Schema apml.xsd

schema location:	C:\Documents and Settings\mbrusnia.ISB\My Documents\Projects\Eclipse_WorkSpace\Corra\APML\trunk\doc\APML\apml.xsd
attribute form default:	unqualified
element form default:	qualified
targetNamespace:	http://www.systemsbiology.org/apml

Elements	Complex types
apml	AlignedFeatureType
	AlignmentType
	ClusterProfileType
	ClusterType
	CoordinateType
	dataType
	elution_profileType
	FeatureType
	PeakListType
	PpidCollectionType
	SoftwareType

element apml

diagram
namespace	http://www.systemsbiology.org/apml
properties	content  complex
children	dataProcessing data
annotation	documentation Collection of annotated features that are the result of feature picking or aligning MS1 spectra.
source	<xs:element name="apml">   <xs:annotation>     <xs:documentation>Collection of annotated features that are the result of feature picking or aligning MS1 spectra.</xs:documentation>   </xs:annotation>   <xs:complexType>     <xs:sequence>       <xs:element name="dataProcessing" type="SoftwareType">         <xs:annotation>           <xs:documentation>Collection of data processing software information.</xs:documentation>         </xs:annotation>       </xs:element>       <xs:element name="data">         <xs:annotation>           <xs:documentation>A collection peak lists OR an alignment result.</xs:documentation>         </xs:annotation>         <xs:complexType>           <xs:sequence>             <xs:element name="cluster_profile" type="ClusterProfileType" minOccurs="0">               <xs:annotation>                 <xs:documentation>Collection of profiling cluster</xs:documentation>               </xs:annotation>             </xs:element>             <xs:choice>               <xs:element name="peak_lists">                 <xs:annotation>                   <xs:documentation>Collection of peak_lists</xs:documentation>                 </xs:annotation>                 <xs:complexType>                   <xs:complexContent>                     <xs:extension base="PeakListType">                       <xs:attribute name="count" type="xs:nonNegativeInteger" use="required"/>                     </xs:extension>                   </xs:complexContent>                 </xs:complexType>               </xs:element>               <xs:element name="alignment">                 <xs:annotation>                   <xs:documentation>An alignment result.</xs:documentation>                 </xs:annotation>                 <xs:complexType>                   <xs:complexContent>                     <xs:extension base="AlignmentType"/>                   </xs:complexContent>                 </xs:complexType>               </xs:element>             </xs:choice>           </xs:sequence>         </xs:complexType>       </xs:element>     </xs:sequence>   </xs:complexType> </xs:element>

element apml/dataProcessing

diagram
namespace	http://www.systemsbiology.org/apml
type	SoftwareType
properties	isRef  0 content  complex
children	software
annotation	documentation Collection of data processing software information.
source	<xs:element name="dataProcessing" type="SoftwareType">   <xs:annotation>     <xs:documentation>Collection of data processing software information.</xs:documentation>   </xs:annotation> </xs:element>

element apml/data

diagram
namespace	http://www.systemsbiology.org/apml
properties	isRef  0 content  complex
children	cluster_profile peak_lists alignment
annotation	documentation A collection peak lists OR an alignment result.
source	<xs:element name="data">   <xs:annotation>     <xs:documentation>A collection peak lists OR an alignment result.</xs:documentation>   </xs:annotation>   <xs:complexType>     <xs:sequence>       <xs:element name="cluster_profile" type="ClusterProfileType" minOccurs="0">         <xs:annotation>           <xs:documentation>Collection of profiling cluster</xs:documentation>         </xs:annotation>       </xs:element>       <xs:choice>         <xs:element name="peak_lists">           <xs:annotation>             <xs:documentation>Collection of peak_lists</xs:documentation>           </xs:annotation>           <xs:complexType>             <xs:complexContent>               <xs:extension base="PeakListType">                 <xs:attribute name="count" type="xs:nonNegativeInteger" use="required"/>               </xs:extension>             </xs:complexContent>           </xs:complexType>         </xs:element>         <xs:element name="alignment">           <xs:annotation>             <xs:documentation>An alignment result.</xs:documentation>           </xs:annotation>           <xs:complexType>             <xs:complexContent>               <xs:extension base="AlignmentType"/>             </xs:complexContent>           </xs:complexType>         </xs:element>       </xs:choice>     </xs:sequence>   </xs:complexType> </xs:element>

element apml/data/cluster_profile

diagram
namespace	http://www.systemsbiology.org/apml
type	ClusterProfileType
properties	isRef  0 minOcc  0 maxOcc  1 content  complex
children	profile_data
attributes	Name   Type   Use   Default   Fixed   annotation id xs:nonNegativeInteger
annotation	documentation Collection of profiling cluster
source	<xs:element name="cluster_profile" type="ClusterProfileType" minOccurs="0">   <xs:annotation>     <xs:documentation>Collection of profiling cluster</xs:documentation>   </xs:annotation> </xs:element>

element apml/data/peak_lists

diagram
namespace	http://www.systemsbiology.org/apml
type	extension of PeakListType
properties	isRef  0 content  complex
children	peak_list
attributes	Name   Type   Use   Default   Fixed   annotation count xs:nonNegativeInteger required
annotation	documentation Collection of peak_lists
source	<xs:element name="peak_lists">   <xs:annotation>     <xs:documentation>Collection of peak_lists</xs:documentation>   </xs:annotation>   <xs:complexType>     <xs:complexContent>       <xs:extension base="PeakListType">         <xs:attribute name="count" type="xs:nonNegativeInteger" use="required"/>       </xs:extension>     </xs:complexContent>   </xs:complexType> </xs:element>

element apml/data/alignment

diagram
namespace	http://www.systemsbiology.org/apml
type	extension of AlignmentType
properties	isRef  0 content  complex
children	feature_source_list aligned_features
annotation	documentation An alignment result.
source	<xs:element name="alignment">   <xs:annotation>     <xs:documentation>An alignment result.</xs:documentation>   </xs:annotation>   <xs:complexType>     <xs:complexContent>       <xs:extension base="AlignmentType"/>     </xs:complexContent>   </xs:complexType> </xs:element>

complexType AlignedFeatureType

diagram
namespace	http://www.systemsbiology.org/apml
children	coordinate features ppids
used by	element  AlignmentType/aligned_features/aligned_feature
attributes	Name   Type   Use   Default   Fixed   annotation id xs:nonNegativeInteger required
annotation	documentation Aligned feature from multiple LCMS runs.
source	<xs:complexType name="AlignedFeatureType">   <xs:annotation>     <xs:documentation>Aligned feature from multiple LCMS runs.</xs:documentation>   </xs:annotation>   <xs:sequence>     <xs:element name="coordinate">       <xs:annotation>         <xs:documentation>Aligned feature coordinate</xs:documentation>       </xs:annotation>       <xs:complexType>         <xs:complexContent>           <xs:extension base="CoordinateType"/>         </xs:complexContent>       </xs:complexType>     </xs:element>     <xs:element name="features">       <xs:complexType>         <xs:sequence>           <xs:element name="feature" maxOccurs="unbounded">             <xs:complexType>               <xs:complexContent>                 <xs:extension base="FeatureType">                   <xs:attribute name="id" type="xs:nonNegativeInteger" use="required"/>                   <xs:attribute name="source" type="xs:anyURI" use="required"/>                 </xs:extension>               </xs:complexContent>             </xs:complexType>           </xs:element>         </xs:sequence>         <xs:attribute name="count" type="xs:nonNegativeInteger" use="required"/>       </xs:complexType>     </xs:element>     <xs:element name="ppids" minOccurs="0">       <xs:complexType>         <xs:complexContent>           <xs:extension base="PpidCollectionType">             <xs:attribute name="count" type="xs:negativeInteger"/>           </xs:extension>         </xs:complexContent>       </xs:complexType>     </xs:element>   </xs:sequence>   <xs:attribute name="id" type="xs:nonNegativeInteger" use="required"/> </xs:complexType>

element AlignedFeatureType/coordinate

diagram
namespace	http://www.systemsbiology.org/apml
type	extension of CoordinateType
properties	isRef  0 content  complex
children	scan_range time_range mz_range
attributes	Name   Type   Use   Default   Fixed   annotation mz xs:float required         rt xs:float required         intensity xs:float optional         charge xs:int required         mass xs:float required         apex_intensity xs:float optional         apex_scan xs:nonNegativeInteger optional
annotation	documentation Aligned feature coordinate
source	<xs:element name="coordinate">   <xs:annotation>     <xs:documentation>Aligned feature coordinate</xs:documentation>   </xs:annotation>   <xs:complexType>     <xs:complexContent>       <xs:extension base="CoordinateType"/>     </xs:complexContent>   </xs:complexType> </xs:element>

element AlignedFeatureType/features

diagram
namespace	http://www.systemsbiology.org/apml
properties	isRef  0 content  complex
children	feature
attributes	Name   Type   Use   Default   Fixed   annotation count xs:nonNegativeInteger required
source	<xs:element name="features">   <xs:complexType>     <xs:sequence>       <xs:element name="feature" maxOccurs="unbounded">         <xs:complexType>           <xs:complexContent>             <xs:extension base="FeatureType">               <xs:attribute name="id" type="xs:nonNegativeInteger" use="required"/>               <xs:attribute name="source" type="xs:anyURI" use="required"/>             </xs:extension>           </xs:complexContent>         </xs:complexType>       </xs:element>     </xs:sequence>     <xs:attribute name="count" type="xs:nonNegativeInteger" use="required"/>   </xs:complexType> </xs:element>

element AlignedFeatureType/features/feature

diagram
namespace	http://www.systemsbiology.org/apml
type	extension of FeatureType
properties	isRef  0 minOcc  1 maxOcc  unbounded content  complex
children	coordinate ppids elution_profile
attributes	Name   Type   Use   Default   Fixed   annotation id xs:nonNegativeInteger required         source xs:anyURI required
source	<xs:element name="feature" maxOccurs="unbounded">   <xs:complexType>     <xs:complexContent>       <xs:extension base="FeatureType">         <xs:attribute name="id" type="xs:nonNegativeInteger" use="required"/>         <xs:attribute name="source" type="xs:anyURI" use="required"/>       </xs:extension>     </xs:complexContent>   </xs:complexType> </xs:element>

element AlignedFeatureType/ppids

diagram
namespace	http://www.systemsbiology.org/apml
type	extension of PpidCollectionType
properties	isRef  0 minOcc  0 maxOcc  1 content  complex
children	ppid
attributes	Name   Type   Use   Default   Fixed   annotation count xs:negativeInteger
source	<xs:element name="ppids" minOccurs="0">   <xs:complexType>     <xs:complexContent>       <xs:extension base="PpidCollectionType">         <xs:attribute name="count" type="xs:negativeInteger"/>       </xs:extension>     </xs:complexContent>   </xs:complexType> </xs:element>

complexType AlignmentType

diagram
namespace	http://www.systemsbiology.org/apml
children	feature_source_list aligned_features
used by	element  apml/data/alignment
annotation	documentation A single alignment containning features from multiple LCMS runs.
source	<xs:complexType name="AlignmentType">   <xs:annotation>     <xs:documentation>A single alignment containning features from multiple LCMS runs.</xs:documentation>   </xs:annotation>   <xs:sequence>     <xs:element name="feature_source_list">       <xs:complexType>         <xs:sequence>           <xs:element name="source" maxOccurs="unbounded">             <xs:complexType>               <xs:attribute name="id" type="xs:nonNegativeInteger" use="optional"/>               <xs:attribute name="location" type="xs:anyURI" use="required"/>             </xs:complexType>           </xs:element>         </xs:sequence>         <xs:attribute name="count" type="xs:int" use="required"/>       </xs:complexType>     </xs:element>     <xs:element name="aligned_features">       <xs:complexType>         <xs:sequence>           <xs:element name="aligned_feature" maxOccurs="unbounded">             <xs:annotation>               <xs:documentation>An aligned feature.</xs:documentation>             </xs:annotation>             <xs:complexType>               <xs:complexContent>                 <xs:extension base="AlignedFeatureType"/>               </xs:complexContent>             </xs:complexType>           </xs:element>         </xs:sequence>         <xs:attribute name="count" type="xs:nonNegativeInteger" use="required"/>       </xs:complexType>     </xs:element>   </xs:sequence> </xs:complexType>

element AlignmentType/feature_source_list

diagram
namespace	http://www.systemsbiology.org/apml
properties	isRef  0 content  complex
children	source
attributes	Name   Type   Use   Default   Fixed   annotation count xs:int required
source	<xs:element name="feature_source_list">   <xs:complexType>     <xs:sequence>       <xs:element name="source" maxOccurs="unbounded">         <xs:complexType>           <xs:attribute name="id" type="xs:nonNegativeInteger" use="optional"/>           <xs:attribute name="location" type="xs:anyURI" use="required"/>         </xs:complexType>       </xs:element>     </xs:sequence>     <xs:attribute name="count" type="xs:int" use="required"/>   </xs:complexType> </xs:element>

element AlignmentType/feature_source_list/source

diagram
namespace	http://www.systemsbiology.org/apml
properties	isRef  0 minOcc  1 maxOcc  unbounded content  complex
attributes	Name   Type   Use   Default   Fixed   annotation id xs:nonNegativeInteger optional         location xs:anyURI required
source	<xs:element name="source" maxOccurs="unbounded">   <xs:complexType>     <xs:attribute name="id" type="xs:nonNegativeInteger" use="optional"/>     <xs:attribute name="location" type="xs:anyURI" use="required"/>   </xs:complexType> </xs:element>

element AlignmentType/aligned_features

diagram
namespace	http://www.systemsbiology.org/apml
properties	isRef  0 content  complex
children	aligned_feature
attributes	Name   Type   Use   Default   Fixed   annotation count xs:nonNegativeInteger required
source	<xs:element name="aligned_features">   <xs:complexType>     <xs:sequence>       <xs:element name="aligned_feature" maxOccurs="unbounded">         <xs:annotation>           <xs:documentation>An aligned feature.</xs:documentation>         </xs:annotation>         <xs:complexType>           <xs:complexContent>             <xs:extension base="AlignedFeatureType"/>           </xs:complexContent>         </xs:complexType>       </xs:element>     </xs:sequence>     <xs:attribute name="count" type="xs:nonNegativeInteger" use="required"/>   </xs:complexType> </xs:element>

element AlignmentType/aligned_features/aligned_feature

diagram
namespace	http://www.systemsbiology.org/apml
type	extension of AlignedFeatureType
properties	isRef  0 minOcc  1 maxOcc  unbounded content  complex
children	coordinate features ppids
attributes	Name   Type   Use   Default   Fixed   annotation id xs:nonNegativeInteger required
annotation	documentation An aligned feature.
source	<xs:element name="aligned_feature" maxOccurs="unbounded">   <xs:annotation>     <xs:documentation>An aligned feature.</xs:documentation>   </xs:annotation>   <xs:complexType>     <xs:complexContent>       <xs:extension base="AlignedFeatureType"/>     </xs:complexContent>   </xs:complexType> </xs:element>

complexType ClusterProfileType

diagram
namespace	http://www.systemsbiology.org/apml
children	profile_data
used by	element  apml/data/cluster_profile
attributes	Name   Type   Use   Default   Fixed   annotation id xs:nonNegativeInteger
annotation	documentation Collection of any type of intensity profile over series of dilution samples or time course samples
source	<xs:complexType name="ClusterProfileType">   <xs:annotation>     <xs:documentation>Collection of any type of intensity profile over series of dilution samples or time course samples</xs:documentation>   </xs:annotation>   <xs:sequence>     <xs:element name="profile_data" maxOccurs="unbounded">       <xs:complexType>         <xs:sequence>           <xs:element name="clusters" type="ClusterType" maxOccurs="unbounded"/>         </xs:sequence>         <xs:attribute name="id" type="xs:nonNegativeInteger" use="required"/>         <xs:attribute name="abundance" type="xs:float" use="required"/>       </xs:complexType>     </xs:element>   </xs:sequence>   <xs:attribute name="id" type="xs:nonNegativeInteger"/> </xs:complexType>

element ClusterProfileType/profile_data

diagram
namespace	http://www.systemsbiology.org/apml
properties	isRef  0 minOcc  1 maxOcc  unbounded content  complex
children	clusters
attributes	Name   Type   Use   Default   Fixed   annotation id xs:nonNegativeInteger required         abundance xs:float required
source	<xs:element name="profile_data" maxOccurs="unbounded">   <xs:complexType>     <xs:sequence>       <xs:element name="clusters" type="ClusterType" maxOccurs="unbounded"/>     </xs:sequence>     <xs:attribute name="id" type="xs:nonNegativeInteger" use="required"/>     <xs:attribute name="abundance" type="xs:float" use="required"/>   </xs:complexType> </xs:element>

element ClusterProfileType/profile_data/clusters

diagram
namespace	http://www.systemsbiology.org/apml
type	ClusterType
properties	isRef  0 minOcc  1 maxOcc  unbounded content  complex
children	cluster
source	<xs:element name="clusters" type="ClusterType" maxOccurs="unbounded"/>

complexType ClusterType

diagram
namespace	http://www.systemsbiology.org/apml
children	cluster
used by	element  ClusterProfileType/profile_data/clusters
annotation	documentation Collection of "feature" or "aligned_feature" references
source	<xs:complexType name="ClusterType">   <xs:annotation>     <xs:documentation>Collection of "feature" or "aligned_feature" references</xs:documentation>   </xs:annotation>   <xs:sequence>     <xs:element name="cluster" maxOccurs="unbounded">       <xs:complexType>         <xs:sequence>           <xs:element name="reference" maxOccurs="unbounded">             <xs:complexType>               <xs:attribute name="ref_element_id" type="xs:nonNegativeInteger" use="required"/>             </xs:complexType>           </xs:element>         </xs:sequence>         <xs:attribute name="id" type="xs:nonNegativeInteger" use="required"/>         <xs:attribute name="classification" type="xs:string" use="required"/>         <xs:attribute name="ref_element" type="xs:string" use="required"/>         <xs:attribute name="count" type="xs:nonNegativeInteger" use="required"/>       </xs:complexType>     </xs:element>   </xs:sequence> </xs:complexType>

element ClusterType/cluster

diagram
namespace	http://www.systemsbiology.org/apml
properties	isRef  0 minOcc  1 maxOcc  unbounded content  complex
children	reference
attributes	Name   Type   Use   Default   Fixed   annotation id xs:nonNegativeInteger required         classification xs:string required         ref_element xs:string required         count xs:nonNegativeInteger required
source	<xs:element name="cluster" maxOccurs="unbounded">   <xs:complexType>     <xs:sequence>       <xs:element name="reference" maxOccurs="unbounded">         <xs:complexType>           <xs:attribute name="ref_element_id" type="xs:nonNegativeInteger" use="required"/>         </xs:complexType>       </xs:element>     </xs:sequence>     <xs:attribute name="id" type="xs:nonNegativeInteger" use="required"/>     <xs:attribute name="classification" type="xs:string" use="required"/>     <xs:attribute name="ref_element" type="xs:string" use="required"/>     <xs:attribute name="count" type="xs:nonNegativeInteger" use="required"/>   </xs:complexType> </xs:element>

element ClusterType/cluster/reference

diagram
namespace	http://www.systemsbiology.org/apml
properties	isRef  0 minOcc  1 maxOcc  unbounded content  complex
attributes	Name   Type   Use   Default   Fixed   annotation ref_element_id xs:nonNegativeInteger required
source	<xs:element name="reference" maxOccurs="unbounded">   <xs:complexType>     <xs:attribute name="ref_element_id" type="xs:nonNegativeInteger" use="required"/>   </xs:complexType> </xs:element>

complexType CoordinateType

diagram
namespace	http://www.systemsbiology.org/apml
children	scan_range time_range mz_range
used by	elements  AlignedFeatureType/coordinate FeatureType/coordinate
attributes	Name   Type   Use   Default   Fixed   annotation mz xs:float required         rt xs:float required         intensity xs:float optional         charge xs:int required         mass xs:float required         apex_intensity xs:float optional         apex_scan xs:nonNegativeInteger optional
annotation	documentation Base definition for a feature / signal coordinate.
source	<xs:complexType name="CoordinateType">   <xs:annotation>     <xs:documentation>Base definition for a feature / signal coordinate.</xs:documentation>   </xs:annotation>   <xs:sequence>     <xs:element name="scan_range" minOccurs="0">       <xs:complexType>         <xs:attribute name="min" type="xs:nonNegativeInteger" use="required"/>         <xs:attribute name="max" type="xs:nonNegativeInteger" use="required"/>       </xs:complexType>     </xs:element>     <xs:element name="time_range" minOccurs="0">       <xs:complexType>         <xs:attribute name="min" type="xs:float" use="required"/>         <xs:attribute name="max" type="xs:float" use="required"/>       </xs:complexType>     </xs:element>     <xs:element name="mz_range" minOccurs="0">       <xs:complexType>         <xs:attribute name="min" type="xs:double" use="required"/>         <xs:attribute name="max" type="xs:double" use="required"/>       </xs:complexType>     </xs:element>   </xs:sequence>   <xs:attribute name="mz" type="xs:float" use="required"/>   <xs:attribute name="rt" type="xs:float" use="required"/>   <xs:attribute name="intensity" type="xs:float" use="optional"/>   <xs:attribute name="charge" type="xs:int" use="required"/>   <xs:attribute name="mass" type="xs:float" use="required"/>   <xs:attribute name="apex_intensity" type="xs:float" use="optional"/>   <xs:attribute name="apex_scan" type="xs:nonNegativeInteger" use="optional"/> </xs:complexType>

element CoordinateType/scan_range

diagram
namespace	http://www.systemsbiology.org/apml
properties	isRef  0 minOcc  0 maxOcc  1 content  complex
attributes	Name   Type   Use   Default   Fixed   annotation min xs:nonNegativeInteger required         max xs:nonNegativeInteger required
source	<xs:element name="scan_range" minOccurs="0">   <xs:complexType>     <xs:attribute name="min" type="xs:nonNegativeInteger" use="required"/>     <xs:attribute name="max" type="xs:nonNegativeInteger" use="required"/>   </xs:complexType> </xs:element>

element CoordinateType/time_range

diagram
namespace	http://www.systemsbiology.org/apml
properties	isRef  0 minOcc  0 maxOcc  1 content  complex
attributes	Name   Type   Use   Default   Fixed   annotation min xs:float required         max xs:float required
source	<xs:element name="time_range" minOccurs="0">   <xs:complexType>     <xs:attribute name="min" type="xs:float" use="required"/>     <xs:attribute name="max" type="xs:float" use="required"/>   </xs:complexType> </xs:element>

element CoordinateType/mz_range

diagram
namespace	http://www.systemsbiology.org/apml
properties	isRef  0 minOcc  0 maxOcc  1 content  complex
attributes	Name   Type   Use   Default   Fixed   annotation min xs:double required         max xs:double required
source	<xs:element name="mz_range" minOccurs="0">   <xs:complexType>     <xs:attribute name="min" type="xs:double" use="required"/>     <xs:attribute name="max" type="xs:double" use="required"/>   </xs:complexType> </xs:element>

complexType dataType

diagram
namespace	http://www.systemsbiology.org/apml
used by	element  elution_profileType/elution_data
attributes	Name   Type   Use   Default   Fixed   annotation rt xs:float required
source	<xs:complexType name="dataType">   <xs:attribute name="rt" type="xs:float" use="required"/> </xs:complexType>

complexType elution_profileType

diagram
namespace	http://www.systemsbiology.org/apml
children	elution_data
used by	element  FeatureType/elution_profile
attributes	Name   Type   Use   Default   Fixed   annotation count xs:nonNegativeInteger required
source	<xs:complexType name="elution_profileType">   <xs:sequence>     <xs:element name="elution_data" maxOccurs="unbounded">       <xs:complexType>         <xs:complexContent>           <xs:extension base="dataType">             <xs:attribute name="intensity" type="xs:float"/>           </xs:extension>         </xs:complexContent>       </xs:complexType>     </xs:element>   </xs:sequence>   <xs:attribute name="count" type="xs:nonNegativeInteger" use="required"/> </xs:complexType>

element elution_profileType/elution_data

diagram
namespace	http://www.systemsbiology.org/apml
type	extension of dataType
properties	isRef  0 minOcc  1 maxOcc  unbounded content  complex
attributes	Name   Type   Use   Default   Fixed   annotation rt xs:float required         intensity xs:float
source	<xs:element name="elution_data" maxOccurs="unbounded">   <xs:complexType>     <xs:complexContent>       <xs:extension base="dataType">         <xs:attribute name="intensity" type="xs:float"/>       </xs:extension>     </xs:complexContent>   </xs:complexType> </xs:element>

complexType FeatureType

diagram
namespace	http://www.systemsbiology.org/apml
children	coordinate ppids elution_profile
used by	elements  PeakListType/peak_list/features/feature AlignedFeatureType/features/feature
annotation	documentation Feature identified from an LCMS run.
source	<xs:complexType name="FeatureType">   <xs:annotation>     <xs:documentation>Feature identified from an LCMS run.</xs:documentation>   </xs:annotation>   <xs:sequence>     <xs:element name="coordinate">       <xs:annotation>         <xs:documentation>Coordinate for the processed feature.</xs:documentation>       </xs:annotation>       <xs:complexType>         <xs:complexContent>           <xs:extension base="CoordinateType"/>         </xs:complexContent>       </xs:complexType>     </xs:element>     <xs:element name="ppids" minOccurs="0">       <xs:annotation>         <xs:documentation>Collection of putative feature identifications.</xs:documentation>       </xs:annotation>       <xs:complexType>         <xs:complexContent>           <xs:extension base="PpidCollectionType">             <xs:attribute name="count" type="xs:nonNegativeInteger" use="required"/>           </xs:extension>         </xs:complexContent>       </xs:complexType>     </xs:element>     <xs:element name="elution_profile" type="elution_profileType" minOccurs="0"/>   </xs:sequence> </xs:complexType>

element FeatureType/coordinate

diagram
namespace	http://www.systemsbiology.org/apml
type	extension of CoordinateType
properties	isRef  0 content  complex
children	scan_range time_range mz_range
attributes	Name   Type   Use   Default   Fixed   annotation mz xs:float required         rt xs:float required         intensity xs:float optional         charge xs:int required         mass xs:float required         apex_intensity xs:float optional         apex_scan xs:nonNegativeInteger optional
annotation	documentation Coordinate for the processed feature.
source	<xs:element name="coordinate">   <xs:annotation>     <xs:documentation>Coordinate for the processed feature.</xs:documentation>   </xs:annotation>   <xs:complexType>     <xs:complexContent>       <xs:extension base="CoordinateType"/>     </xs:complexContent>   </xs:complexType> </xs:element>

element FeatureType/ppids

diagram
namespace	http://www.systemsbiology.org/apml
type	extension of PpidCollectionType
properties	isRef  0 minOcc  0 maxOcc  1 content  complex
children	ppid
attributes	Name   Type   Use   Default   Fixed   annotation count xs:nonNegativeInteger required
annotation	documentation Collection of putative feature identifications.
source	<xs:element name="ppids" minOccurs="0">   <xs:annotation>     <xs:documentation>Collection of putative feature identifications.</xs:documentation>   </xs:annotation>   <xs:complexType>     <xs:complexContent>       <xs:extension base="PpidCollectionType">         <xs:attribute name="count" type="xs:nonNegativeInteger" use="required"/>       </xs:extension>     </xs:complexContent>   </xs:complexType> </xs:element>

element FeatureType/elution_profile

diagram
namespace	http://www.systemsbiology.org/apml
type	elution_profileType
properties	isRef  0 minOcc  0 maxOcc  1 content  complex
children	elution_data
attributes	Name   Type   Use   Default   Fixed   annotation count xs:nonNegativeInteger required
source	<xs:element name="elution_profile" type="elution_profileType" minOccurs="0"/>

complexType PeakListType

diagram
namespace	http://www.systemsbiology.org/apml
children	peak_list
used by	element  apml/data/peak_lists
annotation	documentation Collection of feature picked LCMS runs.
source	<xs:complexType name="PeakListType">   <xs:annotation>     <xs:documentation>Collection of feature picked LCMS runs.</xs:documentation>   </xs:annotation>   <xs:sequence>     <xs:element name="peak_list" maxOccurs="unbounded">       <xs:complexType>         <xs:sequence>           <xs:element name="features">             <xs:annotation>               <xs:documentation>Collection of LCMS features.</xs:documentation>             </xs:annotation>             <xs:complexType>               <xs:sequence>                 <xs:element name="feature" maxOccurs="unbounded">                   <xs:complexType>                     <xs:complexContent>                       <xs:extension base="FeatureType">                         <xs:attribute name="id" type="xs:nonNegativeInteger" use="required"/>                       </xs:extension>                     </xs:complexContent>                   </xs:complexType>                 </xs:element>               </xs:sequence>               <xs:attribute name="count" type="xs:nonNegativeInteger" use="required"/>             </xs:complexType>           </xs:element>         </xs:sequence>         <xs:attribute name="source" type="xs:anyURI" use="required">           <xs:annotation>             <xs:documentation>reference to the mzXML file from which this msrun was generated.</xs:documentation>           </xs:annotation>         </xs:attribute>       </xs:complexType>     </xs:element>   </xs:sequence> </xs:complexType>

element PeakListType/peak_list

diagram
namespace	http://www.systemsbiology.org/apml
properties	isRef  0 minOcc  1 maxOcc  unbounded content  complex
children	features
attributes	Name   Type   Use   Default   Fixed   annotation source xs:anyURI required         documentation reference to the mzXML file from which this msrun was generated.
source	<xs:element name="peak_list" maxOccurs="unbounded">   <xs:complexType>     <xs:sequence>       <xs:element name="features">         <xs:annotation>           <xs:documentation>Collection of LCMS features.</xs:documentation>         </xs:annotation>         <xs:complexType>           <xs:sequence>             <xs:element name="feature" maxOccurs="unbounded">               <xs:complexType>                 <xs:complexContent>                   <xs:extension base="FeatureType">                     <xs:attribute name="id" type="xs:nonNegativeInteger" use="required"/>                   </xs:extension>                 </xs:complexContent>               </xs:complexType>             </xs:element>           </xs:sequence>           <xs:attribute name="count" type="xs:nonNegativeInteger" use="required"/>         </xs:complexType>       </xs:element>     </xs:sequence>     <xs:attribute name="source" type="xs:anyURI" use="required">       <xs:annotation>         <xs:documentation>reference to the mzXML file from which this msrun was generated.</xs:documentation>       </xs:annotation>     </xs:attribute>   </xs:complexType> </xs:element>

element PeakListType/peak_list/features

diagram
namespace	http://www.systemsbiology.org/apml
properties	isRef  0 content  complex
children	feature
attributes	Name   Type   Use   Default   Fixed   annotation count xs:nonNegativeInteger required
annotation	documentation Collection of LCMS features.
source	<xs:element name="features">   <xs:annotation>     <xs:documentation>Collection of LCMS features.</xs:documentation>   </xs:annotation>   <xs:complexType>     <xs:sequence>       <xs:element name="feature" maxOccurs="unbounded">         <xs:complexType>           <xs:complexContent>             <xs:extension base="FeatureType">               <xs:attribute name="id" type="xs:nonNegativeInteger" use="required"/>             </xs:extension>           </xs:complexContent>         </xs:complexType>       </xs:element>     </xs:sequence>     <xs:attribute name="count" type="xs:nonNegativeInteger" use="required"/>   </xs:complexType> </xs:element>

element PeakListType/peak_list/features/feature

diagram
namespace	http://www.systemsbiology.org/apml
type	extension of FeatureType
properties	isRef  0 minOcc  1 maxOcc  unbounded content  complex
children	coordinate ppids elution_profile
attributes	Name   Type   Use   Default   Fixed   annotation id xs:nonNegativeInteger required
source	<xs:element name="feature" maxOccurs="unbounded">   <xs:complexType>     <xs:complexContent>       <xs:extension base="FeatureType">         <xs:attribute name="id" type="xs:nonNegativeInteger" use="required"/>       </xs:extension>     </xs:complexContent>   </xs:complexType> </xs:element>

complexType PpidCollectionType

diagram
namespace	http://www.systemsbiology.org/apml
children	ppid
used by	elements  AlignedFeatureType/ppids FeatureType/ppids
annotation	documentation Collection of putative feature identifications.
source	<xs:complexType name="PpidCollectionType">   <xs:annotation>     <xs:documentation>Collection of putative feature identifications.</xs:documentation>   </xs:annotation>   <xs:sequence>     <xs:element name="ppid" maxOccurs="unbounded">       <xs:annotation>         <xs:documentation>Putative peptide/feature identification.</xs:documentation>       </xs:annotation>       <xs:complexType>         <xs:sequence>           <xs:element name="dta" type="xs:string">             <xs:annotation>               <xs:documentation>Relative path to the dta file.</xs:documentation>             </xs:annotation>           </xs:element>           <xs:element name="search_score" minOccurs="0" maxOccurs="unbounded">             <xs:complexType>               <xs:attribute name="name" type="xs:string" use="required"/>               <xs:attribute name="value" type="xs:anySimpleType" use="required"/>               <xs:attribute name="type" type="xs:anySimpleType"/>             </xs:complexType>           </xs:element>           <xs:element name="peptide_sequence" type="xs:string">             <xs:annotation>               <xs:documentation>Single character alias for peptide amino acid sequence.</xs:documentation>             </xs:annotation>           </xs:element>           <xs:element name="proteins" minOccurs="0">             <xs:complexType>               <xs:sequence maxOccurs="unbounded">                 <xs:element name="protein" maxOccurs="unbounded">                   <xs:complexType>                     <xs:attribute name="accession_num" type="xs:string" use="required"/>                   </xs:complexType>                 </xs:element>               </xs:sequence>             </xs:complexType>           </xs:element>           <xs:element name="modifications" minOccurs="0">             <xs:complexType>               <xs:sequence>                 <xs:element name="modification" maxOccurs="unbounded">                   <xs:complexType>                     <xs:attribute name="position" type="xs:integer" use="required"/>                     <xs:attribute name="value" type="xs:float" use="required"/>                   </xs:complexType>                 </xs:element>               </xs:sequence>             </xs:complexType>           </xs:element>         </xs:sequence>         <xs:attribute name="ms2_scan_num" type="xs:int" use="required"/>         <xs:attribute name="precursor_mz" type="xs:float" use="required"/>         <xs:attribute name="theoretical_mz" type="xs:float" use="optional"/>         <xs:attribute name="charge" type="xs:integer" use="required"/>         <xs:attribute name="previous_aa" type="xs:string" use="optional"/>       </xs:complexType>     </xs:element>   </xs:sequence> </xs:complexType>

element PpidCollectionType/ppid

diagram
namespace	http://www.systemsbiology.org/apml
properties	isRef  0 minOcc  1 maxOcc  unbounded content  complex
children	dta search_score peptide_sequence proteins modifications
attributes	Name   Type   Use   Default   Fixed   annotation ms2_scan_num xs:int required         precursor_mz xs:float required         theoretical_mz xs:float optional         charge xs:integer required         previous_aa xs:string optional
annotation	documentation Putative peptide/feature identification.
source	<xs:element name="ppid" maxOccurs="unbounded">   <xs:annotation>     <xs:documentation>Putative peptide/feature identification.</xs:documentation>   </xs:annotation>   <xs:complexType>     <xs:sequence>       <xs:element name="dta" type="xs:string">         <xs:annotation>           <xs:documentation>Relative path to the dta file.</xs:documentation>         </xs:annotation>       </xs:element>       <xs:element name="search_score" minOccurs="0" maxOccurs="unbounded">         <xs:complexType>           <xs:attribute name="name" type="xs:string" use="required"/>           <xs:attribute name="value" type="xs:anySimpleType" use="required"/>           <xs:attribute name="type" type="xs:anySimpleType"/>         </xs:complexType>       </xs:element>       <xs:element name="peptide_sequence" type="xs:string">         <xs:annotation>           <xs:documentation>Single character alias for peptide amino acid sequence.</xs:documentation>         </xs:annotation>       </xs:element>       <xs:element name="proteins" minOccurs="0">         <xs:complexType>           <xs:sequence maxOccurs="unbounded">             <xs:element name="protein" maxOccurs="unbounded">               <xs:complexType>                 <xs:attribute name="accession_num" type="xs:string" use="required"/>               </xs:complexType>             </xs:element>           </xs:sequence>         </xs:complexType>       </xs:element>       <xs:element name="modifications" minOccurs="0">         <xs:complexType>           <xs:sequence>             <xs:element name="modification" maxOccurs="unbounded">               <xs:complexType>                 <xs:attribute name="position" type="xs:integer" use="required"/>                 <xs:attribute name="value" type="xs:float" use="required"/>               </xs:complexType>             </xs:element>           </xs:sequence>         </xs:complexType>       </xs:element>     </xs:sequence>     <xs:attribute name="ms2_scan_num" type="xs:int" use="required"/>     <xs:attribute name="precursor_mz" type="xs:float" use="required"/>     <xs:attribute name="theoretical_mz" type="xs:float" use="optional"/>     <xs:attribute name="charge" type="xs:integer" use="required"/>     <xs:attribute name="previous_aa" type="xs:string" use="optional"/>   </xs:complexType> </xs:element>

element PpidCollectionType/ppid/dta

diagram
namespace	http://www.systemsbiology.org/apml
type	xs:string
properties	isRef  0 content  simple
annotation	documentation Relative path to the dta file.
source	<xs:element name="dta" type="xs:string">   <xs:annotation>     <xs:documentation>Relative path to the dta file.</xs:documentation>   </xs:annotation> </xs:element>

element PpidCollectionType/ppid/search_score

diagram
namespace	http://www.systemsbiology.org/apml
properties	isRef  0 minOcc  0 maxOcc  unbounded content  complex
attributes	Name   Type   Use   Default   Fixed   annotation name xs:string required         value xs:anySimpleType required         type xs:anySimpleType
source	<xs:element name="search_score" minOccurs="0" maxOccurs="unbounded">   <xs:complexType>     <xs:attribute name="name" type="xs:string" use="required"/>     <xs:attribute name="value" type="xs:anySimpleType" use="required"/>     <xs:attribute name="type" type="xs:anySimpleType"/>   </xs:complexType> </xs:element>

element PpidCollectionType/ppid/peptide_sequence

diagram
namespace	http://www.systemsbiology.org/apml
type	xs:string
properties	isRef  0 content  simple
annotation	documentation Single character alias for peptide amino acid sequence.
source	<xs:element name="peptide_sequence" type="xs:string">   <xs:annotation>     <xs:documentation>Single character alias for peptide amino acid sequence.</xs:documentation>   </xs:annotation> </xs:element>

element PpidCollectionType/ppid/proteins

diagram
namespace	http://www.systemsbiology.org/apml
properties	isRef  0 minOcc  0 maxOcc  1 content  complex
children	protein
source	<xs:element name="proteins" minOccurs="0">   <xs:complexType>     <xs:sequence maxOccurs="unbounded">       <xs:element name="protein" maxOccurs="unbounded">         <xs:complexType>           <xs:attribute name="accession_num" type="xs:string" use="required"/>         </xs:complexType>       </xs:element>     </xs:sequence>   </xs:complexType> </xs:element>

element PpidCollectionType/ppid/proteins/protein

diagram
namespace	http://www.systemsbiology.org/apml
properties	isRef  0 minOcc  1 maxOcc  unbounded content  complex
attributes	Name   Type   Use   Default   Fixed   annotation accession_num xs:string required
source	<xs:element name="protein" maxOccurs="unbounded">   <xs:complexType>     <xs:attribute name="accession_num" type="xs:string" use="required"/>   </xs:complexType> </xs:element>

element PpidCollectionType/ppid/modifications

diagram
namespace	http://www.systemsbiology.org/apml
properties	isRef  0 minOcc  0 maxOcc  1 content  complex
children	modification
source	<xs:element name="modifications" minOccurs="0">   <xs:complexType>     <xs:sequence>       <xs:element name="modification" maxOccurs="unbounded">         <xs:complexType>           <xs:attribute name="position" type="xs:integer" use="required"/>           <xs:attribute name="value" type="xs:float" use="required"/>         </xs:complexType>       </xs:element>     </xs:sequence>   </xs:complexType> </xs:element>

element PpidCollectionType/ppid/modifications/modification

diagram
namespace	http://www.systemsbiology.org/apml
properties	isRef  0 minOcc  1 maxOcc  unbounded content  complex
attributes	Name   Type   Use   Default   Fixed   annotation position xs:integer required         value xs:float required
source	<xs:element name="modification" maxOccurs="unbounded">   <xs:complexType>     <xs:attribute name="position" type="xs:integer" use="required"/>     <xs:attribute name="value" type="xs:float" use="required"/>   </xs:complexType> </xs:element>

complexType SoftwareType

diagram
namespace	http://www.systemsbiology.org/apml
children	software
used by	element  apml/dataProcessing
annotation	documentation Software which processed LCMS either alignment or peak_picking process
source	<xs:complexType name="SoftwareType">   <xs:annotation>     <xs:documentation>Software which processed LCMS either alignment or peak_picking process</xs:documentation>   </xs:annotation>   <xs:sequence>     <xs:element name="software">       <xs:complexType>         <xs:attribute name="name" type="xs:string" use="required">           <xs:annotation>             <xs:documentation>Name of the software used.</xs:documentation>           </xs:annotation>         </xs:attribute>         <xs:attribute name="type" use="required">           <xs:annotation>             <xs:documentation>alignment: softare that aligns multiple LCMS runs. analysis: softare that applies some interpetation of the data. peakpicking: selects LCMS signals of importance. transformation: changes to this document instance by either insertion, deletion, or modification.</xs:documentation>           </xs:annotation>           <xs:simpleType>             <xs:restriction base="xs:string">               <xs:enumeration value="alignment"/>               <xs:enumeration value="peak_picking"/>             </xs:restriction>           </xs:simpleType>         </xs:attribute>         <xs:attribute name="version" type="xs:string" use="optional">           <xs:annotation>             <xs:documentation>Version of the software used.</xs:documentation>           </xs:annotation>         </xs:attribute>       </xs:complexType>     </xs:element>   </xs:sequence> </xs:complexType>

element SoftwareType/software

diagram
namespace	http://www.systemsbiology.org/apml
properties	isRef  0 content  complex
attributes	Name   Type   Use   Default   Fixed   annotation name xs:string required         documentation Name of the software used. type derived by: xs:string required         documentation alignment: softare that aligns multiple LCMS runs. analysis: softare that applies some interpetation of the data. peakpicking: selects LCMS signals of importance. transformation: changes to this document instance by either insertion, deletion, or modification. version xs:string optional         documentation Version of the software used.
source	<xs:element name="software">   <xs:complexType>     <xs:attribute name="name" type="xs:string" use="required">       <xs:annotation>         <xs:documentation>Name of the software used.</xs:documentation>       </xs:annotation>     </xs:attribute>     <xs:attribute name="type" use="required">       <xs:annotation>         <xs:documentation>alignment: softare that aligns multiple LCMS runs. analysis: softare that applies some interpetation of the data. peakpicking: selects LCMS signals of importance. transformation: changes to this document instance by either insertion, deletion, or modification.</xs:documentation>       </xs:annotation>       <xs:simpleType>         <xs:restriction base="xs:string">           <xs:enumeration value="alignment"/>           <xs:enumeration value="peak_picking"/>         </xs:restriction>       </xs:simpleType>     </xs:attribute>     <xs:attribute name="version" type="xs:string" use="optional">       <xs:annotation>         <xs:documentation>Version of the software used.</xs:documentation>       </xs:annotation>     </xs:attribute>   </xs:complexType> </xs:element>

XML Schema documentation generated by XMLSpy Schema Editor http://www.altova.com/xmlspy