Documentation for OME Schemas

Target Namespace	http://www.openmicroscopy.org/Schemas/SA/2008-09
Version	1
Element and Attribute Namespaces	Global element and attribute declarations belong to this schema's target namespace. By default, local element declarations belong to this schema's target namespace. By default, local attribute declarations have no namespace.
Schema Composition	This schema imports schema(s) from the following namespace(s): http://www.openmicroscopy.org/Schemas/OME/2008-09 (at http://www.openmicroscopy.org/Schemas/OME/2008-09/ome.xsd) http://www.openmicroscopy.org/Schemas/BinaryFile/2008-09 (at http://www.openmicroscopy.org/Schemas/BinaryFile/2008-09/BinaryFile.xsd)

Prefix	Namespace
Default namespace	http://www.openmicroscopy.org/Schemas/SA/2008-09
Bin	http://www.openmicroscopy.org/Schemas/BinaryFile/2008-09
xml	http://www.w3.org/XML/1998/namespace
xsd	http://www.w3.org/2001/XMLSchema
OME	http://www.openmicroscopy.org/Schemas/OME/2008-09

Schema Component Representation

<xsd:schema targetNamespace="http://www.openmicroscopy.org/Schemas/SA/2008-09" version="1" elementFormDefault="qualified">

<xsd:import namespace="http://www.openmicroscopy.org/Schemas/OME/2008-09" schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2008-09/ome.xsd"/>

<xsd:import namespace="http://www.openmicroscopy.org/Schemas/BinaryFile/2008-09" schemaLocation="http://www.openmicroscopy.org/Schemas/BinaryFile/2008-09/BinaryFile.xsd"/>

...

</xsd:schema>

Name	BooleanAnnotation
Used by (from the same schema document)	Element StructuredAnnotations
Type	Locally-defined complex type
Nillable	no
Abstract	no

XML Instance Representation

<Link> ... </Link> [1..*]

<Value> xsd:boolean </Value> [1]

</BooleanAnnotation>

Schema Component Representation

<xsd:element name="BooleanAnnotation">

<-- top level definition -->

<xsd:complexType>

<xsd:complexContent>

<xsd:extension base=" CommonAnnotation ">

<xsd:sequence>

<xsd:element name="Value" type=" xsd:boolean " minOccurs="1" maxOccurs="1"/>

</xsd:sequence>

</xsd:extension>

</xsd:complexContent>

</xsd:complexType>

</xsd:element>

Name	DoubleAnnotation
Used by (from the same schema document)	Element StructuredAnnotations
Type	Locally-defined complex type
Nillable	no
Abstract	no

XML Instance Representation

<Link> ... </Link> [1..*]

<Value> xsd:double </Value> [1]

</DoubleAnnotation>

Schema Component Representation

<xsd:element name="DoubleAnnotation">

<-- top level definition -->

<xsd:complexType>

<xsd:complexContent>

<xsd:extension base=" CommonAnnotation ">

<xsd:sequence>

<xsd:element name="Value" type=" xsd:double " minOccurs="1" maxOccurs="1"/>

</xsd:sequence>

</xsd:extension>

</xsd:complexContent>

</xsd:complexType>

</xsd:element>

Name	FileAnnotation
Used by (from the same schema document)	Element StructuredAnnotations
Type	Locally-defined complex type
Nillable	no
Abstract	no

XML Instance Representation

<Link> ... </Link> [1..*]

<FileName> ... </FileName> [1]

<MimeType> OME:MIMEtype </MimeType> [0..1]

Start Choice [1]

<Bin:BinData> ... </Bin:BinData> [1]

<ExternalFile> xsd:string </ExternalFile> [1]

End Choice
</FileAnnotation>

Schema Component Representation

<xsd:element name="FileAnnotation">

<-- top level definition -->

<xsd:complexType>

<xsd:complexContent>

<xsd:extension base=" CommonAnnotation ">

<xsd:sequence>

<xsd:element name="FileName" minOccurs="1" maxOccurs="1"/>

<xsd:element name="MimeType" type=" OME:MIMEtype " minOccurs="0" maxOccurs="1"/>

<xsd:choice minOccurs="1" maxOccurs="1">

<xsd:element ref=" Bin:BinData " minOccurs="1" maxOccurs="1"/>

<xsd:element name="ExternalFile" type=" xsd:string " minOccurs="1" maxOccurs="1"/>

</xsd:choice>

</xsd:sequence>

</xsd:extension>

</xsd:complexContent>

</xsd:complexType>

</xsd:element>

Name	Link
Used by (from the same schema document)	Complex Type CommonAnnotation , Element ListAnnotation
Type	Locally-defined simple type
Nillable	no
Abstract	no

XML Instance Representation

Schema Component Representation

<xsd:element name="Link">

<-- top level definition -->

<xsd:simpleType>

<xsd:restriction base=" OME:LSID "/>

</xsd:simpleType>

</xsd:element>

Name	ListAnnotation
Used by (from the same schema document)	Element StructuredAnnotations
Type	Locally-defined complex type
Nillable	no
Abstract	no

XML Instance Representation

<Link> ... </Link> [1..*]

<List> [1]

<Link> ... </Link> [1..*]

</List>

</ListAnnotation>

Schema Component Representation

<xsd:element name="ListAnnotation">

<-- top level definition -->

<xsd:complexType>

<xsd:complexContent>

<xsd:extension base=" CommonAnnotation ">

<xsd:sequence>

<xsd:element name="List" minOccurs="1" maxOccurs="1">

<xsd:complexType>

<xsd:sequence>

<xsd:element ref=" Link " minOccurs="1" maxOccurs="unbounded"/>

</xsd:sequence>

</xsd:complexType>

</xsd:element>

</xsd:sequence>

</xsd:extension>

</xsd:complexContent>

</xsd:complexType>

</xsd:element>

Name	LongAnnotation
Used by (from the same schema document)	Element StructuredAnnotations
Type	Locally-defined complex type
Nillable	no
Abstract	no

XML Instance Representation

<Link> ... </Link> [1..*]

<Value> xsd:long </Value> [1]

</LongAnnotation>

Schema Component Representation

<xsd:element name="LongAnnotation">

<-- top level definition -->

<xsd:complexType>

<xsd:complexContent>

<xsd:extension base=" CommonAnnotation ">

<xsd:sequence>

<xsd:element name="Value" type=" xsd:long " minOccurs="1" maxOccurs="1"/>

</xsd:sequence>

</xsd:extension>

</xsd:complexContent>

</xsd:complexType>

</xsd:element>

Name	StringAnnotation
Used by (from the same schema document)	Element StructuredAnnotations
Type	Locally-defined complex type
Nillable	no
Abstract	no

XML Instance Representation

<Link> ... </Link> [1..*]

<Value> xsd:string </Value> [1]

</StringAnnotation>

Schema Component Representation

<xsd:element name="StringAnnotation">

<-- top level definition -->

<xsd:complexType>

<xsd:complexContent>

<xsd:extension base=" CommonAnnotation ">

<xsd:sequence>

<xsd:element name="Value" type=" xsd:string " minOccurs="1" maxOccurs="1"/>

</xsd:sequence>

</xsd:extension>

</xsd:complexContent>

</xsd:complexType>

</xsd:element>

Name	StructuredAnnotations
Type	Locally-defined complex type
Nillable	no
Abstract	no

XML Instance Representation

<StructuredAnnotations>
Start Choice [0..*]

<XmlAnnotation> ... </XmlAnnotation> [1]

<FileAnnotation> ... </FileAnnotation> [1]

<ListAnnotation> ... </ListAnnotation> [1]

<LongAnnotation> ... </LongAnnotation> [1]

<DoubleAnnotation> ... </DoubleAnnotation> [1]

<StringAnnotation> ... </StringAnnotation> [1]

<BooleanAnnotation> ... </BooleanAnnotation> [1]

<TimestampAnnotation> ... </TimestampAnnotation> [1]

End Choice
</StructuredAnnotations>

Schema Component Representation

<xsd:element name="StructuredAnnotations">

<-- top level definition -->

<xsd:complexType>

<xsd:choice minOccurs="0" maxOccurs="unbounded">

<xsd:element ref=" XmlAnnotation " minOccurs="1" maxOccurs="1"/>

<xsd:element ref=" FileAnnotation " minOccurs="1" maxOccurs="1"/>

<xsd:element ref=" ListAnnotation " minOccurs="1" maxOccurs="1"/>

<xsd:element ref=" LongAnnotation " minOccurs="1" maxOccurs="1"/>

<xsd:element ref=" DoubleAnnotation " minOccurs="1" maxOccurs="1"/>

<xsd:element ref=" StringAnnotation " minOccurs="1" maxOccurs="1"/>

<xsd:element ref=" BooleanAnnotation " minOccurs="1" maxOccurs="1"/>

<xsd:element ref=" TimestampAnnotation " minOccurs="1" maxOccurs="1"/>

</xsd:choice>

</xsd:complexType>

</xsd:element>

Name	TimestampAnnotation
Used by (from the same schema document)	Element StructuredAnnotations
Type	Locally-defined complex type
Nillable	no
Abstract	no

XML Instance Representation

<Link> ... </Link> [1..*]

<Value> xsd:dateTime </Value> [1]

</TimestampAnnotation>

Schema Component Representation

<xsd:element name="TimestampAnnotation">

<-- top level definition -->

<xsd:complexType>

<xsd:complexContent>

<xsd:extension base=" CommonAnnotation ">

<xsd:sequence>

<xsd:element name="Value" type=" xsd:dateTime " minOccurs="1" maxOccurs="1"/>

</xsd:sequence>

</xsd:extension>

</xsd:complexContent>

</xsd:complexType>

</xsd:element>

Name	XmlAnnotation
Used by (from the same schema document)	Element StructuredAnnotations
Type	Locally-defined complex type
Nillable	no
Abstract	no

XML Instance Representation

<Link> ... </Link> [1..*]

<Value> [1]

Allow any elements from any namespace (lax validation). [0..*]

</Value>

</XmlAnnotation>

Schema Component Representation

<xsd:element name="XmlAnnotation">

<-- top level definition -->

<xsd:complexType>

<xsd:complexContent>

<xsd:extension base=" CommonAnnotation ">

<xsd:sequence>

<xsd:element name="Value" minOccurs="1" maxOccurs="1">

<xsd:complexType>

<xsd:sequence>

<xsd:any processContents="lax" minOccurs="0" maxOccurs="unbounded"/>

</xsd:sequence>

</xsd:complexType>

</xsd:element>

</xsd:sequence>

</xsd:extension>

</xsd:complexContent>

</xsd:complexType>

</xsd:element>

Super-types:	None
Sub-types:	None

Name	CommonAnnotation
Abstract	yes

XML Instance Representation

<...
ID=" AnnotationID [1]"
Namespace=" xsd:anyURI [1]">

<Link> ... </Link> [1..*]

</...>

Schema Component Representation

<xsd:complexType name="CommonAnnotation" abstract="true">

<xsd:sequence>

<xsd:element ref=" Link " minOccurs="1" maxOccurs="unbounded"/>

</xsd:sequence>

<xsd:attribute name="ID" type=" AnnotationID " use="required"/>

<xsd:attribute name="Namespace" type=" xsd:anyURI " use="required"/>

</xsd:complexType>

Super-types:	OME:LSID < AnnotationID (by restriction)
Sub-types:	None

Name	AnnotationID
Used by (from the same schema document)	Complex Type CommonAnnotation
Content	Base XSD Type: string pattern = (urn:lsid:([\w\-\.]+\.[\w\-\.]+)+:\S+:\S+)\|(\S+:\S+) pattern = (urn:lsid:([\w\-\.]+\.[\w\-\.]+)+:Annotation:\S+)\|(Annotation:\S+)

Schema Component Representation

<xsd:simpleType name="AnnotationID">

<xsd:restriction base=" OME:LSID ">

<xsd:pattern value="(urn:lsid:([\w\-\.]+\.[\w\-\.]+)+:Annotation:\S+)|(Annotation:\S+)"/>

</xsd:restriction>

</xsd:simpleType>

Legend

Complex Type:

Schema Component Type

AusAddress

Schema Component Name

Super-types:	Address < AusAddress (by extension)
Sub-types:	QLDAddress (by restriction)

If this schema component is a type definition, its type hierarchy is shown in a gray-bordered box.

Name	AusAddress
Abstract	no

The table above displays the properties of this schema component.

XML Instance Representation

<... country="Australia" >
<unitNo> string </unitNo> [0..1]
<houseNo> string </houseNo> [1]
<street> string </street> [1]
Start Choice [1]
<city> string </city> [1]
<town> string </town> [1]
End Choice
<state> AusStates </state> [1]
<postcode> string <<pattern = [1-9][0-9]{3}>> </postcode> [1] ?
</...>

The XML Instance Representation table above shows the schema component's content as an XML instance.

The minimum and maximum occurrence of elements and attributes are provided in square brackets, e.g. [0..1].
Model group information are shown in gray, e.g. Start Choice ... End Choice.
For type derivations, the elements and attributes that have been added to or changed from the base type's content are shown in bold.
If an element/attribute has a fixed value, the fixed value is shown in green, e.g. country="Australia".
Otherwise, the type of the element/attribute is displayed.
- If the element/attribute's type is in the schema, a link is provided to it.
- For local simple type definitions, the constraints are displayed in angle brackets, e.g. <<pattern = [1-9][0-9]{3}>>.
If a local element/attribute has documentation, it will be displayed in a window that pops up when the question mark inside the attribute or next to the element is clicked, e.g. <postcode>.

Schema Component Representation

The Schema Component Representation table above displays the underlying XML representation of the schema component. (Annotations are not shown.)

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Glossary

Abstract (Applies to complex type definitions and element declarations). An abstract element or complex type cannot used to validate an element instance. If there is a reference to an abstract element, only element declarations that can substitute the abstract element can be used to validate the instance. For references to abstract type definitions, only derived types can be used.

All Model Group Child elements can be provided in any order in instances. See: http://www.w3.org/TR/xmlschema-1/#element-all.

Choice Model Group Only one from the list of child elements and model groups can be provided in instances. See: http://www.w3.org/TR/xmlschema-1/#element-choice.

Collapse Whitespace Policy Replace tab, line feed, and carriage return characters with space character (Unicode character 32). Then, collapse contiguous sequences of space characters into single space character, and remove leading and trailing space characters.

Disallowed Substitutions (Applies to element declarations). If substitution is specified, then substitution group members cannot be used in place of the given element declaration to validate element instances. If derivation methods, e.g. extension, restriction, are specified, then the given element declaration will not validate element instances that have types derived from the element declaration's type using the specified derivation methods. Normally, element instances can override their declaration's type by specifying an xsi:type attribute.

Key Constraint Like Uniqueness Constraint, but additionally requires that the specified value(s) must be provided. See: http://www.w3.org/TR/xmlschema-1/#cIdentity-constraint_Definitions.

Key Reference Constraint Ensures that the specified value(s) must match value(s) from a Key Constraint or Uniqueness Constraint. See: http://www.w3.org/TR/xmlschema-1/#cIdentity-constraint_Definitions.

Model Group Groups together element content, specifying the order in which the element content can occur and the number of times the group of element content may be repeated. See: http://www.w3.org/TR/xmlschema-1/#Model_Groups.

Nillable (Applies to element declarations). If an element declaration is nillable, instances can use the xsi:nil attribute. The xsi:nil attribute is the boolean attribute, nil, from the http://www.w3.org/2001/XMLSchema-instance namespace. If an element instance has an xsi:nil attribute set to true, it can be left empty, even though its element declaration may have required content.

Notation A notation is used to identify the format of a piece of data. Values of elements and attributes that are of type, NOTATION, must come from the names of declared notations. See: http://www.w3.org/TR/xmlschema-1/#cNotation_Declarations.

Preserve Whitespace Policy Preserve whitespaces exactly as they appear in instances.

Prohibited Derivations (Applies to type definitions). Derivation methods that cannot be used to create sub-types from a given type definition.

Prohibited Substitutions (Applies to complex type definitions). Prevents sub-types that have been derived using the specified derivation methods from validating element instances in place of the given type definition.

Replace Whitespace Policy Replace tab, line feed, and carriage return characters with space character (Unicode character 32).

Sequence Model Group Child elements and model groups must be provided in the specified order in instances. See: http://www.w3.org/TR/xmlschema-1/#element-sequence.

Substitution Group Elements that are members of a substitution group can be used wherever the head element of the substitution group is referenced.

Substitution Group Exclusions (Applies to element declarations). Prohibits element declarations from nominating themselves as being able to substitute a given element declaration, if they have types that are derived from the original element's type using the specified derivation methods.

Target Namespace The target namespace identifies the namespace that components in this schema belongs to. If no target namespace is provided, then the schema components do not belong to any namespace.

Uniqueness Constraint Ensures uniqueness of an element/attribute value, or a combination of values, within a specified scope. See: http://www.w3.org/TR/xmlschema-1/#cIdentity-constraint_Definitions.

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Documentation for OME Schemas

Table of Contents

Master schema documentation file: ome.xsd.html

Schema Document Properties

Declared Namespaces

Global Declarations

Element: BooleanAnnotation

Element: DoubleAnnotation

Element: FileAnnotation

Element: Link

Element: ListAnnotation

Element: LongAnnotation

Element: StringAnnotation

Element: StructuredAnnotations

Element: TimestampAnnotation

Element: XmlAnnotation

Global Definitions

Complex Type: CommonAnnotation

Simple Type: AnnotationID

Legend

Complex Type:

AusAddress

Glossary