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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 / protein

| 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 amino acid 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. 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

AAChar

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 must be an identifier ("id") that is of type xs:nonNegativeInteger to define the column number.

Inheritance

AAChar restricts AbstractChar.

Attributes

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

Substructures

an element called "dict", instance of Dict (0..unbounded).

Definition source

  <xs:complexType name="AAChar" sawsdl:modelReference="http://evolutionaryontology-dev.nescent.org/cdao.owl#AminoAcidResidueCharacter">
    <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="prohibited"/>
        <xs:attribute name="id" type="xs:NCName" use="required"/>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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AAFormat

Description

The AAFormat class is the container of amino acid column definitions.

Inheritance

AAFormat restricts AbstractFormat.

Substructures

an element called "char", instance of AAChar (1..unbounded).

Definition source

  <xs:complexType abstract="false" name="AAFormat">
    <xs:complexContent>
      <xs:restriction base="AbstractFormat">
        <xs:sequence maxOccurs="1" minOccurs="1">
          <xs:element maxOccurs="unbounded" minOccurs="1" name="char" type="AAChar"/>
        </xs:sequence>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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AAMatrixObsRow

Description

This is a row in a matrix of amino acid data containing granular observations.

Inheritance

AAMatrixObsRow restricts AbstractObsRow.

Substructures

an element called "dict", instance of Dict (0..unbounded).
an element called "cell", instance of AAObs (1..unbounded).

Definition source

  <xs:complexType abstract="false" name="AAMatrixObsRow">
    <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="AAObs"/>
        </xs:sequence>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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AAMatrixSeqRow

Description

This is a row in a matrix of amino acid data containing raw sequence data.

Inheritance

AAMatrixSeqRow restricts AbstractSeqRow.

Substructures

an element called "dict", instance of Dict (0..unbounded).
an element called "seq", instance of AASeq (1..1).

Definition source

  <xs:complexType abstract="false" name="AAMatrixSeqRow">
    <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="AASeq"/>
        </xs:sequence>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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AAObs

Description

This is a single cell in a matrix containing an amino acid observation.

Inheritance

AAObs restricts AbstractObs.

Attributes

Name	Type	Usage
char	xs:nonNegativeInteger	required
state	AAToken	required

Substructures

an element called "dict", instance of Dict (0..unbounded).

Definition source

  <xs:complexType abstract="false" name="AAObs" sawsdl:modelReference="http://evolutionaryontology-dev.nescent.org/cdao.owl#AminoAcidResidueStateDatum">
    <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="AAToken" use="required"/>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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AAObsMatrix

Description

A matrix of rows with single character observations.

Inheritance

AAObsMatrix restricts AbstractObsMatrix.

Substructures

an element called "row", instance of AAMatrixObsRow (1..unbounded).

Definition source

  <xs:complexType abstract="false" name="AAObsMatrix">
    <xs:complexContent>
      <xs:restriction base="AbstractObsMatrix">
        <xs:sequence maxOccurs="1" minOccurs="1">
          <xs:element maxOccurs="unbounded" minOccurs="1" name="row" type="AAMatrixObsRow"/>
        </xs:sequence>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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AASeqMatrix

Description

A matrix of rows with amino acid data as sequence strings.

Inheritance

AASeqMatrix restricts AbstractSeqMatrix.

Substructures

an element called "row", instance of AAMatrixSeqRow (1..unbounded).

Definition source

  <xs:complexType abstract="false" name="AASeqMatrix">
    <xs:complexContent>
      <xs:restriction base="AbstractSeqMatrix">
        <xs:sequence maxOccurs="1" minOccurs="1">
          <xs:element maxOccurs="unbounded" minOccurs="1" name="row" type="AAMatrixSeqRow"/>
        </xs:sequence>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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ProteinCells

Description

An amino acid characters block consisting of granular cells preceded by metadata.

Inheritance

ProteinCells restricts AbstractCells.

Substructures

an element called "dict", instance of Dict (0..unbounded).
an element called "format", instance of AAFormat (0..1).
an element called "matrix", instance of AAObsMatrix (1..1).

Definition source

  <xs:complexType abstract="false" name="ProteinCells">
    <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="AAFormat"/>
          <xs:element maxOccurs="1" minOccurs="1" name="matrix" type="AAObsMatrix"/>
        </xs:sequence>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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ProteinSeqs

Description

An amino acid characters block consisting of sequences preceded by metadata.

Inheritance

ProteinSeqs restricts AbstractSeqs.

Substructures

an element called "dict", instance of Dict (0..unbounded).
an element called "format", instance of AAFormat (0..1).
an element called "matrix", instance of AASeqMatrix (1..1).

Definition source

  <xs:complexType abstract="false" name="ProteinSeqs">
    <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="AAFormat"/>
          <xs:element maxOccurs="1" minOccurs="1" name="matrix" type="AASeqMatrix"/>
        </xs:sequence>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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Simple types

AASeq

Description

This is a simple type that specifies a sequence of amino acid characters, following IUPAC single character symbols for aa (and ambiguities).

Inheritance

AASeq restricts AbstractSeq.

Facets

Type	Value
pattern	[ABCDEFGHIKLMNPQRSTUVWXYZ\s]*

Definition source

  <xs:simpleType name="AASeq">
    <xs:restriction base="AbstractSeq">
      <xs:pattern value="[ABCDEFGHIKLMNPQRSTUVWXYZ\s]*"/>
    </xs:restriction>
  </xs:simpleType>

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AAToken

Description

The AAToken simple type is a restriction of AbstractSymbol that defines an IUPAC single character amino acid symbol.

Inheritance

AAToken restricts AbstractSymbol.

Facets

Type	Value
pattern	[ABCDEFGHIKLMNPQRSTUVWXYZ]
length	1

Definition source

  <xs:simpleType name="AAToken">
    <xs:restriction base="AbstractSymbol">
      <xs:pattern value="[ABCDEFGHIKLMNPQRSTUVWXYZ]"/>
      <xs:length value="1"/>
    </xs:restriction>
  </xs:simpleType>

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nexml schema 1.0 ~/nexml/xsd/characters/protein.xsd

[nexml]

The future data exchange standard is here!

Schema module documentation

Description

Complex types

AAChar

Description

Inheritance

Attributes

Substructures

Definition source

AAFormat

Description

Inheritance

Substructures

Definition source

AAMatrixObsRow

Description

Inheritance

Substructures

Definition source

AAMatrixSeqRow

Description

Inheritance

Substructures

Definition source

AAObs

Description

Inheritance

Attributes

Substructures

Definition source

AAObsMatrix

Description

Inheritance

Substructures

Definition source

AASeqMatrix

Description

Inheritance

Substructures

Definition source

ProteinCells

Description

Inheritance

Substructures

Definition source

ProteinSeqs

Description

Inheritance

Substructures

Definition source

Simple types

AASeq

Description

Inheritance

Facets

Definition source

AAToken

Description

Inheritance

Facets

Definition source

See also

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External links