Target Namespace | http://www.phyloxml.org |
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Element and Attribute Namespaces |
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Documentation | phyloXML is an XML language to describe phylogenies and associated data. Version: 1.00. License: LGPL. Copyright (c) 2008-2009 Christian M Zmasek. |
Prefix | Namespace |
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xml | http://www.w3.org/XML/1998/namespace |
phy | http://www.phyloxml.org |
xs | http://www.w3.org/2001/XMLSchema |
Name | phyloxml |
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Type | phy:Phyloxml |
Nillable | no |
Abstract | no |
Super-types: | xs:token < Accession (by extension) |
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Sub-types: | None |
Name | Accession |
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Used by (from the same schema document) | Complex Type Sequence |
Abstract | no |
Documentation | Element Accession is used to capture the local part in a sequence identifier (e.g. 'P17304' in 'UniProtKB:P17304', in which case the 'source' attribute would be 'UniProtKB'). |
Super-types: | None |
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Sub-types: | None |
Name | Annotation |
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Used by (from the same schema document) | Complex Type Sequence |
Abstract | no |
Documentation | The annotation of a molecular sequence. It is recommended to annotate by using the optional 'ref' attribute (some examples of acceptable values for the ref attribute: 'GO:0008270', 'KEGG:Tetrachloroethene degradation', 'EC:1.1.1.1'). Optional element 'desc' allows for a free text description. Optional element 'confidence' is used to state the type and value of support for a annotation. Similarly, optional attribute 'evidence' is used to describe the evidence for a annotation as free text (e.g. 'experimental'). Optional element 'property' allows for further, typed and referenced annotations from external resources. |
Super-types: | None |
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Sub-types: | None |
Name | BinaryCharacterList |
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Used by (from the same schema document) | Complex Type BinaryCharacters , Complex Type BinaryCharacters , Complex Type BinaryCharacters , Complex Type BinaryCharacters |
Abstract | no |
Super-types: | None |
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Sub-types: | None |
Name | BinaryCharacters |
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Used by (from the same schema document) | Complex Type Clade |
Abstract | no |
Documentation | The names and/or counts of binary characters present, gained, and lost at the root of a clade. |
Super-types: | None |
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Sub-types: | None |
Name | BranchColor |
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Used by (from the same schema document) | Complex Type Clade |
Abstract | no |
Documentation | This indicates the color of a clade when rendered (the color applies to the whole clade unless overwritten by the color(s) of sub clades). |
Super-types: | None |
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Sub-types: | None |
Name | Clade |
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Used by (from the same schema document) | Complex Type Phylogeny , Complex Type Clade |
Abstract | no |
Documentation | Element Clade is used in a recursive manner to describe the topology of a phylogenetic tree. The parent branch length of a clade can be described either with the 'branch_length' element or the 'branch_length' attribute (it is not recommended to use both at the same time, though). Usage of the 'branch_length' attribute allows for a less verbose description. Element 'confidence' is used to indicate the support for a clade/parent branch. Element 'events' is used to describe such events as gene-duplications at the root node/parent branch of a clade. Element 'width' is the branch width for this clade (including parent branch). Both 'color' and 'width' elements apply for the whole clade unless overwritten in-sub clades. Attribute 'id_source' is used to link other elements to a clade (on the xml-level). |
Super-types: | None |
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Sub-types: | None |
Name | CladeRelation |
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Used by (from the same schema document) | Complex Type Phylogeny |
Abstract | no |
Documentation | This is used to express a typed relationship between two clades. For example it could be used to describe multiple parents of a clade. |
Super-types: | xs:double < Confidence (by extension) |
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Sub-types: | None |
Name | Confidence |
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Used by (from the same schema document) | Complex Type Phylogeny , Complex Type Clade , Complex Type Events , Complex Type Annotation , Complex Type SequenceRelation , Complex Type CladeRelation |
Abstract | no |
Documentation | A general purpose confidence element. For example this can be used to express the bootstrap support value of a clade (in which case the 'type' attribute is 'bootstrap'). |
Super-types: | None |
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Sub-types: | None |
Name | Date |
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Used by (from the same schema document) | Complex Type Clade |
Abstract | no |
Documentation | A date associated with a clade/node. Its value can be numerical by using the 'value' element and/or free text with the 'desc' element' (e.g. 'Silurian'). If a numerical value is used, it is recommended to employ the 'unit' attribute to indicate the type of the numerical value (e.g. 'mya' for 'million years ago'). |
Super-types: | None |
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Sub-types: | None |
Name | Distribution |
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Used by (from the same schema document) | Complex Type Clade |
Abstract | no |
Documentation | The geographic distribution of the items of a clade (species, sequences), intended for phylogeographic applications. The location can be described either by free text in the 'desc' element and/or by the coordinates of one or more 'Points' (similar to the 'Point' element in Google's KML format) or by 'Polygons'. |
Super-types: | None |
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Sub-types: | None |
Name | DomainArchitecture |
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Used by (from the same schema document) | Complex Type Sequence |
Abstract | no |
Documentation | This is used describe the domain architecture of a protein. Attribute 'length' is the total length of the protein |
Super-types: | None |
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Sub-types: | None |
Name | Events |
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Used by (from the same schema document) | Complex Type Clade |
Abstract | no |
Documentation | Events at the root node of a clade (e.g. one gene duplication). |
Super-types: | xs:token < Id (by extension) |
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Sub-types: | None |
Name | Id |
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Used by (from the same schema document) | Complex Type Phylogeny , Complex Type Clade , Complex Type Taxonomy |
Abstract | no |
Documentation | A general purpose identifier element. Allows to indicate the type (or source) of an identifier. |
Super-types: | None |
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Sub-types: | None |
Name | Phylogeny |
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Used by (from the same schema document) | Complex Type Phyloxml |
Abstract | no |
Documentation | Element Phylogeny is used to represent a phylogeny. The required attribute 'rooted' is used to indicate whether the phylogeny is rooted or not. The attribute 'rerootable' can be used to indicate that the phylogeny is not allowed to be rooted differently (i.e. because it is associated with root dependent data, such as gene duplications). The attribute 'type' can be used to indicate the type of phylogeny (i.e. 'gene tree'). It is recommended to use the attribute 'branch_length_unit' if the phylogeny has branch lengths. Element clade is used in a recursive manner to describe the topology of a phylogenetic tree. |
Super-types: | None |
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Sub-types: | None |
Name | Phyloxml |
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Used by (from the same schema document) | Element phyloxml |
Abstract | no |
Documentation | 'phyloxml' is the name of the root element. Phyloxml contains an arbitrary number of 'phylogeny' elements (each representing one phylogeny) possibly followed by elements from other namespaces. |
Super-types: | None |
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Sub-types: | None |
Name | Point |
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Used by (from the same schema document) | Complex Type Distribution , Complex Type Polygon |
Abstract | no |
Documentation | The coordinates of a point with an optional altitude (used by element 'Distribution'). Required attribute 'geodetic_datum' is used to indicate the geodetic datum (also called 'map datum'), for example Google's KML uses 'WGS84'. |
Super-types: | None |
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Sub-types: | None |
Name | Polygon |
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Used by (from the same schema document) | Complex Type Distribution |
Abstract | no |
Documentation | A polygon defined by a list of 'Points' (used by element 'Distribution'). |
Super-types: | None |
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Sub-types: | None |
Name | Property |
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Used by (from the same schema document) | Complex Type Phylogeny , Complex Type Clade , Complex Type Annotation |
Abstract | no |
Documentation | Property allows for typed and referenced properties from external resources to be attached to 'Phylogeny', 'Clade', and 'Annotation'. The value of a property is its mixed (free text) content. Attribute 'datatype' indicates the type of a property and is limited to xsd-datatypes (e.g. 'xsd:string', 'xsd:boolean', 'xsd:integer', 'xsd:decimal', 'xsd:float', 'xsd:double', 'xsd:date', 'xsd:anyURI'). Attribute 'applies_to' indicates the item to which a property applies to (e.g. 'node' for the parent node of a clade, 'parent_branch' for the parent branch of a clade). Attribute 'id_ref' allows to attached a property specifically to one element (on the xml-level). Optional attribute 'unit' is used to indicate the unit of the property. An example: <property datatype="xsd:integer" ref="NOAA:depth" applies_to="clade" unit="METRIC:m"> 200 </property> |
Super-types: | xs:token < ProteinDomain (by extension) |
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Sub-types: | None |
Name | ProteinDomain |
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Used by (from the same schema document) | Complex Type DomainArchitecture |
Abstract | no |
Documentation | To represent an individual domain in a domain architecture. The name/unique identifier is described via the 'id' attribute. 'confidence' can be used to store (i.e.) E-values. |
Super-types: | None |
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Sub-types: | None |
Name | Reference |
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Used by (from the same schema document) | Complex Type Clade |
Abstract | no |
Documentation | A literature reference for a clade. It is recommended to use the 'doi' attribute instead of the free text 'desc' element whenever possible. |
Super-types: | None |
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Sub-types: | None |
Name | Sequence |
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Used by (from the same schema document) | Complex Type Clade |
Abstract | no |
Documentation | Element Sequence is used to represent a molecular sequence (Protein, DNA, RNA) associated with a node. 'symbol' is a short (maximal ten characters) symbol of the sequence (e.g. 'ACTM') whereas 'name' is used for the full name (e.g. 'muscle Actin'). 'location' is used for the location of a sequence on a genome/chromosome. The actual sequence can be stored with the 'mol_seq' element. Attribute 'type' is used to indicate the type of sequence ('dna', 'rna', or 'aa'). One intended use for 'id_ref' is to link a sequence to a taxonomy (via the taxonomy's 'id_source') in case of multiple sequences and taxonomies per node. |
Super-types: | None |
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Sub-types: | None |
Name | SequenceRelation |
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Used by (from the same schema document) | Complex Type Phylogeny |
Abstract | no |
Documentation | This is used to express a typed relationship between two sequences. For example it could be used to describe an orthology (in which case attribute 'type' is 'orthology'). |
Super-types: | None |
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Sub-types: | None |
Name | Taxonomy |
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Used by (from the same schema document) | Complex Type Clade |
Abstract | no |
Documentation | Element Taxonomy is used to describe taxonomic information for a clade. Element 'code' is intended to store UniProt/Swiss-Prot style organism codes (e.g. 'APLCA' for the California sea hare 'Aplysia californica'). Element 'id' is used for a unique identifier of a taxon (for example '6500' with 'ncbi_taxonomy' as 'type' for the California sea hare). Attribute 'id_source' is used to link other elements to a taxonomy (on the xml-level). |
Super-types: | xs:anyURI < Uri (by extension) |
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Sub-types: | None |
Name | Uri |
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Used by (from the same schema document) | Complex Type Taxonomy , Complex Type Sequence , Complex Type Annotation |
Abstract | no |
Documentation | A uniform resource identifier. In general, this is expected to be an URL (for example, to link to an image on a website, in which case the 'type' attribute might be 'image' and 'desc' might be 'image of a California sea hare'). |
Super-types: | xs:token < AppliesTo (by restriction) |
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Sub-types: | None |
Name | AppliesTo |
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Used by (from the same schema document) | Complex Type Property |
Content |
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Super-types: | xs:token < Doi (by restriction) |
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Sub-types: | None |
Name | Doi |
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Used by (from the same schema document) | Complex Type Reference |
Content |
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Super-types: | xs:token < EventType (by restriction) |
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Sub-types: | None |
Name | EventType |
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Used by (from the same schema document) | Complex Type Events |
Content |
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Super-types: | xs:token < MolSeq (by restriction) |
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Sub-types: | None |
Name | MolSeq |
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Used by (from the same schema document) | Complex Type Sequence |
Content |
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Super-types: | xs:token < PropertyDataType (by restriction) |
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Sub-types: | None |
Name | PropertyDataType |
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Used by (from the same schema document) | Complex Type Property |
Content |
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Super-types: | xs:token < Rank (by restriction) |
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Sub-types: | None |
Name | Rank |
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Used by (from the same schema document) | Complex Type Taxonomy |
Content |
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Super-types: | xs:token < SequenceRelationType (by restriction) |
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Sub-types: | None |
Name | SequenceRelationType |
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Used by (from the same schema document) | Complex Type SequenceRelation |
Content |
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Super-types: | xs:token < SequenceSymbol (by restriction) |
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Sub-types: | None |
Name | SequenceSymbol |
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Used by (from the same schema document) | Complex Type Sequence |
Content |
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Super-types: | xs:token < SequenceType (by restriction) |
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Sub-types: | None |
Name | SequenceType |
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Used by (from the same schema document) | Complex Type Sequence |
Content |
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Super-types: | xs:token < TaxonomyCode (by restriction) |
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Sub-types: | None |
Name | TaxonomyCode |
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Used by (from the same schema document) | Complex Type Taxonomy |
Content |
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Super-types: | xs:IDREF < id_ref (by restriction) |
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Sub-types: | None |
Name | id_ref |
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Used by (from the same schema document) | Complex Type Sequence , Complex Type Property , Complex Type SequenceRelation , Complex Type SequenceRelation , Complex Type CladeRelation , Complex Type CladeRelation |
Content |
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Super-types: | xs:ID < id_source (by restriction) |
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Sub-types: | None |
Name | id_source |
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Used by (from the same schema document) | Complex Type Clade , Complex Type Taxonomy , Complex Type Sequence |
Content |
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Super-types: | xs:token < ref (by restriction) |
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Sub-types: | None |
Name | ref |
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Used by (from the same schema document) | Complex Type Annotation , Complex Type Property , Complex Type Property |
Content |
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Super-types: | Address < AusAddress (by extension) |
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Sub-types: |
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Name | AusAddress |
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Abstract | no |
The XML Instance Representation table above shows the schema component's content as an XML instance.
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.