Documentation for POML

Table of Contents

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Schema Document Properties

Target Namespace None
Element and Attribute Namespaces
  • Global element and attribute declarations belong to this schema's target namespace.
  • By default, local element declarations have no namespace.
  • By default, local attribute declarations have no namespace.
Documentation Proteomic Objects Markup Language schema.

Declared Namespaces

Prefix Namespace
xml http://www.w3.org/XML/1998/namespace
xs http://www.w3.org/2001/XMLSchema
Schema Component Representation
<xs:schema>
...
</xs:schema>
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Global Declarations

Element: project

Name project
Type Project
Nillable no
Abstract no
Logical Diagram
XML Instance Representation
<project
name=" xs:string [0..1]"
author=" xs:string [0..1]"
date=" xs:date [0..1]"
description=" xs:string [0..1]">
<experiment_2DE-MS> Experiment_2DEMS </experiment_2DE-MS> [0..*]
<experiment_LC-MS> Experiment_LCMS </experiment_LC-MS> [0..*]
</project>
Diagram
h-1089254180 h1351109946
Schema Component Representation
<xs:element name="project" type=" Project "/>
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Global Definitions

Complex Type: Category

Super-types: None
Sub-types: None
Name Category
Used by (from the same schema document) Complex Type Experiment_2DEMS
Abstract no
Documentation Category of gels matched sets (e.g., normal, treated, diseased).
XML Instance Representation
<...
name=" xs:string [1]"
description=" xs:string [0..1]">
<gel> Gel </gel> [1..*]
</...>
Diagram
h-676026199
Schema Component Representation
<xs:complexType name="Category">
<xs:sequence>
<xs:element name="gel" type=" Gel " minOccurs="1" maxOccurs="unbounded"/>
</xs:sequence>
<xs:attribute name="name" type=" xs:string " use="required"/>
<xs:attribute name="description" type=" xs:string " use="optional"/>
</xs:complexType>
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Complex Type: Experiment_2DEMS

Super-types: None
Sub-types: None
Name Experiment_2DEMS
Used by (from the same schema document) Complex Type Project
Abstract no
Documentation 2-Dimensional Electrophoresis - Mass Spectrometry (2DE-MS) experiment.
XML Instance Representation
<...
name=" xs:string [0..1]"
description=" xs:string [0..1]">
<proteomic_step> Step </proteomic_step> [0..*]
<category> Category </category> [1..*]
</...>
Diagram
h518396113 h1201685635
Schema Component Representation
<xs:complexType name="Experiment_2DEMS">
<xs:sequence>
<xs:element name="proteomic_step" type=" Step " minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="category" type=" Category " minOccurs="1" maxOccurs="unbounded"/>
</xs:sequence>
<xs:attribute name="name" type=" xs:string " use="optional"/>
<xs:attribute name="description" type=" xs:string " use="optional"/>
</xs:complexType>
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Complex Type: Experiment_LCMS

Super-types: None
Sub-types: None
Name Experiment_LCMS
Used by (from the same schema document) Complex Type Project
Abstract no
Documentation Liquid Chromatography - Mass Spectrometry (LC-MS) experiment.
XML Instance Representation
<...
name=" xs:string [0..1]"
description=" xs:string [0..1]">
<proteomic_step> Step </proteomic_step> [0..*]
<peptides> Peptides </peptides> [0..*]
<proteins> Proteins </proteins> [0..*]
</...>
Diagram
h518396113 h1537815751 h161718485
Schema Component Representation
<xs:complexType name="Experiment_LCMS">
<xs:sequence>
<xs:element name="proteomic_step" type=" Step " minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="peptides" type=" Peptides " minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="proteins" type=" Proteins " minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
<xs:attribute name="name" type=" xs:string " use="optional"/>
<xs:attribute name="description" type=" xs:string " use="optional"/>
</xs:complexType>
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Complex Type: Feature

Super-types: None
Sub-types: None
Name Feature
Used by (from the same schema document) Complex Type Features_set
Abstract no
Documentation A proteomic feature is a value assigned to a proteomic object during a proteomic step.
XML Instance Representation
<...
name=" xs:string [1]"
description=" xs:string [0..1]">
Start Choice [1]
<num_discrete> ND_Feature </num_discrete> [1]
<num_continuous> NC_Feature </num_continuous> [1]
<text> T_Feature </text> [1]
End Choice
</...>
Diagram
h-1568633998 h238820465 h864055078
Schema Component Representation
<xs:complexType name="Feature">
<xs:choice>
<xs:element name="num_discrete" type=" ND_Feature " minOccurs="1" maxOccurs="1"/>
<xs:element name="num_continuous" type=" NC_Feature " minOccurs="1" maxOccurs="1"/>
<xs:element name="text" type=" T_Feature " minOccurs="1" maxOccurs="1"/>
</xs:choice>
<xs:attribute name="name" type=" xs:string " use="required"/>
<xs:attribute name="description" type=" xs:string " use="optional"/>
</xs:complexType>
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Complex Type: Features_set

Super-types: None
Sub-types: None
Name Features_set
Used by (from the same schema document) Complex Type Proteomic_object
Abstract no
Documentation Group of proteomic features.
XML Instance Representation
<...
proteomic_step=" xs:string [1]">
<feature> Feature </feature> [1..*]
</...>
Diagram
h-249336111
Schema Component Representation
<xs:complexType name="Features_set">
<xs:sequence>
<xs:element name="feature" type=" Feature " minOccurs="1" maxOccurs="unbounded"/>
</xs:sequence>
<xs:attribute name="proteomic_step" type=" xs:string " use="required"/>
<-- Edw tha prepei na yparxoun kapoies default times, opws "Data generation", "Differential analysis" klp. -->
</xs:complexType>
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Complex Type: Gel

Super-types: None
Sub-types: None
Name Gel
Used by (from the same schema document) Complex Type Category
Abstract no
Documentation 2-Dimensional Electrophoresis Gel.
XML Instance Representation
<...
id=" xs:string [1]"
description=" xs:string [0..1]"
reference=" xs:boolean [0..1]">
<proteomic_object> Proteomic_object </proteomic_object> [1..*]
</...>
Diagram
h668950477
Schema Component Representation
<xs:complexType name="Gel">
<xs:sequence>
<xs:element name="proteomic_object" type=" Proteomic_object " minOccurs="1" maxOccurs="unbounded"/>
</xs:sequence>
<xs:attribute name="id" type=" xs:string " use="required"/>
<xs:attribute name="description" type=" xs:string " use="optional"/>
<xs:attribute name="reference" type=" xs:boolean " use="optional"/>
</xs:complexType>
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Complex Type: NC_Feature

Super-types: None
Sub-types: None
Name NC_Feature
Used by (from the same schema document) Complex Type Feature
Abstract no
Documentation Numerical Continuous feature.
XML Instance Representation
<...
value=" xs:double [1]"/>
Diagram
Schema Component Representation
<xs:complexType name="NC_Feature">
<xs:attribute name="value" type=" xs:double " use="required"/>
</xs:complexType>
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Complex Type: ND_Feature

Super-types: None
Sub-types: None
Name ND_Feature
Used by (from the same schema document) Complex Type Feature
Abstract no
Documentation Numerical Discrete feature.
XML Instance Representation
<...
value=" xs:integer [1]"/>
Diagram
Schema Component Representation
<xs:complexType name="ND_Feature">
<xs:attribute name="value" type=" xs:integer " use="required"/>
</xs:complexType>
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Complex Type: Parameter

Super-types: None
Sub-types: None
Name Parameter
Used by (from the same schema document) Complex Type Step
Abstract no
Documentation A parameter of a proteomic step (e.g., instrument, software, resolution, method).
XML Instance Representation
<...
name=" xs:string [1]"
value=" xs:string [1]"/>
Diagram
Schema Component Representation
<xs:complexType name="Parameter">
<xs:attribute name="name" type=" xs:string " use="required"/>
<xs:attribute name="value" type=" xs:string " use="required"/>
</xs:complexType>
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Complex Type: Peptides

Super-types: None
Sub-types: None
Name Peptides
Used by (from the same schema document) Complex Type Experiment_LCMS
Abstract no
Documentation Group of peptides identified by an LC-MS expriment.
XML Instance Representation
<...
name=" xs:string [0..1]"
description=" xs:string [0..1]">
<proteomic_object> Proteomic_object </proteomic_object> [1..*]
</...>
Diagram
h668950477
Schema Component Representation
<xs:complexType name="Peptides">
<xs:sequence>
<xs:element name="proteomic_object" type=" Proteomic_object " minOccurs="1" maxOccurs="unbounded"/>
</xs:sequence>
<xs:attribute name="name" type=" xs:string " use="optional"/>
<xs:attribute name="description" type=" xs:string " use="optional"/>
</xs:complexType>
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Complex Type: Project

Super-types: None
Sub-types: None
Name Project
Used by (from the same schema document) Element project
Abstract no
Documentation Proteomics project.
XML Instance Representation
<...
name=" xs:string [0..1]"
author=" xs:string [0..1]"
date=" xs:date [0..1]"
description=" xs:string [0..1]">
<experiment_2DE-MS> Experiment_2DEMS </experiment_2DE-MS> [0..*]
<experiment_LC-MS> Experiment_LCMS </experiment_LC-MS> [0..*]
</...>
Diagram
h-1089254180 h1351109946
Schema Component Representation
<xs:complexType name="Project">
<xs:sequence>
<xs:element name="experiment_2DE-MS" type=" Experiment_2DEMS " minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="experiment_LC-MS" type=" Experiment_LCMS " minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
<xs:attribute name="name" type=" xs:string " use="optional"/>
<xs:attribute name="author" type=" xs:string " use="optional"/>
<xs:attribute name="date" type=" xs:date " use="optional"/>
<xs:attribute name="description" type=" xs:string " use="optional"/>
</xs:complexType>
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Complex Type: Proteins

Super-types: None
Sub-types: None
Name Proteins
Used by (from the same schema document) Complex Type Experiment_LCMS
Abstract no
Documentation Group of proteins identified by an LC-MS expriment.
XML Instance Representation
<...
name=" xs:string [0..1]"
description=" xs:string [0..1]">
<proteomic_object> Proteomic_object </proteomic_object> [1..*]
</...>
Diagram
h668950477
Schema Component Representation
<xs:complexType name="Proteins">
<xs:sequence>
<xs:element name="proteomic_object" type=" Proteomic_object " minOccurs="1" maxOccurs="unbounded"/>
</xs:sequence>
<xs:attribute name="name" type=" xs:string " use="optional"/>
<xs:attribute name="description" type=" xs:string " use="optional"/>
</xs:complexType>
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Complex Type: Proteomic_object

Super-types: None
Sub-types: None
Name Proteomic_object
Used by (from the same schema document) Complex Type Gel , Complex Type Proteins , Complex Type Peptides
Abstract no
Documentation Proteomic object can be a spot, a protein or a peptide.
XML Instance Representation
<...
id=" xs:string [1]">
<features_set> Features_set </features_set> [1..*]
</...>
Diagram
h1828169317
Schema Component Representation
<xs:complexType name="Proteomic_object">
<xs:sequence>
<xs:element name="features_set" type=" Features_set " minOccurs="1" maxOccurs="unbounded"/>
</xs:sequence>
<xs:attribute name="id" type=" xs:string " use="required"/>
</xs:complexType>
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Complex Type: Step

Super-types: None
Sub-types: None
Name Step
Used by (from the same schema document) Complex Type Experiment_2DEMS , Complex Type Experiment_LCMS
Abstract no
Documentation Step of a proteomics analysis workflow (e.g., Data generation, Differential analysis, Identification, Metadata analysis).
XML Instance Representation
<...
name=" xs:string [1]">
<parameter> Parameter </parameter> [1..*]
</...>
Diagram
h-1013834556
Schema Component Representation
<xs:complexType name="Step">
<xs:sequence>
<xs:element name="parameter" type=" Parameter " minOccurs="1" maxOccurs="unbounded"/>
</xs:sequence>
<xs:attribute name="name" type=" xs:string " use="required"/>
</xs:complexType>
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Complex Type: T_Feature

Super-types: None
Sub-types: None
Name T_Feature
Used by (from the same schema document) Complex Type Feature
Abstract no
Documentation Text feature.
XML Instance Representation
<...
value=" xs:string [1]"/>
Diagram
Schema Component Representation
<xs:complexType name="T_Feature">
<xs:attribute name="value" type=" xs:string " use="required"/>
</xs:complexType>
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