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phylogenetic data in xml

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nexml is an exchange standard for representing phylogenetic data — inspired by the commonly used NEXUS format, but more robust and easier to process.

Schema module documentation

~ / nexml / html / doc / schema-1 / characters / rna

| Tue Dec 16 16:26:28 2008 —

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 of the <cell> element, whose value-space is limited to the IUPAC single character nucleotide symbols (except T). 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. In this implementation there is no reference to explicitly defined states, as we use the IUPAC standard. There may be a CodonPosition ("codon") attribute, and there must be an identifier ("id") that is of type xs:nonNegativeInteger to define the column number.

Inheritance

RNAChar restricts AbstractChar.

Attributes

Name	Type	Usage
tokens	MSTokenLength	prohibited
states	xs:NCName	prohibited
codon	CodonPosition	optional
id	xs:NCName	required

Substructures

an element called "dict", instance of Dict (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="dict" type="Dict"/>
        </xs:sequence>
        <xs:attribute name="tokens" type="MSTokenLength" use="prohibited"/>
        <xs:attribute name="states" type="xs:NCName" use="prohibited"/>
        <xs:attribute name="codon" type="CodonPosition" use="optional"/>
        <xs:attribute name="id" type="xs:NCName" 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 "char", instance of RNAChar (1..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="char" type="RNAChar"/>
        </xs:sequence>
      </xs:restriction>
    </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 "dict", instance of Dict (0..unbounded).
an element called "cell", instance of RNAObs (1..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="dict" type="Dict"/>
          <xs:element maxOccurs="unbounded" minOccurs="1" name="cell" type="RNAObs"/>
        </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 "dict", instance of Dict (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="dict" type="Dict"/>
          <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 a nucleotide observation.

Inheritance

RNAObs restricts AbstractObs.

Attributes

Name	Type	Usage
char	xs:nonNegativeInteger	required
state	RNAToken	required

Substructures

an element called "dict", instance of Dict (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="dict" type="Dict"/>
        </xs:sequence>
        <xs:attribute name="char" type="xs:nonNegativeInteger" use="required"/>
        <xs:attribute name="state" type="RNAToken" 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).

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:sequence>
      </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).

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:sequence>
      </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 "dict", instance of Dict (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="dict" type="Dict"/>
          <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 "dict", instance of Dict (0..unbounded).
an element called "format", instance of RNAFormat (0..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="dict" type="Dict"/>
          <xs:element maxOccurs="1" minOccurs="0" 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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nexml schema 1.0 ~/nexml/xsd/characters/rna.xsd

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The future data exchange standard is here!

Schema module documentation

Description

Complex types

RNAChar

Description

Inheritance

Attributes

Substructures

Definition source

RNAFormat

Description

Inheritance

Substructures

Definition source

RNAMatrixObsRow

Description

Inheritance

Substructures

Definition source

RNAMatrixSeqRow

Description

Inheritance

Substructures

Definition source

RNAObs

Description

Inheritance

Attributes

Substructures

Definition source

RNAObsMatrix

Description

Inheritance

Substructures

Definition source

RNASeqMatrix

Description

Inheritance

Substructures

Definition source

RnaCells

Description

Inheritance

Substructures

Definition source

RnaSeqs

Description

Inheritance

Substructures

Definition source

Simple types

RNASeq

Description

Inheritance

Facets

Definition source

RNAToken

Description

Inheritance

Facets

Definition source

See also

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