[NeXML]
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NeXML is an exchange standard for representing phyloinformatic data — inspired by the commonly used NEXUS format, but more robust and easier to process.
Schema module documentation
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Description
This module defines concrete subclasses for the abstract character matrix components that all character matrices must implement. The subclasses defined here apply to RNA character data. In a verbose notation, this data is represented as the "state" attribute which references an explicit state definition. In a compact notation, the same data is represented as a sequence of tokens (whitespace is allowed but has no meaning).
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schema source
Complex types
RNAChar
Description
A concrete implementation of the AbstractChar element, i.e. a single column in an alignment.
Inheritance
RNAChar restricts AbstractChar.
Attributes
| Name | Type | Usage |
| tokens | MSTokenLength | prohibited |
| states | xs:IDREF | required |
| codon | CodonPosition | optional |
| id | xs:ID | required |
Substructures
- an element called "meta", instance of Meta (0..unbounded).
Definition source
<xs:complexType name="RNAChar" sawsdl:modelReference="http://evolutionaryontology-dev.nescent.org/cdao.owl#RNAResidueCharacter"> <xs:complexContent> <xs:restriction base="AbstractChar"> <xs:sequence maxOccurs="1" minOccurs="1"> <xs:element maxOccurs="unbounded" minOccurs="0" name="meta" type="Meta"/> </xs:sequence> <xs:attribute name="tokens" type="MSTokenLength" use="prohibited"/> <xs:attribute name="states" type="xs:IDREF" use="required"/> <xs:attribute name="codon" type="CodonPosition" use="optional"/> <xs:attribute name="id" type="xs:ID" use="required"/> </xs:restriction> </xs:complexContent> </xs:complexType>
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RNAFormat
Description
The RNAFormat class is the container of RNA column definitions.
Inheritance
RNAFormat restricts AbstractFormat.
Substructures
- an element called "states", instance of RNAStates (1..unbounded).
- an element called "char", instance of RNAChar (1..unbounded).
- an element called "set", instance of CharSet (0..unbounded).
Definition source
<xs:complexType abstract="false" name="RNAFormat"> <xs:complexContent> <xs:restriction base="AbstractFormat"> <xs:sequence maxOccurs="1" minOccurs="1"> <xs:element maxOccurs="unbounded" minOccurs="1" name="states" type="RNAStates"/> <xs:element maxOccurs="unbounded" minOccurs="1" name="char" type="RNAChar"/> <xs:element maxOccurs="unbounded" minOccurs="0" name="set" type="CharSet"/> </xs:sequence> </xs:restriction> </xs:complexContent> </xs:complexType>
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RNAMapping
Description
An IUPAC RNA ambiguity mapping.
Inheritance
RNAMapping restricts AbstractMapping.
Definition source
<xs:complexType name="RNAMapping"> <xs:complexContent> <xs:restriction base="AbstractMapping"/> </xs:complexContent> </xs:complexType>
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RNAMatrixObsRow
Description
This is a row in a matrix of RNA data containing granular observations.
Inheritance
RNAMatrixObsRow restricts AbstractObsRow.
Substructures
- an element called "meta", instance of Meta (0..unbounded).
- an element called "cell", instance of RNAObs (1..unbounded).
- an element called "set", instance of CellSet (0..unbounded).
Definition source
<xs:complexType abstract="false" name="RNAMatrixObsRow"> <xs:complexContent> <xs:restriction base="AbstractObsRow"> <xs:sequence maxOccurs="1" minOccurs="1"> <xs:element maxOccurs="unbounded" minOccurs="0" name="meta" type="Meta"/> <xs:element maxOccurs="unbounded" minOccurs="1" name="cell" type="RNAObs"/> <xs:element maxOccurs="unbounded" minOccurs="0" name="set" type="CellSet"/> </xs:sequence> </xs:restriction> </xs:complexContent> </xs:complexType>
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RNAMatrixSeqRow
Description
This is a row in a matrix of RNA data containing raw sequence data.
Inheritance
RNAMatrixSeqRow restricts AbstractSeqRow.
Substructures
- an element called "meta", instance of Meta (0..unbounded).
- an element called "seq", instance of RNASeq (1..1).
Definition source
<xs:complexType abstract="false" name="RNAMatrixSeqRow"> <xs:complexContent> <xs:restriction base="AbstractSeqRow"> <xs:sequence maxOccurs="1" minOccurs="1"> <xs:element maxOccurs="unbounded" minOccurs="0" name="meta" type="Meta"/> <xs:element maxOccurs="1" minOccurs="1" name="seq" type="RNASeq"/> </xs:sequence> </xs:restriction> </xs:complexContent> </xs:complexType>
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RNAObs
Description
This is a single cell in a matrix containing an RNA nucleotide observation.
Inheritance
RNAObs restricts AbstractObs.
Attributes
| Name | Type | Usage |
| char | xs:IDREF | required |
| state | xs:IDREF | required |
Substructures
- an element called "meta", instance of Meta (0..unbounded).
Definition source
<xs:complexType abstract="false" name="RNAObs" sawsdl:modelReference="http://evolutionaryontology-dev.nescent.org/cdao.owl#RNAResidueStateDatum"> <xs:complexContent> <xs:restriction base="AbstractObs"> <xs:sequence maxOccurs="1" minOccurs="1"> <xs:element maxOccurs="unbounded" minOccurs="0" name="meta" type="Meta"/> </xs:sequence> <xs:attribute name="char" type="xs:IDREF" use="required"/> <xs:attribute name="state" type="xs:IDREF" use="required"/> </xs:restriction> </xs:complexContent> </xs:complexType>
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RNAObsMatrix
Description
A matrix of rows with single character observations.
Inheritance
RNAObsMatrix restricts AbstractObsMatrix.
Substructures
- an element called "row", instance of RNAMatrixObsRow (1..unbounded).
- an element called "set", instance of RowSet (0..unbounded).
Definition source
<xs:complexType abstract="false" name="RNAObsMatrix"> <xs:complexContent> <xs:restriction base="AbstractObsMatrix"> <xs:sequence maxOccurs="1" minOccurs="1"> <xs:element maxOccurs="unbounded" minOccurs="1" name="row" type="RNAMatrixObsRow"/> <xs:element maxOccurs="unbounded" minOccurs="0" name="set" type="RowSet"/> </xs:sequence> </xs:restriction> </xs:complexContent> </xs:complexType>
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RNAPolymorphicStateSet
Description
The RNAPolymorphicStateSet describes a single polymorphic IUPAC ambiguity mapping.
Inheritance
RNAPolymorphicStateSet restricts AbstractPolymorphicStateSet.
Attributes
| Name | Type | Usage |
| symbol | RNAToken | required |
Substructures
- an element called "member", instance of RNAMapping (0..unbounded).
- an element called "uncertain_state_set", instance of RNAUncertainStateSet (0..unbounded).
Definition source
<xs:complexType name="RNAPolymorphicStateSet"> <xs:complexContent> <xs:restriction base="AbstractPolymorphicStateSet"> <xs:sequence maxOccurs="1" minOccurs="1"> <xs:element maxOccurs="unbounded" minOccurs="0" name="member" type="RNAMapping"/> <xs:element maxOccurs="unbounded" minOccurs="0" name="uncertain_state_set" type="RNAUncertainStateSet"/> </xs:sequence> <xs:attribute name="symbol" type="RNAToken" use="required"/> </xs:restriction> </xs:complexContent> </xs:complexType>
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RNASeqMatrix
Description
A matrix of rows with seq strings of type RNA.
Inheritance
RNASeqMatrix restricts AbstractSeqMatrix.
Substructures
- an element called "row", instance of RNAMatrixSeqRow (1..unbounded).
- an element called "set", instance of RowSet (0..unbounded).
Definition source
<xs:complexType abstract="false" name="RNASeqMatrix"> <xs:complexContent> <xs:restriction base="AbstractSeqMatrix"> <xs:sequence maxOccurs="1" minOccurs="1"> <xs:element maxOccurs="unbounded" minOccurs="1" name="row" type="RNAMatrixSeqRow"/> <xs:element maxOccurs="unbounded" minOccurs="0" name="set" type="RowSet"/> </xs:sequence> </xs:restriction> </xs:complexContent> </xs:complexType>
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RNAState
Description
This is a concrete implementation of the state element, which requires a symbol attribute, in this case restricted to RNAToken, i.e. a single IUPAC nucleotide symbol, and optional mapping elements to refer to other states.
Inheritance
RNAState restricts AbstractState.
Attributes
| Name | Type | Usage |
| symbol | RNAToken | required |
Definition source
<xs:complexType name="RNAState"> <xs:complexContent> <xs:restriction base="AbstractState"> <xs:sequence maxOccurs="1" minOccurs="1"/> <xs:attribute name="symbol" type="RNAToken" use="required"/> </xs:restriction> </xs:complexContent> </xs:complexType>
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RNAStates
Description
A container for a set of states.
Inheritance
RNAStates restricts AbstractStates.
Substructures
- an element called "meta", instance of Meta (0..unbounded).
- an element called "state", instance of RNAState (0..unbounded).
- an element called "polymorphic_state_set", instance of RNAPolymorphicStateSet (0..unbounded).
- an element called "uncertain_state_set", instance of RNAUncertainStateSet (0..unbounded).
- an element called "set", instance of StateSet (0..unbounded).
Definition source
<xs:complexType name="RNAStates"> <xs:complexContent> <xs:restriction base="AbstractStates"> <xs:sequence maxOccurs="1" minOccurs="1"> <xs:element maxOccurs="unbounded" minOccurs="0" name="meta" type="Meta"/> <xs:element maxOccurs="unbounded" minOccurs="0" name="state" type="RNAState"/> <xs:element maxOccurs="unbounded" minOccurs="0" name="polymorphic_state_set" type="RNAPolymorphicStateSet"/> <xs:element maxOccurs="unbounded" minOccurs="0" name="uncertain_state_set" type="RNAUncertainStateSet"/> <xs:element maxOccurs="unbounded" minOccurs="0" name="set" type="StateSet"/> </xs:sequence> </xs:restriction> </xs:complexContent> </xs:complexType>
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RNAUncertainStateSet
Description
The RNAUncertainStateSet describes a single uncertain IUPAC ambiguity mapping.
Inheritance
RNAUncertainStateSet restricts AbstractUncertainStateSet.
Attributes
| Name | Type | Usage |
| symbol | RNAToken | required |
Substructures
- an element called "member", instance of RNAMapping (0..unbounded).
Definition source
<xs:complexType name="RNAUncertainStateSet"> <xs:complexContent> <xs:restriction base="AbstractUncertainStateSet"> <xs:sequence maxOccurs="1" minOccurs="1"> <xs:element maxOccurs="unbounded" minOccurs="0" name="member" type="RNAMapping"/> </xs:sequence> <xs:attribute name="symbol" type="RNAToken" use="required"/> </xs:restriction> </xs:complexContent> </xs:complexType>
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RnaCells
Description
A RNA characters block consisting of granular cells preceded by metadata.
Inheritance
RnaCells restricts AbstractCells.
Substructures
- an element called "meta", instance of Meta (0..unbounded).
- an element called "format", instance of RNAFormat (0..1).
- an element called "matrix", instance of RNAObsMatrix (1..1).
Definition source
<xs:complexType abstract="false" name="RnaCells"> <xs:complexContent> <xs:restriction base="AbstractCells"> <xs:sequence maxOccurs="1" minOccurs="1"> <xs:element maxOccurs="unbounded" minOccurs="0" name="meta" type="Meta"/> <xs:element maxOccurs="1" minOccurs="0" name="format" type="RNAFormat"/> <xs:element maxOccurs="1" minOccurs="1" name="matrix" type="RNAObsMatrix"/> </xs:sequence> </xs:restriction> </xs:complexContent> </xs:complexType>
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RnaSeqs
Description
A RNA characters block consisting of sequences preceded by metadata.
Inheritance
RnaSeqs restricts AbstractSeqs.
Substructures
- an element called "meta", instance of Meta (0..unbounded).
- an element called "format", instance of RNAFormat (1..1).
- an element called "matrix", instance of RNASeqMatrix (1..1).
Definition source
<xs:complexType abstract="false" name="RnaSeqs"> <xs:complexContent> <xs:restriction base="AbstractSeqs"> <xs:sequence maxOccurs="1" minOccurs="1"> <xs:element maxOccurs="unbounded" minOccurs="0" name="meta" type="Meta"/> <xs:element maxOccurs="1" minOccurs="1" name="format" type="RNAFormat"/> <xs:element maxOccurs="1" minOccurs="1" name="matrix" type="RNASeqMatrix"/> </xs:sequence> </xs:restriction> </xs:complexContent> </xs:complexType>
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Simple types
RNASeq
Description
This is a simple type that specifies a sequence of RNA characters, following IUPAC single character symbols for nucleotides (and ambiguities).
Inheritance
RNASeq restricts AbstractSeq.
Facets
| Type | Value |
| pattern | [\-\?ABCDGHKMNRSUVWXY\s]* |
Definition source
<xs:simpleType name="RNASeq"> <xs:restriction base="AbstractSeq"> <xs:pattern value="[\-\?ABCDGHKMNRSUVWXY\s]*"/> </xs:restriction> </xs:simpleType>
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RNAToken
Description
The RNAToken simple type is a restriction of AbstractSymbol that defines a token of a IUPAC single character nucleotide token.
Inheritance
RNAToken restricts AbstractSymbol.
Facets
| Type | Value |
| pattern | [\-\?ABCDGHKMNRSUVWXY] |
| length | 1 |
Definition source
<xs:simpleType name="RNAToken"> <xs:restriction base="AbstractSymbol"> <xs:pattern value="[\-\?ABCDGHKMNRSUVWXY]"/> <xs:length value="1"/> </xs:restriction> </xs:simpleType>
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See also
~/nexml/xsd/characters/rna.xsd includes the following other files:
~/nexml/xsd/characters/rna.xsd is included in:
This page summarizes the contents of schema file "~/nexml/xsd/characters/rna.xsd". Generated on Tue Sep 23 12:49:34 2014.