">
        <xs:annotation>
          <xs:documentation>Index for non sequential data access</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:sequence>
            <xs:element name="offset" maxOccurs="unbounded">
              <xs:annotation>
                <xs:documentation>Offset of the element identified by name (index attribute) and id</xs:documentation>
              </xs:annotation>
              <xs:complexType>
                <xs:simpleContent>
                  <xs:extension base="xs:long">
                    <xs:attribute name="id" type="xs:positiveInteger" use="required">
                      <xs:annotation>
                        <xs:documentation>This is a unique identifier for the elements of type "name" present in the index (e.g.: for an element of type scan, this will be the scan number)</xs:documentation>
                      </xs:annotation>
                    </xs:attribute>
                  </xs:extension>
                </xs:simpleContent>
              </xs:complexType>
            </xs:element>
          </xs:sequence>
          <xs:attribute name="name" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>name of the element the index entries are pointing to (e.g: scan)</xs:documentation>
            </xs:annotation>
          </xs:attribute>
        </xs:complexType>
      </xs:element>
      <xs:element name="indexOffset" type="xs:long" nillable="1">
        <xs:annotation>
          <xs:documentation>offset of the index element (if 0 no index present)</xs:documentation>
        </xs:annotation>
      </xs:element>
      <xs:element name="sha1" minOccurs="0">
        <xs:annotation>
          <xs:documentation>sha-1 sum for this file (from the beginning of the file up to (and including) the opening tag of sha1</xs:documentation>
        </xs:annotation>
        <xs:simpleType>
          <xs:restriction base="xs:string">
            <xs:length value="40"/>
          </xs:restriction>
        </xs:simpleType>
      </xs:element>
    </xs:sequence>
  </xs:complexType>
</xs:element>

element mzXML/index
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
children offset
attributes
Name  Type  Use  Default  Fixed  Annotation
name  xs:string  required      
documentation 
name of the element the index entries are pointing to (e.g: scan)
annotation
documentation 
Index for non sequential data access
source 
<xs:element name="index" minOccurs="0">
  <xs:annotation>
    <xs:documentation>Index for non sequential data access</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:sequence>
      <xs:element name="offset" maxOccurs="unbounded">
        <xs:annotation>
          <xs:documentation>Offset of the element identified by name (index attribute) and id</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:simpleContent>
            <xs:extension base="xs:long">
              <xs:attribute name="id" type="xs:positiveInteger" use="required">
                <xs:annotation>
                  <xs:documentation>This is a unique identifier for the elements of type "name" present in the index (e.g.: for an element of type scan, this will be the scan number)</xs:documentation>
                </xs:annotation>
              </xs:attribute>
            </xs:extension>
          </xs:simpleContent>
        </xs:complexType>
      </xs:element>
    </xs:sequence>
    <xs:attribute name="name" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>name of the element the index entries are pointing to (e.g: scan)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
</xs:element>

element mzXML/index/offset
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
type extension of xs:long
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:positiveInteger  required      
documentation 
This is a unique identifier for the elements of type "name" present in the index (e.g.: for an element of type scan, this will be the scan number)
annotation
documentation 
Offset of the element identified by name (index attribute) and id
source 
<xs:element name="offset" maxOccurs="unbounded">
  <xs:annotation>
    <xs:documentation>Offset of the element identified by name (index attribute) and id</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:simpleContent>
      <xs:extension base="xs:long">
        <xs:attribute name="id" type="xs:positiveInteger" use="required">
          <xs:annotation>
            <xs:documentation>This is a unique identifier for the elements of type "name" present in the index (e.g.: for an element of type scan, this will be the scan number)</xs:documentation>
          </xs:annotation>
        </xs:attribute>
      </xs:extension>
    </xs:simpleContent>
  </xs:complexType>
</xs:element>

element mzXML/indexOffset
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
type xs:long
annotation
documentation 
offset of the index element (if 0 no index present)
source 
<xs:element name="indexOffset" type="xs:long" nillable="1">
  <xs:annotation>
    <xs:documentation>offset of the index element (if 0 no index present)</xs:documentation>
  </xs:annotation>
</xs:element>

element mzXML/sha1
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
type restriction of xs:string
facets
length 40
annotation
documentation 
sha-1 sum for this file (from the beginning of the file up to (and including) the opening tag of sha1
source 
<xs:element name="sha1" minOccurs="0">
  <xs:annotation>
    <xs:documentation>sha-1 sum for this file (from the beginning of the file up to (and including) the opening tag of sha1</xs:documentation>
  </xs:annotation>
  <xs:simpleType>
    <xs:restriction base="xs:string">
      <xs:length value="40"/>
    </xs:restriction>
  </xs:simpleType>
</xs:element>

element msRun
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
children parentFile msInstrument dataProcessing separation spotting scan sha1
used by
element mzXML
attributes
Name  Type  Use  Default  Fixed  Annotation
scanCount  xs:positiveInteger  optional      
documentation 
Total number of scans contained in the XML instance document. This number should be equal to the total number of scans in the original RAW data, unless some were not converted (e.g.: signal below threshold)..
startTime  xs:duration  optional      
documentation 
The time at which the run was started.
endTime  xs:duration  optional      
documentation 
The time at which the run was ended.
source 
<xs:element name="msRun">
  <xs:complexType>
    <xs:sequence>
      <xs:element name="parentFile" maxOccurs="unbounded">
        <xs:annotation>
          <xs:documentation>Path to all the ancestor files (up to the native acquisition file) used to generate the current XML instance document.</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:simpleContent>
            <xs:extension base="xs:anySimpleType">
              <xs:attribute name="fileName" type="xs:anyURI" use="required">
                <xs:annotation>
                  <xs:documentation>Name of the parent file</xs:documentation>
                </xs:annotation>
              </xs:attribute>
              <xs:attribute name="fileType" use="required">
                <xs:annotation>
                  <xs:documentation>Was the parent file a native acquisition file? Or was it processed data?</xs:documentation>
                </xs:annotation>
                <xs:simpleType>
                  <xs:restriction base="xs:string">
                    <xs:enumeration value="RAWData"/>
                    <xs:enumeration value="processedData"/>
                  </xs:restriction>
                </xs:simpleType>
              </xs:attribute>
              <xs:attribute name="fileSha1" use="required">
                <xs:annotation>
                  <xs:documentation>sha-1 sum of the parent file</xs:documentation>
                </xs:annotation>
                <xs:simpleType>
                  <xs:restriction base="xs:string">
                    <xs:length value="40"/>
                  </xs:restriction>
                </xs:simpleType>
              </xs:attribute>
            </xs:extension>
          </xs:simpleContent>
        </xs:complexType>
        <xs:key name="parentFileKey">
          <xs:selector xpath="."/>
          <xs:field xpath="@fileSha1"/>
        </xs:key>
      </xs:element>
      <xs:element name="msInstrument" minOccurs="0">
        <xs:annotation>
          <xs:documentation>General information about the MS instrument.</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:sequence>
            <xs:element name="msManufacturer">
              <xs:complexType>
                <xs:complexContent>
                  <xs:extension base="cff:ontologyEntryType"/>
                </xs:complexContent>
              </xs:complexType>
            </xs:element>
            <xs:element name="msModel" type="cff:ontologyEntryType"/>
            <xs:element name="msIonisation" type="cff:ontologyEntryType"/>
            <xs:element name="msMassAnalyzer">
              <xs:complexType>
                <xs:complexContent>
                  <xs:extension base="cff:ontologyEntryType"/>
                </xs:complexContent>
              </xs:complexType>
            </xs:element>
            <xs:element name="msDetector" type="cff:ontologyEntryType"/>
            <xs:element ref="cff:software"/>
            <xs:element name="msResolution" type="cff:ontologyEntryType" minOccurs="0"/>
            <xs:element ref="cff:operator" minOccurs="0"/>
            <xs:sequence minOccurs="0" maxOccurs="unbounded">
              <xs:element name="nameValue" type="cff:namevalueType">
                <xs:annotation>
                  <xs:documentation>Any additional property of the instrument not included elsewhere in the instrument element.</xs:documentation>
                </xs:annotation>
              </xs:element>
              <xs:element name="comment" type="xs:string" minOccurs="0">
                <xs:annotation>
                  <xs:documentation>Additional comments.</xs:documentation>
                </xs:annotation>
              </xs:element>
            </xs:sequence>
          </xs:sequence>
        </xs:complexType>
      </xs:element>
      <xs:element name="dataProcessing" maxOccurs="unbounded">
        <xs:annotation>
          <xs:documentation>Description of any manipulation (from the first conversion to mzXML format until the creation of the current mzXML instance document) applied to the data.</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:sequence>
            <xs:element ref="cff:software">
              <xs:annotation>
                <xs:documentation>Software used to convert the data. If data has been processed (e.g. profile > centroid) by any additional progs these should be added too.</xs:documentation>
              </xs:annotation>
            </xs:element>
            <xs:sequence minOccurs="0" maxOccurs="unbounded">
              <xs:element name="processingOperation" type="cff:namevalueType">
                <xs:annotation>
                  <xs:documentation>Any additional manipulation not included elsewhere in the dataProcessing element.</xs:documentation>
                </xs:annotation>
              </xs:element>
              <xs:element name="comment" type="xs:string" minOccurs="0">
                <xs:annotation>
                  <xs:documentation>Additional comments</xs:documentation>
                </xs:annotation>
              </xs:element>
            </xs:sequence>
          </xs:sequence>
          <xs:attribute name="intensityCutoff" type="xs:float" use="optional">
            <xs:annotation>
              <xs:documentation>Intensity threshold for including a peak in the XML output</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="centroided" type="xs:boolean" use="optional">
            <xs:annotation>
              <xs:documentation>Is the data centroided</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="deisotoped" type="xs:boolean" use="optional">
            <xs:annotation>
              <xs:documentation>Is the data deisotoped</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="chargeDeconvoluted" type="xs:boolean" use="optional">
            <xs:annotation>
              <xs:documentation>Has the charge state been deconvoluted</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="spotIntegration" type="xs:boolean" use="optional"/>
        </xs:complexType>
      </xs:element>
      <xs:element name="separation" minOccurs="0">
        <xs:annotation>
          <xs:documentation>Information about the separation technique, if any, used right before the acquisition.</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:sequence>
            <xs:element ref="cff:separationTechnique" maxOccurs="unbounded"/>
          </xs:sequence>
        </xs:complexType>
      </xs:element>
      <xs:element name="spotting" minOccurs="0">
        <xs:annotation>
          <xs:documentation>Acquisition independent properties of a MALDI experiment.</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:sequence>
            <xs:element name="plate" maxOccurs="unbounded">
              <xs:annotation>
                <xs:documentation>Information about a MALDI plate.</xs:documentation>
              </xs:annotation>
              <xs:complexType>
                <xs:sequence>
                  <xs:element name="plateManufacturer" type="cff:ontologyEntryType"/>
                  <xs:element name="plateModel" type="cff:ontologyEntryType"/>
                  <xs:element name="pattern" minOccurs="0">
                    <xs:complexType>
                      <xs:sequence>
                        <xs:element name="spottingPattern" type="cff:ontologyEntryType"/>
                        <xs:element name="orientation">
                          <xs:annotation>
                            <xs:documentation>Defines the orientation of the spotting pattern, with the IDs of the fist two consecutive spotted spots.</xs:documentation>
                          </xs:annotation>
                          <xs:complexType>
                            <xs:attribute name="firstSpotID" type="xs:string" use="required">
                              <xs:annotation>
                                <xs:documentation>ID of the first spot spotted using "spottingPattern". This ID must have been defined also in the spot element.</xs:documentation>
                              </xs:annotation>
                            </xs:attribute>
                            <xs:attribute name="secondSpotID" type="xs:string" use="required">
                              <xs:annotation>
                                <xs:documentation>ID of the second spot spotted using "spottingPattern". This ID must have been defined also in the spot element.</xs:documentation>
                              </xs:annotation>
                            </xs:attribute>
                          </xs:complexType>
                          <xs:keyref name="onlyValidFirstSpotID" refer="cff:spotKey">
                            <xs:selector xpath="."/>
                            <xs:field xpath="@spotID"/>
                          </xs:keyref>
                          <xs:keyref name="onlyValidSecondSpotID" refer="cff:spotKey">
                            <xs:selector xpath="."/>
                            <xs:field xpath="@spotID"/>
                          </xs:keyref>
                        </xs:element>
                      </xs:sequence>
                    </xs:complexType>
                  </xs:element>
                  <xs:element name="spot" maxOccurs="unbounded">
                    <xs:annotation>
                      <xs:documentation>Information about individual spots.</xs:documentation>
                    </xs:annotation>
                    <xs:complexType>
                      <xs:sequence>
                        <xs:element name="maldiMatrix" type="cff:ontologyEntryType"/>
                      </xs:sequence>
                      <xs:attribute name="spotID" type="xs:string" use="required">
                        <xs:annotation>
                          <xs:documentation>Unique identifier for the spot.</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="spotXPosition" type="xs:string" use="required">
                        <xs:annotation>
                          <xs:documentation>X cartesian position of the spot.</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="spotYPosition" type="xs:string" use="required">
                        <xs:annotation>
                          <xs:documentation>Y cartesian position of the spot.</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="spotDiameter" type="xs:positiveInteger" use="optional"/>
                    </xs:complexType>
                    <xs:key name="spotKey">
                      <xs:selector xpath="."/>
                      <xs:field xpath="@spotID"/>
                    </xs:key>
                  </xs:element>
                </xs:sequence>
                <xs:attribute name="plateID" type="xs:positiveInteger" use="required">
                  <xs:annotation>
                    <xs:documentation>Unique identifier for the plate.</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="spotXCount" type="xs:positiveInteger" use="required"/>
                <xs:attribute name="spotYCount" type="xs:positiveInteger" use="required"/>
              </xs:complexType>
              <xs:key name="plateKey">
                <xs:selector xpath="."/>
                <xs:field xpath="@plateID"/>
              </xs:key>
            </xs:element>
            <xs:element name="robot" minOccurs="0">
              <xs:annotation>
                <xs:documentation>Information about the robot, if any, used to spot the plates.</xs:documentation>
              </xs:annotation>
              <xs:complexType>
                <xs:sequence>
                  <xs:element name="robotManufacturer" type="cff:ontologyEntryType"/>
                  <xs:element name="robotModel" type="cff:ontologyEntryType"/>
                </xs:sequence>
                <xs:attribute name="timePerSpot" type="xs:duration" use="required"/>
                <xs:attribute name="deadVolume" type="xs:nonNegativeInteger" use="optional">
                  <xs:annotation>
                    <xs:documentation>Dead volume in ul of the spotting robot.</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
              </xs:complexType>
            </xs:element>
          </xs:sequence>
        </xs:complexType>
      </xs:element>
      <xs:element ref="cff:scan" maxOccurs="unbounded"/>
      <xs:element name="sha1" minOccurs="0">
        <xs:annotation>
          <xs:documentation>sha-1 sum for this file (from the beginning of the file up to (and including) the opening tag of sha1</xs:documentation>
        </xs:annotation>
        <xs:simpleType>
          <xs:restriction base="xs:string">
            <xs:length value="40"/>
          </xs:restriction>
        </xs:simpleType>
      </xs:element>
    </xs:sequence>
    <xs:attribute name="scanCount" type="xs:positiveInteger" use="optional">
      <xs:annotation>
        <xs:documentation>Total number of scans contained in the XML instance document. This number should be equal to the total number of scans in the original RAW data, unless some were not converted (e.g.: signal below threshold)..</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="startTime" type="xs:duration" use="optional">
      <xs:annotation>
        <xs:documentation