BioTypes 1.1

From BioSchemas

Attention: Discussions about the further development of this specification should be held on the discussion page. Click here to edit the specification.

Contents

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Introduction

For better reading and editing this schema is divided into different sections:

  • Basic: Basic type definitions.
  • Source: Type definitions for specifying the source of biological data.
  • Sequence: Type definitions for sequence data
  • Structure: Type definitions for structure data.
  • Classification: Type definitions for classification schemes.
  • Pattern: Type definitions for sequence patterns.
  • Alignment: Type definitions for sequence alignments.

The final release of this schema can be downloaded from http://schemas.bioservices.net/2005/.

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Specification

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schema http://schemas.bioservices.net/2005/biotypes

code 

<xs:schema xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xmlns:xs="http://www.w3.org/2001/XMLSchema" targetNamespace="http://schemas.bioservices.net/2005/biotypes" elementFormDefault="qualified" attributeFormDefault="unqualified" id="BioTypes" version="1.1" xml:lang="en"/>

documentation

The BioTypes schema provides a common XML type framework for biological data in analogy to the predefined XML Schema types. The recommended prefix for the BioTypes namespace is bt. For further information on usage visit <a href="http://schemas.bioservices.net">BioSchemas </a>.

To use BioTypes in an XML schema download a local copy of the BioTypes schema and include it via the import statement:

<xs:import xmlns:xs="http://www.w3.org/2001/XMLSchema" schemaLocation="biotypes.xsd" namespace="http://schemas.bioservices.net/2005/biotypes"/>

Content is available under <a href="http://creativecommons.org/licenses/by-sa/2.0/">Creative Commons Attribution-ShareAlike License</a>.

appinfo biotypes/tests/tests.xsd 

<xs:schema xmlns:bt="http://schemas.bioservices.net/2005/biotypes" targetNamespace="http://schemas.bioservices.net/2005/biotypes/tests" elementFormDefault="qualified" attributeFormDefault="unqualified">
  <xs:import schemaLocation="../../biotypes.xsd" namespace="http://schemas.bioservices.net/2005/biotypes"/>
  <xs:element name="root">
    <xs:complexType>
      <xs:sequence>
        <xs:any namespace="##any" processContents="strict" minOccurs="0" maxOccurs="unbounded"/>
      </xs:sequence>
      <xs:anyAttribute namespace="##any" processContents="lax"/>
    </xs:complexType>
  </xs:element>
  <xs:element name="index" type="bt:index"/>
  <xs:element name="alphaIndex" type="bt:alphanumericIndex"/>
  <xs:element name="version" type="bt:version"/>
  <xs:element name="lsid" type="bt:lsid"/>
  <xs:element name="sourceUri" type="bt:sourceUri"/>
  <xs:element name="seq" type="bt:sequence"/>
  <xs:element name="atomName" type="bt:atomName"/>
  <xs:element name="container">
    <xs:complexType>
      <xs:complexContent>
        <xs:extension base="bt:anyContent"/>
      </xs:complexContent>
    </xs:complexType>
  </xs:element>
  <xs:element name="item">
    <xs:complexType>
      <xs:attributeGroup ref="bt:dataAttrs"/>
    </xs:complexType>
  </xs:element>
  <xs:element name="coord">
    <xs:complexType>
      <xs:attributeGroup ref="bt:coordinates3D"/>
    </xs:complexType>
  </xs:element>
  <xs:element name="source" type="bt:source"/>
  <xs:element name="atom" type="bt:atom" substitutionGroup="bt:abstractAtom"/>
  <xs:element name="atomSeq" type="bt:atomSequence"/>
  <xs:element name="patternProfile" type="bt:patternProfile"/>
  <xs:element name="pattern" type="bt:pattern"/>
  <xs:element name="aaMultipleAlignment" type="bt:multipleAlignment"/>
</xs:schema>

appinfo 

<xs:appinfo>
  <bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="##missing">
    <bt:mapping to="url"/>
    <bt:mapping to="caption">Unknown</bt:mapping>
  </bt:source>
  <bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:">
    <bt:mapping to="url"/>
    <bt:mapping to="caption">
      <bt:attribute name="source"/>
    </bt:mapping>
  </bt:source>
  <bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:lsid:">
    <bt:mapping to="url">lsidres:
      <bt:attribute name="source"/>
    </bt:mapping>
    <bt:mapping to="caption">
      <bt:attribute name="source"/>
    </bt:mapping>
  </bt:source>
  <bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:embl">
    <bt:mapping to="caption">EMBL Nucleotide Sequence Database</bt:mapping>
    <bt:mapping to="url">http://www.ebi.ac.uk/embl/</bt:mapping>
  </bt:source>
  <bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:entrez">
    <bt:mapping to="caption">NCBI Entrez Gene</bt:mapping>
    <bt:mapping to="url">http://www.ncbi.nih.gov/entrez/query.fcgi?db=gene</bt:mapping>
  </bt:source>
  <bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:genbank">
    <bt:mapping to="caption">NCBI GenBank</bt:mapping>
    <bt:mapping to="url">http://www.ncbi.nlm.nih.gov/Genbank/</bt:mapping>
  </bt:source>
  <bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:hugo">
    <bt:mapping to="caption">The Human Genome Organisation</bt:mapping>
    <bt:mapping to="url">http://www.hugo-international.org/</bt:mapping>
  </bt:source>
  <bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:locuslink">
    <bt:mapping to="caption">NCBI LocusLink</bt:mapping>
    <bt:mapping to="url">http://www.ncbi.nlm.nih.gov/projects/LocusLink/</bt:mapping>
  </bt:source>
  <bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:mgd">
    <bt:mapping to="caption">Mouse Genome Informatics</bt:mapping>
    <bt:mapping to="url">http://www.informatics.jax.org/</bt:mapping>
  </bt:source>
  <bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:mgi">
    <bt:mapping to="caption">Mouse Genome Informatics</bt:mapping>
    <bt:mapping to="url">http://www.informatics.jax.org/</bt:mapping>
  </bt:source>
  <bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:rgd">
    <bt:mapping to="caption">Rat Genome Database</bt:mapping>
    <bt:mapping to="url">http://rgd.mcw.edu/</bt:mapping>
  </bt:source>
  <bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:sgd">
    <bt:mapping to="caption">Saccharomyces Genome Database</bt:mapping>
    <bt:mapping to="url">http://www.yeastgenome.org/</bt:mapping>
  </bt:source>
  <bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:pdb">
    <bt:mapping to="caption">RCSB Protein Data Bank</bt:mapping>
    <bt:mapping to="url">http://www.rcsb.org/pdb/</bt:mapping>
  </bt:source>
  <bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:swissprot">
    <bt:mapping to="caption">Swiss-Prot</bt:mapping>
    <bt:mapping to="url">http://au.expasy.org/sprot/</bt:mapping>
  </bt:source>
  <bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:dssp">
    <bt:mapping to="caption">DSSP</bt:mapping>
    <bt:mapping to="url">http://www.cmbi.kun.nl/gv/dssp/</bt:mapping>
  </bt:source>
  <bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:pdb">
    <bt:mapping to="caption">RCSB Protein Data Bank</bt:mapping>
    <bt:mapping to="url">http://www.rcsb.org/pdb/</bt:mapping>
  </bt:source>
  <bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:pdb">
    <bt:mapping to="caption">RCSB Protein Data Bank</bt:mapping>
    <bt:mapping to="url">http://www.rcsb.org/pdb/</bt:mapping>
  </bt:source>
  <bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:cath">
    <bt:mapping to="caption">CATH</bt:mapping>
    <bt:mapping to="url">http://www.ccbb.re.kr/irs/2_cath/</bt:mapping>
  </bt:source>
  <bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:scop">
    <bt:mapping to="caption">SCOP</bt:mapping>
    <bt:mapping to="url">http://scop.mrc-lmb.cam.ac.uk/scop/</bt:mapping>
  </bt:source>
  <bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:interpro">
    <bt:mapping to="caption">EMBL Interpro</bt:mapping>
    <bt:mapping to="url">http://www.ebi.ac.uk/interpro/</bt:mapping>
  </bt:source>
  <bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:pfam">
    <bt:mapping to="caption">PFAM</bt:mapping>
    <bt:mapping to="url">http://www.sanger.ac.uk/Software/Pfam/</bt:mapping>
  </bt:source>
  <bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:prodom">
    <bt:mapping to="caption">ProDom</bt:mapping>
    <bt:mapping to="url">http://protein.toulouse.inra.fr/prodom/current/html/home.php</bt:mapping>
  </bt:source>
  <bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:prosite">
    <bt:mapping to="caption">ExPASy PROSITE</bt:mapping>
    <bt:mapping to="url">http://au.expasy.org/prosite/</bt:mapping>
  </bt:source>
  <bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:clustalw">
    <bt:mapping to="caption">ClustalW</bt:mapping>
    <bt:mapping to="url">http://www.ebi.ac.uk/clustalw/</bt:mapping>
  </bt:source>
</xs:appinfo>


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Basic

This section contains basic type definitions.


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simpleType index

code 

<xs:simpleType name="index">
  <xs:restriction base="xs:positiveInteger"/>
</xs:simpleType>

documentation

An one-based index. Indices should begin with 1 because zero-based indices might be confusing for humans and are a common source for errors, e.g. when a user assumes the numeration begins with 1.

appinfo biotypes/tests/TestIndex.xml 

<root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
  <test:case test="with" result="pass" desc="index may be 1.">
    <index>1</index>
  </test:case>
  <test:case test="with" result="fail" desc="index starts with 1.">
    <index>0</index>
  </test:case>
  <test:case test="with" result="fail" desc="index must not be negative.">
    <index>-1</index>
  </test:case>
</root>


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simpleType alphanumericIndex

code 

<xs:simpleType name="alphanumericIndex">
  <xs:union memberTypes="bt:index">
    <xs:simpleType>
      <xs:restriction base="xs:string">
        <xs:pattern value="[a-z]"/>
      </xs:restriction>
    </xs:simpleType>
  </xs:union>
</xs:simpleType>

documentation

An alphanumeric index. Numeric indices should begin with 1. Alternatively the indices could be numbered using small letters: "a", "b", etc. A combination of letters is not allowed.

appinfo biotypes/tests/TestAlphanumericIndex.xml 

<root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
     <test:case test="with" result="pass" desc="alphaIndex may be 1.">
          <alphaIndex>1</alphaIndex>
     </test:case>
     <test:case test="with" result="fail" desc="alphaIndex starts with 1.">
          <alphaIndex>0</alphaIndex>
     </test:case>
     <test:case test="with" result="fail" desc="alphaIndex must not be negative.">
          <alphaIndex>-1</alphaIndex>
     </test:case>
     <test:case test="with" result="pass" desc="alphaIndex may be a.">
          <alphaIndex>a</alphaIndex>
     </test:case>
     <test:case test="with" result="fail" desc="alphaIndex must not be a uppercase letter.">
          <alphaIndex>A</alphaIndex>
     </test:case>
     <test:case test="with" result="fail" desc="alphaIndex must not be empty.">
          <alphaIndex/>
     </test:case>
     <test:case test="with" result="fail" desc="alphaIndex must not be a combination of letters.">
          <alphaIndex>ab</alphaIndex>
     </test:case>
</root>


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simpleType version

code 

<xs:simpleType name="version">
  <xs:restriction base="xs:token">
    <xs:pattern value="\d+(\.\d+)*"/>
  </xs:restriction>
</xs:simpleType>

documentation

A versioning number.

appinfo biotypes/tests/TestVersion.xml 

<root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
  <test:case test="with" result="pass" desc="version may be a single digit.">
    <version>1</version>
  </test:case>
  <test:case test="with" result="pass" desc="version may be a number.">
    <version>11</version>
  </test:case>
  <test:case test="with" result="pass" desc="version may be a sequence of numbers.">
    <version>11.0.1</version>
  </test:case>
  <test:case test="with" result="fail" desc="version must not be empty.">
    <version/>
  </test:case>
  <test:case test="with" result="fail" desc="version must not end with a dot.">
    <version>1.</version>
  </test:case>
  <test:case test="with" result="fail" desc="version must not contain characters other than digits.">
    <version>1.x</version>
  </test:case>
  <test:case test="with" result="fail" desc="version must not contain two or more points in sequence.">
    <version>1..1</version>
  </test:case>
</root>


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simpleType score

code 

<xs:simpleType name="score">
  <xs:restriction base="xs:double"/>
</xs:simpleType>

documentation

A scoring value. Scores can be positive or negative.


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complexType anyContent

code 

<xs:complexType name="anyContent" mixed="true" abstract="true">
  <xs:sequence minOccurs="0" maxOccurs="unbounded">
    <xs:any namespace="##any" processContents="lax"/>
  </xs:sequence>
</xs:complexType>

documentation

Allows any mixed content, i.e. text and elements from any namespace.

appinfo biotypes/tests/TestContainer.xml 

<root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
  <test:case test="with" result="pass" desc="A container may contain elements from foreign namespaces and text.">
    <container>Prefix
        <ext:item xmlns:ext="urn:other"/>
        Infix
        <ext2:item xmlns:ext2="urn:other2"/>
        Postfix
      </container>
  </test:case>
  <test:case test="with" result="pass" desc="A container may contain elements from the target namespace.">
    <container>Prefix
        <item/>
        Infix
        <item/>
        Postfix
      </container>
  </test:case>
</root>


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simpleType dateOptionalTime

code 

<xs:simpleType name="dateOptionalTime">
  <xs:union memberTypes="xs:date xs:dateTime"/>
</xs:simpleType>

documentation

A date and eventually a time information.


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simpleType missing

code 

<xs:simpleType name="missing">
  <xs:restriction base="xs:token">
    <xs:enumeration value="##missing"/>
  </xs:restriction>
</xs:simpleType>

documentation

Marks an optional attribute value as missing. This should be the default value for the attribute. This special enumeration value is necessary because optional attributes without a default value could not be used within a key declaration.


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simpleType sourceDate

code 

<xs:simpleType name="sourceDate">
  <xs:restriction base="bt:dateOptionalTime"/>
</xs:simpleType>

documentation

The date (and eventually time) the corresponding data item was retrieved from the data source.


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simpleType optionalSourceDate

code 

<xs:simpleType name="optionalSourceDate">
  <xs:union memberTypes="bt:sourceDate bt:missing"/>
</xs:simpleType>

documentation

The date (and eventually time) the corresponding data item was retrieved from the data source, or ##missing as the default value.


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simpleType sourceVersion

code 

<xs:simpleType name="sourceVersion">
  <xs:restriction base="bt:version"/>
</xs:simpleType>

documentation

The version of the data source from whom the data item was retrieved.


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simpleType optionalSourceVersion

code 

<xs:simpleType name="optionalSourceVersion">
  <xs:union memberTypes="bt:sourceVersion bt:missing"/>
</xs:simpleType>

documentation

The version of the data source from whom the data item was retrieved, or ##missing as the default value.


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attributeGroup dataAttrs

code 

<xs:attributeGroup name="dataAttrs">
  <xs:attribute name="version" type="bt:optionalSourceVersion" use="optional" default="##missing"/>
  <xs:attribute name="date" type="bt:optionalSourceVersion" use="optional" default="##missing"/>
</xs:attributeGroup>

documentation

The attributes for a data item. A data item is an element which holds data that should be regarded as a single unit in contrast to a data collection which holds multiple units of data, i.e. data items. In addition to the optional version and date attributes, specifying the version of the data source and the date (and eventually the time) the data item was retrieved, a data item should declare a source attribute of type sourceUri and a accNumber attribute of type accessionNumber, specifying the data source of the data item and its accession number within the data source.


references

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attributeGroup scopeAttrs

code 

<xs:attributeGroup name="scopeAttrs">
  <xs:attribute name="from" type="bt:index" use="required"/>
  <xs:attribute name="to" type="bt:index" use="required"/>
</xs:attributeGroup>

documentation

Attributes for setting a range. from should be less than to.


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Source

This section contains type declarations for specifying the source of biological data.


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simpleType lsid

code 

<xs:simpleType name="lsid">
  <xs:restriction base="xs:anyURI">
    <xs:pattern value="urn:lsid:(\c|/)+:(\c|/)+:\c+(:\c+)?"/>
  </xs:restriction>
</xs:simpleType>

documentation

A Life Sciences Identifier (LSID) is a URN that uniquely names an object. According to the <a href="http://lsid.sourceforge.net/">LSID Resolution Protocol Project</a> the syntax is urn:lsid:<authority>:<namespace>:<value>:<version> where authority is the name of the organization that has defined an entity, namespace is a namespace within the authority for the Id, value is an alpha-numeric sequence that uniquely identifies an object to its authority, and version is an optional version number for an Id. authority and namespace can have hierarchical path elements separated by "/".

appinfo biotypes/tests/TestLSID.xml 

<root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
  <test:case test="with" result="pass" desc="lsid need not to have a revision.">
    <lsid>urn:lsid:authority:namespace:identifier</lsid>
  </test:case>
  <test:case test="with" result="pass" desc="lsid may have a revision. ">
    <lsid>urn:lsid:authority:namespace:identifier:1</lsid>
  </test:case>
  <test:case test="with" result="fail" desc="lsid must a have an urn prefix.">
    <lsid>lsid:authority:namespace:identifier</lsid>
  </test:case>
  <test:case test="with" result="fail" desc="lsid must have a lsid prefix.">
    <lsid>urn:authority:namespace:identifier</lsid>
  </test:case>
  <test:case test="with" result="fail" desc="lsid must have an identifier.">
    <lsid>urn:lsid:authority:namespace</lsid>
  </test:case>
  <test:case test="with" result="fail" desc="lsid must have a namespace.">
    <lsid>urn:lsid:authority::identifier</lsid>
  </test:case>
  <test:case test="with" result="fail" desc="lsid must have an authority.">
    <lsid>urn:lsid::namespace:identifier</lsid>
  </test:case>
  <test:case test="with" result="pass" desc="authority and namespace may include slashes.">
    <lsid>urn:lsid:authority/sub:namespace/sub:identifier</lsid>
  </test:case>
</root>


references


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simpleType sourceUri

code 

<xs:simpleType name="sourceUri" final="restriction">
  <xs:union memberTypes="bt:lsid">
    <xs:simpleType>
      <xs:restriction base="xs:anyURI">
        <xs:minLength value="1"/>
      </xs:restriction>
    </xs:simpleType>
  </xs:union>
</xs:simpleType>

documentation

The URI of a data source. This may be an URL, an URN or a LSID.


references


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simpleType optionalSourceUri

code 

<xs:simpleType name="optionalSourceUri">
  <xs:union memberTypes="bt:sourceUri bt:missing"/>
</xs:simpleType>

documentation

The URI of a data source. This may be an URL, an URN or a LSID or ##missing as the default value.


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simpleType accessionNumber

code 

<xs:simpleType name="accessionNumber">
  <xs:restriction base="xs:token">
    <xs:minLength value="1"/>
  </xs:restriction>
</xs:simpleType>

documentation

Specifies the accession number of a data item relative to its data source. The format of the accession number depends on the data source.


references

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complexType source

code 

<xs:complexType name="source" mixed="true">
  <xs:complexContent>
    <xs:extension base="bt:anyContent">
      <xs:attribute name="uri" type="bt:optionalSourceUri" use="required" form="unqualified"/>
    </xs:extension>
  </xs:complexContent>
</xs:complexType>

documentation

The description of a data source. The data source is identified by the uri attribute. The content may be source specific. It may consist e.g. of one or more mapping elements which map the source URI to an URL or a caption. Such a mapping is demonstrated by the <a href="http://schemas.bioservices.net/index.php?title=BioTypes_stylesheet">BioTypes stylesheet</a>.


references

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element source

code 

<xs:element name="source">
  <xs:complexType>
    <xs:complexContent>
      <xs:extension base="bt:source">
        <xs:anyAttribute namespace="##other" processContents="lax"/>
      </xs:extension>
    </xs:complexContent>
  </xs:complexType>
</xs:element>

documentation

The description of a data source.

appinfo biotypes/tests/TestSource.xml 

<bst:root xmlns:bst="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
  <bst:source uri="test">
    <test:attribute name="uri" result="fail" desc="source must have a uri."/>
    <test:attribute name="uri" value="urn:bts:cath" result="pass" desc="source uri may be a predefined name."/>
    <test:attribute name="uri" value="urn:org.db:id" result="pass" desc="source uri may be a custom URN."/>
    <test:attribute name="uri" value="http://www.db.org/id" result="pass" desc="source uri may be a custom URL."/>
    <test:attribute name="uri" value="urn:lsid:authority:namespace:identifier" result="pass" desc="source uri may be a LSID."/>
    <test:attribute name="uri" value="##missing" result="pass" desc="source uri may be ##missing."/>
    <test:case test="with" result="pass" desc="source may contain any content.">
        Prefix<ext:item xmlns:ext="urn:other">Infix</ext:item>Postfix
      </test:case>
  </bst:source>
</bst:root>


references

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[edit]

element mapping

code 

<xs:element name="mapping">
  <xs:complexType>
    <xs:complexContent>
      <xs:extension base="bt:anyContent">
        <xs:attribute name="to" use="required">
          <xs:simpleType>
            <xs:union memberTypes="xs:token">
              <xs:simpleType>
                <xs:restriction base="xs:token">
                  <xs:enumeration value="url"/>
                  <xs:enumeration value="caption"/>
                </xs:restriction>
              </xs:simpleType>
            </xs:union>
          </xs:simpleType>
        </xs:attribute>
        <xs:anyAttribute namespace="##other" processContents="lax"/>
      </xs:extension>
    </xs:complexContent>
  </xs:complexType>
</xs:element>

documentation

The mapping of a value to another representation. The to attribute specifies the representation. A mapping is used e.g. within a source element to map the data source URI to an URL. It is used by the <a href="http://schemas.bioservices.net/index.php?title=BioTypes_stylesheet">BioTypes stylesheet</a>. Its content may be mapping specific, e.g. text and one or more attribute elements. For each subordinated element the processing application or stylesheet should be ready to process it, i.e. there must be appropiate template.


references

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[edit]

element attribute

code 

<xs:element name="attribute">
  <xs:complexType>
    <xs:attribute name="name" type="xs:Name" use="required"/>
    <xs:attribute name="namespace" type="xs:anyURI" use="optional"/>
    <xs:anyAttribute namespace="##other" processContents="lax"/>
  </xs:complexType>
</xs:element>

documentation

Evaluates an attribute. This element can be used e.g. inside a mapping element. During the mapping process it should be replaced by the concrete value of the attribute.


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[edit]

Sequence

This section contains type declarations for biological sequence data.


[edit]

simpleType sequence

code 

<xs:simpleType name="sequence">
  <xs:restriction base="xs:string">
    <xs:minLength value="1"/>
    <xs:whiteSpace value="preserve"/>
  </xs:restriction>
</xs:simpleType>

documentation

A sequence of character data of length greater than zero.

appinfo biotypes/tests/TestSequence.xml 

<root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
  <seq>
    <test:case test="with" result="fail" desc="sequence must not be empty."/>
    <test:case test="with" result="pass" desc="sequence may contain any number of characters.">ABCDEFGHIJKLMNOPQRSTVWXYZabcdefghijklmnopqrstvwxyz</test:case>
    <test:case test="with" result="pass" desc="sequence may contain whitespace and line breaks.">
AA
AA
     </test:case>
  </seq>
</root>


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simpleType gappedAmbiguousNucleotideSequence

code 

<xs:simpleType name="gappedAmbiguousNucleotideSequence">
  <xs:restriction base="bt:sequence">
    <xs:pattern value="(A|G|C|T|U|R|Y|M|K|S|W|H|B|V|D|N|X|\-)+"/>
    <xs:whiteSpace value="collapse"/>
  </xs:restriction>
</xs:simpleType>

documentation

A sequence of nucleotides (RNA and DNA) or its placeholders in upper case letters and gap characters. Only leading and trailing whitespace is allowed.

appinfo biotypes/tests/TestGappedAmbiguousNucleotideSequence.xml 

<root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
  <seq xsi:type="bt:gappedAmbiguousNucleotideSequence">
    <test:case test="with" result="fail" desc="gapped ambiguous nucleotide sequence must not be empty."/>
    <test:case test="with" result="fail" desc="gapped ambiguous nucleotide sequence must not contain lower case characters.">a</test:case>
    <test:case test="with" result="pass" desc="gapped ambiguous nucleotide sequence may contain any number of nucleotides, ambiguous characters and gaps.">ACGTURYMKSWHBVDNX-</test:case>
    <test:case test="with" result="pass" desc="gapped ambiguous nucleotide sequence may contain line breaks at the beginning and at the end.">
  AAAA
       </test:case>
    <test:case test="with" result="fail" desc="gapped ambiguous nucleotide must not contain line breaks in between.">
  AA
  AA
       </test:case>
  </seq>
</root>


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[edit]

simpleType gappedNucleotideSequence

code 

<xs:simpleType name="gappedNucleotideSequence">
  <xs:restriction base="bt:gappedAmbiguousNucleotideSequence">
    <xs:pattern value="(A|G|C|T|U|\-)+"/>
  </xs:restriction>
</xs:simpleType>

documentation

A sequence of nucleotides (RNA and DNA) in upper case letters and gap characters. Only leading and trailing whitespace is allowed.

appinfo biotypes/tests/TestGappedNucleotideSequence.xml 

<root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
  <seq xsi:type="bt:gappedNucleotideSequence">
    <test:case test="with" result="fail" desc="gapped nucleotide sequence must not contain ambiguous characters.">RYMKSWHBVDNX</test:case>
  </seq>
</root>


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[edit]

simpleType ambiguousNucleotideSequence

code 

<xs:simpleType name="ambiguousNucleotideSequence">
  <xs:restriction base="bt:gappedAmbiguousNucleotideSequence">
    <xs:pattern value="(A|G|C|T|U|R|Y|M|K|S|W|H|B|V|D|N|X)+"/>
  </xs:restriction>
</xs:simpleType>

documentation

A sequence of nucleotides (RNA and DNA) or its placeholders in upper case letters. Only leading and trailing whitespace is allowed.

appinfo biotypes/tests/TestAmbiguousNucleotideSequence.xml 

<root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
  <seq xsi:type="bt:ambiguousNucleotideSequence">
    <test:case test="with" result="fail" desc="ambiguous nucleotide sequence must not contain gap characters.">-</test:case>
  </seq>
</root>


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[edit]

simpleType nucleotideSequence

code 

<xs:simpleType name="nucleotideSequence">
  <xs:restriction base="bt:ambiguousNucleotideSequence">
    <xs:pattern value="(A|G|C|T|U)+"/>
  </xs:restriction>
</xs:simpleType>

documentation

A sequence of nucleotides (RNA and DNA) in upper case letters. Only leading and trailing whitespace is allowed.

appinfo biotypes/tests/TestNucleotideSequence.xml 

<root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
  <seq xsi:type="bt:nucleotideSequence">
    <test:case test="with" result="fail" desc="nucleotide sequence must not contain gap characters or ambiguous characters.">-X</test:case>
  </seq>
</root>


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[edit]

simpleType nucleotideSequenceSources

code 

<xs:simpleType name="nucleotideSequenceSources">
  <xs:restriction base="xs:token">
    <xs:enumeration value="urn:bts:embl"/>
    <xs:enumeration value="urn:bts:entrez"/>
    <xs:enumeration value="urn:bts:genbank"/>
    <xs:enumeration value="urn:bts:hugo"/>
    <xs:enumeration value="urn:bts:locuslink"/>
    <xs:enumeration value="urn:bts:mgd"/>
    <xs:enumeration value="urn:bts:mgi"/>
    <xs:enumeration value="urn:bts:rgd"/>
    <xs:enumeration value="urn:bts:sgd"/>
  </xs:restriction>
</xs:simpleType>

documentation

A list of predefined nucleotide sequence source names.


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[edit]

simpleType nucleotideSequenceSource

code 

<xs:simpleType name="nucleotideSequenceSource">
  <xs:union memberTypes="bt:sourceUri bt:nucleotideSequenceSources"/>
</xs:simpleType>

documentation

The source of a nucleotide sequence. May be an URI, a LSID or one of the predefined source names.


references


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[edit]

attributeGroup nucleotideSequenceAttrs

code 

<xs:attributeGroup name="nucleotideSequenceAttrs">
  <xs:attributeGroup ref="bt:dataAttrs"/>
  <xs:attribute name="accNumber" type="bt:accessionNumber" use="optional"/>
  <xs:attribute name="source" type="bt:nucleotideSequenceSource" use="optional"/>
</xs:attributeGroup>

documentation

Attributes for nucleotide sequences. source specifies the source of the sequence. In addition accNumber can be set to an accession number dependant on the data source if source identifies only the data source (e.g. database) but not the data item itself.


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[edit]

simpleType gappedAmbiguousDnaSequence

code 

<xs:simpleType name="gappedAmbiguousDnaSequence">
  <xs:restriction base="bt:gappedAmbiguousNucleotideSequence">
    <xs:pattern value="(A|G|C|T|R|Y|M|K|S|W|H|B|V|D|N|X|\-)+"/>
    <xs:whiteSpace value="collapse"/>
  </xs:restriction>
</xs:simpleType>

documentation

A sequence of DNAs or its placeholders in upper case letters and gap characters. Only leading and trailing whitespace is allowed.

appinfo biotypes/tests/TestGappedAmbiguousDnaSequence.xml 

<root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
  <seq xsi:type="bt:gappedAmbiguousDnaSequence">
    <test:case test="with" result="fail" desc="gapped ambiguous dna sequence must not contain Uracil.">U</test:case>
  </seq>
</root>


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[edit]

simpleType gappedDnaSequence

code 

<xs:simpleType name="gappedDnaSequence">
  <xs:restriction base="bt:gappedAmbiguousDnaSequence">
    <xs:pattern value="(A|G|C|T|\-)+"/>
  </xs:restriction>
</xs:simpleType>

documentation

A sequence of DNAs in upper case letters and gap characters. Only leading and trailing whitespace is allowed.

appinfo biotypes/tests/TestGappedDnaSequence.xml 

<root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
  <seq xsi:type="bt:gappedDnaSequence">
    <test:case test="with" result="fail" desc="gapped dna sequence must not contain ambiguous characters.">RYMKSWHBVDNX</test:case>
  </seq>
</root>


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[edit]

simpleType ambiguousDnaSequence

code 

<xs:simpleType name="ambiguousDnaSequence">
  <xs:restriction base="bt:gappedAmbiguousDnaSequence">
    <xs:pattern value="(A|G|C|T|R|Y|M|K|S|W|H|B|V|D|N|X)+"/>
  </xs:restriction>
</xs:simpleType>

documentation

A sequence of DNAs or its placeholders in upper case letters. Only leading and trailing whitespace is allowed.

appinfo biotypes/tests/TestAmbiguousDnaSequence.xml 

<root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
  <seq xsi:type="bt:ambiguousDnaSequence">
    <test:case test="with" result="fail" desc="ambiguous dna sequence must not contain gap characters.">-</test:case>
  </seq>
</root>


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[edit]

simpleType dnaSequence

code 

<xs:simpleType name="dnaSequence">
  <xs:restriction base="bt:ambiguousDnaSequence">
    <xs:pattern value="(A|G|C|T)+"/>
  </xs:restriction>
</xs:simpleType>

documentation

A sequence of DNAs in upper case letters. Only leading and trailing whitespace is allowed.

appinfo biotypes/tests/TestDnaSequence.xml 

<root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
  <seq xsi:type="bt:dnaSequence">
    <test:case test="with" result="fail" desc="dna sequence must not contain gap characters or ambiguous characters.">-X</test:case>
  </seq>
</root>


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[edit]

simpleType gappedAmbiguousRnaSequence

code 

<xs:simpleType name="gappedAmbiguousRnaSequence">
  <xs:restriction base="bt:gappedAmbiguousNucleotideSequence">
    <xs:pattern value="(A|G|C|U|R|Y|M|K|S|W|H|B|V|D|N|X|\-)+"/>
    <xs:whiteSpace value="collapse"/>
  </xs:restriction>
</xs:simpleType>

documentation

A sequence of RNAs or its placeholders in upper case letters and gap characters. Only leading and trailing whitespace is allowed.

appinfo biotypes/tests/TestGappedAmbiguousRnaSequence.xml 

<root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
  <seq xsi:type="bt:gappedAmbiguousRnaSequence">
    <test:case test="with" result="fail" desc="gapped ambiguous rna sequence must not contain Thymin.">T</test:case>
  </seq>
</root>


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[edit]

simpleType gappedRnaSequence

code 

<xs:simpleType name="gappedRnaSequence">
  <xs:restriction base="bt:gappedAmbiguousRnaSequence">
    <xs:pattern value="(A|G|C|U|\-)+"/>
  </xs:restriction>
</xs:simpleType>

documentation

A sequence of DNAs in upper case letters and gap characters. Only leading and trailing whitespace is allowed.

appinfo biotypes/tests/TestGappedRnaSequence.xml 

<root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
  <seq xsi:type="bt:gappedRnaSequence">
    <test:case test="with" result="fail" desc="gapped rna sequence must not contain ambiguous characters.">RYMKSWHBVDNX</test:case>
  </seq>
</root>


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[edit]

simpleType ambiguousRnaSequence

code 

<xs:simpleType name="ambiguousRnaSequence">
  <xs:restriction base="bt:gappedAmbiguousRnaSequence">
    <xs:pattern value="(A|G|C|U|R|Y|M|K|S|W|H|B|V|D|N|X)+"/>
  </xs:restriction>
</xs:simpleType>

documentation

A sequence of RNAs or its placeholders in upper case letters. Only leading and trailing whitespace is allowed.

appinfo biotypes/tests/TestAmbiguousRnaSequence.xml 

<root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
  <seq xsi:type="bt:ambiguousRnaSequence">
    <test:case test="with" result="fail" desc="ambiguous rna sequence must not contain gap characters.">-</test:case>
  </seq>
</root>


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[edit]

simpleType rnaSequence

code 

<xs:simpleType name="rnaSequence">
  <xs:restriction base="bt:ambiguousRnaSequence">
    <xs:pattern value="(A|G|C|U)+"/>
  </xs:restriction>
</xs:simpleType>

documentation

A sequence of RNAs in upper case letters. Only leading and trailing whitespace is allowed.

appinfo biotypes/tests/TestRnaSequence.xml 

<root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
  <seq xsi:type="bt:rnaSequence">
    <test:case test="with" result="fail" desc="rna sequence must not contain gap characters or ambiguous characters.">-X</test:case>
  </seq>
</root>


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[edit]

simpleType gappedAmbiguousTerminalAminoAcidOneLetterSequence

code 

<xs:simpleType name="gappedAmbiguousTerminalAminoAcidOneLetterSequence">
  <xs:restriction base="bt:sequence">
    <xs:pattern value="(A|R|N|D|C|Q|E|G|H|I|L|K|M|F|P|S|T|U|W|Y|V|X|B|Z|\-|\*)+"/>
    <xs:whiteSpace value="collapse"/>
  </xs:restriction>
</xs:simpleType>

documentation

A sequence of amino acids in upper case one letter code including the terminal symbol *, ambigiuous and gap characters. Only leading and trailing whitespace is allowed.


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[edit]

simpleType gappedAmbiguousAminoAcidOneLetterSequence

code 

<xs:simpleType name="gappedAmbiguousAminoAcidOneLetterSequence">
  <xs:restriction base="bt:gappedAmbiguousTerminalAminoAcidOneLetterSequence">
    <xs:pattern value="(A|R|N|D|C|Q|E|G|H|I|L|K|M|F|P|S|T|U|W|Y|V|X|B|Z|\-)+"/>
  </xs:restriction>
</xs:simpleType>

documentation

A sequence of amino acids in upper case one letter code, ambigiuous and gap characters. Only leading and trailing whitespace is allowed.


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[edit]

simpleType ambiguousAminoAcidOneLetterSequence

code 

<xs:simpleType name="ambiguousAminoAcidOneLetterSequence">
  <xs:restriction base="bt:gappedAmbiguousTerminalAminoAcidOneLetterSequence">
    <xs:pattern value="(A|R|N|D|C|Q|E|G|H|I|L|K|M|F|P|S|T|U|W|Y|V|X|B|Z)+"/>
  </xs:restriction>
</xs:simpleType>

documentation

A sequence of amino acids in upper case one letter code and ambigiuous characters. Only leading and trailing whitespace is allowed.


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[edit]

simpleType gappedAminoAcidOneLetterSequence

code 

<xs:simpleType name="gappedAminoAcidOneLetterSequence">
  <xs:restriction base="bt:gappedAmbiguousTerminalAminoAcidOneLetterSequence">
    <xs:pattern value="(A|R|N|D|C|Q|E|G|H|I|L|K|M|F|P|S|T|U|W|Y|V|\-)+"/>
  </xs:restriction>
</xs:simpleType>

documentation

A sequence of amino acids in upper case one letter code and gap characters. Only leading and trailing whitespace is allowed.


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[edit]

simpleType terminalAminoAcidOneLetterSequence

code 

<xs:simpleType name="terminalAminoAcidOneLetterSequence">
  <xs:restriction base="bt:gappedAmbiguousTerminalAminoAcidOneLetterSequence">
    <xs:pattern value="(A|R|N|D|C|Q|E|G|H|I|L|K|M|F|P|S|T|U|W|Y|V|\*)+"/>
  </xs:restriction>
</xs:simpleType>

documentation

A sequence of amino acids in upper case one letter code including the terminal symbol *. Only leading and trailing whitespace is allowed.


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[edit]

simpleType aminoAcidOneLetterSequence

code 

<xs:simpleType name="aminoAcidOneLetterSequence">
  <xs:restriction base="bt:ambiguousAminoAcidOneLetterSequence">
    <xs:pattern value="(A|R|N|D|C|Q|E|G|H|I|L|K|M|F|P|S|T|U|W|Y|V)+"/>
  </xs:restriction>
</xs:simpleType>

documentation

A sequence of amino acids in upper case one letter code. Only leading and trailing whitespace is allowed.


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[edit]

simpleType terminalAminoAcidThreeLetterSequence

code 

<xs:simpleType name="terminalAminoAcidThreeLetterSequence">
  <xs:restriction base="bt:sequence">
    <xs:pattern value="(ALA|ARG|ASN|ASP|CYS|GLN|GLU|GLY|HIS|ILE|LEU|LYS|MET|PHE|PRO|SER|THR|SEC|TRP|TYR|VAL|TER)+"/>
    <xs:whiteSpace value="collapse"/>
  </xs:restriction>
</xs:simpleType>

documentation

A sequence of amino acids in upper case three letter code including the terminal symbol TER. Only leading and trailing whitespace is allowed.

appinfo biotypes/tests/TestTerminalAminoAcidThreeLetterSequence.xml 

<root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
  <seq xsi:type="bt:terminalAminoAcidThreeLetterSequence">
    <test:case test="with" result="fail" desc="terminal amino acid three letter sequence must not be empty."/>
    <test:case test="with" result="fail" desc="terminal amino acid three letter sequence must not contain lower case characters.">ala</test:case>
    <test:case test="with" result="fail" desc="terminal amino acid three letter sequence must not contain illegal character combinations.">XZY</test:case>
    <test:case test="with" result="pass" desc="terminal amino acid thre letter sequence may contain any number of amino acids in three letter code and the terminal signal.">ALAARGASNASPCYSGLNGLUGLYHISILELEULYSMETPHEPROSERTHRSECTRPTYRVALTER</test:case>
  </seq>
</root>


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[edit]

simpleType aminoAcidThreeLetterSequence

code 

<xs:simpleType name="aminoAcidThreeLetterSequence">
  <xs:restriction base="bt:terminalAminoAcidThreeLetterSequence">
    <xs:pattern value="(ALA|ARG|ASN|ASP|CYS|GLN|GLU|GLY|HIS|ILE|LEU|LYS|MET|PHE|PRO|SER|THR|SEC|TRP|TYR|VAL)+"/>
  </xs:restriction>
</xs:simpleType>

documentation

A sequence of amino acids in upper case three letter code. Only leading and trailing whitespace is allowed.

appinfo biotypes/tests/TestAminoAcidThreeLetterSequence.xml 

<root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
  <seq xsi:type="bt:aminoAcidThreeLetterSequence">
    <test:case test="with" result="fail" desc="amino acid three letter sequence must not contain the terminal signal.">TER</test:case>
  </seq>
</root>


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[edit]

simpleType aminoAcidSequenceSources

code 

<xs:simpleType name="aminoAcidSequenceSources">
  <xs:restriction base="xs:token">
    <xs:enumeration value="urn:bts:pdb"/>
    <xs:enumeration value="urn:bts:swissprot"/>
  </xs:restriction>
</xs:simpleType>

documentation

A list of predefined amino acid sequence source names.


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[edit]

simpleType aminoAcidSequenceSource

code 

<xs:simpleType name="aminoAcidSequenceSource">
  <xs:union memberTypes="bt:sourceUri bt:aminoAcidSequenceSources"/>
</xs:simpleType>

documentation

The source of a amino acid sequence. May be an URI, a LSID or one of the predefined source names.


references


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[edit]

attributeGroup aminoAcidSequenceAttrs

code 

<xs:attributeGroup name="aminoAcidSequenceAttrs">
  <xs:attributeGroup ref="bt:dataAttrs"/>
  <xs:attribute name="accNumber" type="bt:accessionNumber" use="optional"/>
  <xs:attribute name="source" type="bt:aminoAcidSequenceSource" use="optional"/>
</xs:attributeGroup>

documentation

Attributes for amino acid sequences. source specifies the source of the sequence. In addition accNumber can be set to an accession number dependant on the data source if source identifies only the data source (e.g. database) but not the data item itself.


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[edit]

simpleType gappedAmbiguousSecondaryStructureSequence

code 

<xs:simpleType name="gappedAmbiguousSecondaryStructureSequence">
  <xs:restriction base="bt:sequence">
    <xs:pattern value="(C|H|G|I|E|B|T|S|_|X|\-)+"/>
    <xs:whiteSpace value="replace"/>
  </xs:restriction>
</xs:simpleType>

documentation

A sequence of secondary structure assignments or its placeholder in upper case letters and gap characters. Only leading and trailing whitespace is allowed.

appinfo biotypes/tests/TestGappedAmbiguousSecondaryStructureSequence.xml 

<root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
  <seq xsi:type="bt:gappedAmbiguousSecondaryStructureSequence">
    <test:case test="with" result="fail" desc="gapped ambiguous secondary structure sequence must not be empty."/>
    <test:case test="with" result="fail" desc="gapped ambiguous secondary structure sequence must not contain lower case characters.">a</test:case>
    <test:case test="with" result="pass" desc="gapped ambiguous secondary structure sequence may contain any number of secondary structures, ambiguous characters and gaps.">CHGIEBTS_X-</test:case>
    <test:case test="with" result="fail" desc="gapped ambiguous secondary structure must not contain line breaks in between.">
  SS
  SS
       </test:case>
  </seq>
</root>


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[edit]

simpleType ambiguousSecondaryStructureSequence

code 

<xs:simpleType name="ambiguousSecondaryStructureSequence">
  <xs:restriction base="bt:gappedAmbiguousSecondaryStructureSequence">
    <xs:pattern value="(C|H|G|I|E|B|T|S|_|X)+"/>
  </xs:restriction>
</xs:simpleType>

documentation

A sequence of secondary structure assignments or its placeholder in upper case letters. Only leading and trailing whitespace is allowed.

appinfo biotypes/tests/TestAmbiguousSecondaryStructureSequence.xml 

<root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
  <seq xsi:type="bt:ambiguousSecondaryStructureSequence">
    <test:case test="with" result="fail" desc="ambiguous secondary structure sequence must not contain gap characters.">-</test:case>
  </seq>
</root>


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[edit]

simpleType gappedSecondaryStructureSequence

code 

<xs:simpleType name="gappedSecondaryStructureSequence">
  <xs:restriction base="bt:gappedAmbiguousSecondaryStructureSequence">
    <xs:pattern value="(C|H|G|I|E|B|T|S|_|\-)+"/>
  </xs:restriction>
</xs:simpleType>

documentation

A sequence of secondary structure assignments in upper case letters and gap characters. Only leading and trailing whitespace is allowed.

appinfo biotypes/tests/TestGappedSecondaryStructureSequence.xml 

<root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
  <seq xsi:type="bt:gappedSecondaryStructureSequence">
    <test:case test="with" result="fail" desc="gapped secondary structure sequence must not contain ambiguous character.">X</test:case>
  </seq>
</root>


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[edit]

simpleType secondaryStructureSequence

code 

<xs:simpleType name="secondaryStructureSequence">
  <xs:restriction base="bt:gappedAmbiguousSecondaryStructureSequence">
    <xs:pattern value="(C|H|G|I|E|B|T|S|_)+"/>
  </xs:restriction>
</xs:simpleType>

documentation

A sequence of secondary structure assignments in upper case letters. Only leading and trailing whitespace is allowed.

appinfo biotypes/tests/TestSecondaryStructureSequence.xml 

<root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
  <seq xsi:type="bt:secondaryStructureSequence">
    <test:case test="with" result="fail" desc="secondary structure sequence must not contain ambiguous character or gap character.">X-</test:case>
  </seq>
</root>


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[edit]

simpleType secondaryStructureSequenceSources

code 

<xs:simpleType name="secondaryStructureSequenceSources">
  <xs:restriction base="xs:token">
    <xs:enumeration value="urn:bts:dssp"/>
    <xs:enumeration value="urn:bts:pdb"/>
  </xs:restriction>
</xs:simpleType>

documentation

A list of predefined secondary structure sequence source names.


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[edit]

simpleType secondaryStructureSequenceSource

code 

<xs:simpleType name="secondaryStructureSequenceSource">
  <xs:union memberTypes="bt:sourceUri bt:secondaryStructureSequenceSources"/>
</xs:simpleType>

documentation

The source of a secondary structure sequence. May be an URI, a LSID or one of the predefined source names.


references


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[edit]

attributeGroup secondaryStructureSequenceAttrs

code 

<xs:attributeGroup name="secondaryStructureSequenceAttrs">
  <xs:attributeGroup ref="bt:dataAttrs"/>
  <xs:attribute name="accNumber" type="bt:accessionNumber" use="optional"/>
  <xs:attribute name="source" type="bt:secondaryStructureSequenceSource" use="optional"/>
</xs:attributeGroup>

documentation

Attributes for secondary structure sequences. source specifies the source of the sequence. In addition accNumber can be set to an accession number dependant on the data source if source identifies only the data source (e.g. database) but not the data item itself.


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[edit]

simpleType gappedRnaSecondaryStructureSequence

code 

<xs:simpleType name="gappedRnaSecondaryStructureSequence">
  <xs:restriction base="bt:sequence">
    <xs:pattern value="(\(|\)|\[|\]|\{|\}|&lt;|&gt;|\.|\-)+"/>
  </xs:restriction>
</xs:simpleType>

documentation

A sequence of secondary structure assignments in dot-bracket format and gap characters. Only leading and trailing whitespace is allowed.


change log

  • 01/02/06 by Kai Loewenthal: added bracket-pair < > for pseudoknot structures
  • 11/04/05 by Jan Krueger: add additional bracket-pairs for pseudoknot structures
  • 10/19/05 by Philipp Seibel: Initial declaration.
[edit]

simpleType rnaSecondaryStructureSequence

code 

<xs:simpleType name="rnaSecondaryStructureSequence">
  <xs:restriction base="bt:gappedRnaSecondaryStructureSequence">
    <xs:pattern value="(\(|\)|\[|\]|\{|\}|&lt;|&gt;|\.)+"/>
  </xs:restriction>
</xs:simpleType>

documentation

A sequence of rna secondary structure assignments in dot-bracket notation. Only leading and trailing whitespace is allowed.


change log

  • 01/02/06 by Kai Loewenthal: added bracket-pair < > for pseudoknot structures
  • 11/04/05 by Jan Krueger: add additional bracket-pairs for pseudoknot structures
  • 10/19/05 by Philipp Seibel: Initial declaration.
[edit]

simpleType rnaSecondaryStructureSequenceClass

code 

<xs:simpleType name="rnaSecondaryStructureSequenceClass">
  <xs:restriction base="bt:sequence">
    <xs:pattern value="(\(|\)|\[|\]|\{|\}|&lt;|&gt;|_)+"/>
  </xs:restriction>
</xs:simpleType>

documentation

A class of rna secondary structure sequences in shape notation.


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[edit]

Structure

This section contains type, attribute and element declarations for atom structures.


[edit]

simpleType atomNames

code 

<xs:simpleType name="atomNames">
  <xs:restriction base="xs:token">
    <xs:enumeration value="H"/>
    <xs:enumeration value="C"/>
    <xs:enumeration value="CA"/>
    <xs:enumeration value="CB"/>
    <xs:enumeration value="O"/>
    <xs:enumeration value="N"/>
    <xs:enumeration value="S"/>
  </xs:restriction>
</xs:simpleType>

documentation

A list of predefined atom names.

This list contains the following atom names:

  • H: hydrogen atom
  • C: carbon atom
  • CA: alpha carbon atom
  • CB: beta carbon atom
  • O: oxygen atom
  • N: nitrogen atom
  • S: sulphur atom


references


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[edit]

simpleType atomName

code 

<xs:simpleType name="atomName">
  <xs:union memberTypes="bt:atomNames">
    <xs:simpleType>
      <xs:restriction base="xs:token">
        <xs:minLength value="1"/>
      </xs:restriction>
    </xs:simpleType>
  </xs:union>
</xs:simpleType>

documentation

The (abbreviated) name of an atom within a biological molecule. The name must be at least one character long and may contain numbers but not at the beginning.

appinfo biotypes/tests/TestAtomName.xml 

<root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
  <test:case test="with" result="fail" desc="atom name must not be empty.">
    <atomName/>
  </test:case>
  <test:case test="with" result="pass" desc="atom name may contain any number of token characters.">
    <atomName>B1</atomName>
  </test:case>
  <test:case test="with" result="pass" desc="atom name must not start with a digit.">
    <atomName>1B</atomName>
  </test:case>
</root>


references


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[edit]

simpleType coordinate

code 

<xs:simpleType name="coordinate">
  <xs:restriction base="xs:double"/>
</xs:simpleType>

documentation

A coordinate in a n-dimensional space.


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[edit]

simpleType distance

code 

<xs:simpleType name="distance">
  <xs:restriction base="xs:double">
    <xs:minInclusive value="0.0"/>
  </xs:restriction>
</xs:simpleType>

documentation

A distance in a n-dimensional space. A distance may not be negative.


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[edit]

simpleType distanceUnits

code 

<xs:simpleType name="distanceUnits">
  <xs:restriction base="xs:token">
    <xs:enumeration value="angstroem"/>
  </xs:restriction>
</xs:simpleType>

documentation

A list of possible distance units.

This list contains the following entries:

  • angstroem: Angstroem


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[edit]

simpleType atomStructureSources

code 

<xs:simpleType name="atomStructureSources">
  <xs:restriction base="xs:token">
    <xs:enumeration value="urn:bts:pdb"/>
  </xs:restriction>
</xs:simpleType>

documentation

A list of predefined atom structure source names.


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[edit]

simpleType atomStructureSource

code 

<xs:simpleType name="atomStructureSource">
  <xs:union memberTypes="bt:sourceUri bt:atomStructureSources"/>
</xs:simpleType>

documentation

The source of an atom structure. May be an URI, a LSID or one of the predefined source names.


references


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[edit]

attributeGroup coordinates3D

code 

<xs:attributeGroup name="coordinates3D">
  <xs:attribute name="x" type="bt:coordinate" use="required" form="unqualified"/>
  <xs:attribute name="y" type="bt:coordinate" use="required" form="unqualified"/>
  <xs:attribute name="z" type="bt:coordinate" use="required" form="unqualified"/>
</xs:attributeGroup>

documentation

Coordinates in a 3-dimensional space.

appinfo biotypes/tests/TestCoordinates3D.xml 

<coord xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" y="1.0" z="1.0" x="1.0" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
  <test:attribute id="x" name="x" result="fail" desc="3-D-coordinates must have a x value."/>
  <test:attribute name="y" result="fail" desc="3-D-coordinates must have a y value."/>
  <test:attribute name="z" result="fail" desc="3-D-coordinates must have a z value."/>
</coord>


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[edit]

complexType atom

code 

<xs:complexType name="atom" block="restriction" final="restriction">
  <xs:attributeGroup ref="bt:coordinates3D"/>
  <xs:attribute name="type" type="bt:atomName" use="required" form="unqualified"/>
</xs:complexType>

documentation

A single atom including its coordinates in 3-dimensional space and its type.

appinfo biotypes/tests/TestAtom.xml 

<atom xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd" x="1.0" y="1.0" z="1.0" type="C">
  <test:attribute name="type" result="fail" desc="atom must have a type."/>
</atom>


references


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[edit]

element abstractAtom

code 

<xs:element name="abstractAtom" type="bt:atom" abstract="true" block="restriction" final="restriction"/>

documentation

An abstract atom element for the atomSeq element.


references


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[edit]

attributeGroup structureAttrs

code 

<xs:attributeGroup name="structureAttrs">
  <xs:attributeGroup ref="bt:dataAttrs"/>
  <xs:attribute name="accNumber" type="bt:accessionNumber" use="optional"/>
  <xs:attribute name="source" type="bt:atomStructureSource" use="optional"/>
</xs:attributeGroup>

documentation

Attributes for structure data. source specifies the source of the structure data. In addition accNumber can be set to an accession number dependant on the data source if source identifies only the data source (e.g. database) but not the data item itself.


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[edit]

complexType atomSequence

code 

<xs:complexType name="atomSequence" block="restriction" final="restriction">
  <xs:sequence>
    <xs:element ref="bt:abstractAtom" minOccurs="1" maxOccurs="unbounded"/>
  </xs:sequence>
  <xs:attributeGroup ref="bt:structureAttrs"/>
  <xs:attribute name="unit" type="bt:distanceUnits" use="optional" default="angstroem"/>
</xs:complexType>

documentation

A sequence of atoms. An atom sequence must contain at least one atom. The abstractAtom element must be replaced by a concrete element of type atom. This is done via a substitution group:

<xs:element xmlns:xs="http://www.w3.org/2001/XMLSchema" name="atom" type="bt:atom" substitutionGroup="bt:abstractAtom"/>.

The coordinates of each atom are relative to the specified distance unit (default is Angstroem).

appinfo biotypes/tests/TestAtomSeq.xml 

<atomSeq xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
  <test:case test="with" result="fail" desc="atomSeq must not be empty."/>
  <test:case test="with" result="pass" desc="atomSeq may contain one or more atoms.">
    <atom y="1.0" z="1.0" type="C" x="1.0"/>
    <atom y="1.0" z="1.0" type="C" x="1.0"/>
  </test:case>
</atomSeq>


references


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[edit]

complexType atomConnection

code 

<xs:complexType name="atomConnection" abstract="true" block="restriction" final="restriction">
  <xs:attribute name="atomType1" type="bt:atomName" use="required"/>
  <xs:attribute name="atomType2" type="bt:atomName" use="required"/>
</xs:complexType>

documentation

Specifies a connection between two atoms identified by atomType1 and atomType2. A connection can be e.g. a bond or a contact.


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[edit]

complexType atomContact

code 

<xs:complexType name="atomContact">
  <xs:complexContent>
    <xs:extension base="bt:atomConnection">
      <xs:attribute name="distance" type="bt:distance" use="required"/>
      <xs:attribute name="unit" type="bt:distanceUnits" use="optional" default="angstroem"/>
    </xs:extension>
  </xs:complexContent>
</xs:complexType>

documentation

Specifies a (close) contact between two atoms. The distance of the two atoms is specified by distance. The unit of the distance depends on unit. The default setting for unit is angstroem.


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[edit]

Classification

This section contains type declaration for the classification of biological objects.


[edit]

simpleType classificationSources

code 

<xs:simpleType name="classificationSources">
  <xs:restriction base="xs:token">
    <xs:enumeration value="urn:bts:cath"/>
    <xs:enumeration value="urn:bts:scop"/>
  </xs:restriction>
</xs:simpleType>

documentation

A list of predefined classification source names.


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[edit]

simpleType classificationSource

code 

<xs:simpleType name="classificationSource">
  <xs:union memberTypes="bt:sourceUri bt:classificationSources"/>
</xs:simpleType>

documentation

The source of a classification. May be an URI, a LSID or one of the predefined source names.


references


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[edit]

simpleType classificationValue

code 

<xs:simpleType name="classificationValue">
  <xs:restriction base="xs:token">
    <xs:minLength value="1"/>
  </xs:restriction>
</xs:simpleType>

documentation

Obsolete.


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[edit]

complexType classification

code 

<xs:complexType name="classification">
  <xs:attributeGroup ref="bt:dataAttrs"/>
  <xs:attribute name="source" type="bt:classificationSource" use="required"/>
  <xs:attribute name="accNumber" type="bt:classificationValue" use="required"/>
</xs:complexType>

documentation

Specifies a classification. The classification scheme is identified by source. The classification itself is specified by accNumber.


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[edit]

Pattern

This section contains type declaration for sequence patterns.


[edit]

simpleType patternSources

code 

<xs:simpleType name="patternSources">
  <xs:restriction base="xs:token">
    <xs:enumeration value="urn:bts:interpro"/>
    <xs:enumeration value="urn:bts:pfam"/>
    <xs:enumeration value="urn:bts:prodom"/>
    <xs:enumeration value="urn:bts:prosite"/>
  </xs:restriction>
</xs:simpleType>

documentation

A list of predefined sequence pattern source names.


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[edit]

simpleType patternSource

code 

<xs:simpleType name="patternSource">
  <xs:union memberTypes="bt:sourceUri bt:patternSources"/>
</xs:simpleType>

documentation

The source of a sequence pattern. May be an URI, a LSID or one of the predefined source names.


references


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[edit]

attributeGroup patternAttrs

code 

<xs:attributeGroup name="patternAttrs">
  <xs:attributeGroup ref="bt:dataAttrs"/>
  <xs:attribute name="source" type="bt:patternSource" use="required"/>
  <xs:attribute name="accNumber" type="bt:accessionNumber" use="required"/>
</xs:attributeGroup>

documentation

Attributes for pattern data. source specifies the source of the pattern data. In addition accNumber can be set to an accession number dependant on the data source if source identifies only the data source (e.g. database) but not the data item itself.


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[edit]

complexType patternBase

code 

<xs:complexType name="patternBase" mixed="true">
  <xs:complexContent>
    <xs:extension base="bt:anyContent">
      <xs:attributeGroup ref="bt:patternAttrs"/>
    </xs:extension>
  </xs:complexContent>
</xs:complexType>

documentation

A sequence pattern. The content of a pattern element is the pattern itself, e.g. a consensus sequence or a HMM, and may contain elements from any namespace and text.


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[edit]

complexType patternProfile

code 

<xs:complexType name="patternProfile">
  <xs:sequence>
    <xs:element ref="bt:abstractPatternProfileMember" minOccurs="1" maxOccurs="unbounded"/>
  </xs:sequence>
  <xs:attributeGroup ref="bt:dataAttrs"/>
  <xs:attribute name="source" type="bt:patternSource" use="optional"/>
  <xs:attribute name="accNumber" type="bt:accessionNumber" use="optional"/>
</xs:complexType>

documentation

A sequence pattern profile. A profile must contain at least one pattern reference.


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[edit]

complexType patternProfileMember

code 

<xs:complexType name="patternProfileMember" block="restriction" final="restriction">
  <xs:complexContent>
    <xs:extension base="bt:patternBase">
      <xs:attribute name="occurence" type="xs:positiveInteger" use="required"/>
    </xs:extension>
  </xs:complexContent>
</xs:complexType>

documentation

A member of a pattern profile. The number of occurences of the pattern in the sequence(s) must be specified.


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[edit]

element abstractPatternProfileMember

code 

<xs:element name="abstractPatternProfileMember" type="bt:patternProfileMember" abstract="true" block="restriction" final="restriction"/>

documentation

Abstract pattern element for a pattern profile.


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[edit]

complexType pattern

code 

<xs:complexType name="pattern" mixed="true">
  <xs:complexContent>
    <xs:extension base="bt:patternBase">
      <xs:attributeGroup ref="bt:scopeAttrs"/>
    </xs:extension>
  </xs:complexContent>
</xs:complexType>

documentation

A single sequence pattern. The location of the pattern inside the sequence is identified by the attributes from and to.


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[edit]

Alignment

This section contains type declaration for sequence alignments.


[edit]

simpleType alignmentSources

code 

<xs:simpleType name="alignmentSources">
  <xs:restriction base="xs:token">
    <xs:enumeration value="urn:bts:clustalw"/>
  </xs:restriction>
</xs:simpleType>

documentation

A list of predefined sequence alignment source names.


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[edit]

simpleType alignmentSource

code 

<xs:simpleType name="alignmentSource">
  <xs:union memberTypes="bt:sourceUri bt:alignmentSources"/>
</xs:simpleType>

documentation

The source of a sequence alignment. May be an URI, a LSID or one of the predefined source names.


references


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[edit]

complexType multipleAlignment

code 

<xs:complexType name="multipleAlignment" final="restriction" block="restriction">
  <xs:choice>
    <xs:sequence minOccurs="2" maxOccurs="unbounded">
      <xs:element ref="bt:abstractAlignedRnaSequence"/>
    </xs:sequence>
    <xs:sequence minOccurs="2" maxOccurs="unbounded">
      <xs:element ref="bt:abstractAlignedDnaSequence"/>
    </xs:sequence>
    <xs:sequence minOccurs="2" maxOccurs="unbounded">
      <xs:element ref="bt:abstractAlignedSecondaryStructureSequence"/>
    </xs:sequence>
    <xs:sequence minOccurs="2" maxOccurs="unbounded">
      <xs:element ref="bt:abstractAlignedAminoAcidSequence"/>
    </xs:sequence>
    <xs:sequence minOccurs="2" maxOccurs="unbounded">
      <xs:element ref="bt:abstractAlignedRnaSecondaryStructureSequence"/>
    </xs:sequence>
  </xs:choice>
  <xs:attributeGroup ref="bt:dataAttrs"/>
  <xs:attribute name="score" type="bt:score" use="optional"/>
  <xs:attribute name="source" type="bt:alignmentSource" use="optional"/>
  <xs:attribute name="accNumber" type="bt:accessionNumber" use="optional"/>
</xs:complexType>

documentation

A multiple sequence alignment. A overall score may be assigned to the multiple alignment using the score attribute. The source of the multiple alignment can be specified using the attributes source and accNumber. A multiple alignment must contain at least two aligned sequences. Thus one or more of the abstract elements abstractAlignedRnaSequence, abstractAlignedDnaSequence, abstractAlignedSecondaryStructureSequence,abstractAlignedAminoAcidSequence or abstractAlignedRnaSecondaryStructureSequence must be replaced by a concrete element. This can be done via a substitution group.


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[edit]

attributeGroup alignedSequenceAttrs

code 

<xs:attributeGroup name="alignedSequenceAttrs">
  <xs:attribute name="score" type="bt:score" use="optional"/>
</xs:attributeGroup>

documentation

The attributes for an aligned sequence. The individual score for an aligned sequence may be set using the score attribute.


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[edit]

complexType alignedRnaSequence

code 

<xs:complexType name="alignedRnaSequence">
  <xs:simpleContent>
    <xs:extension base="bt:gappedAmbiguousRnaSequence">
      <xs:attributeGroup ref="bt:alignedSequenceAttrs"/>
    </xs:extension>
  </xs:simpleContent>
</xs:complexType>

documentation

An aligned RNA sequence.


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[edit]

element abstractAlignedRnaSequence

code 

<xs:element name="abstractAlignedRnaSequence" type="bt:alignedRnaSequence" abstract="true" final="restriction" block="restriction"/>

documentation

An abstract aligned RNA sequence element for the multiple alignment.


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[edit]

complexType alignedDnaSequence

code 

<xs:complexType name="alignedDnaSequence">
  <xs:simpleContent>
    <xs:extension base="bt:gappedAmbiguousDnaSequence">
      <xs:attributeGroup ref="bt:alignedSequenceAttrs"/>
    </xs:extension>
  </xs:simpleContent>
</xs:complexType>

documentation

An aligned DNA sequence.


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element abstractAlignedDnaSequence

code 

<xs:element name="abstractAlignedDnaSequence" type="bt:alignedDnaSequence" abstract="true" final="restriction" block="restriction"/>

documentation

An abstract aligned DNA sequence element for the multiple alignment.


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complexType alignedSecondaryStructureSequence

code 

<xs:complexType name="alignedSecondaryStructureSequence">
  <xs:simpleContent>
    <xs:extension base="bt:gappedAmbiguousSecondaryStructureSequence">
      <xs:attributeGroup ref="bt:alignedSequenceAttrs"/>
    </xs:extension>
  </xs:simpleContent>
</xs:complexType>

documentation

An aligned secondary structure sequence.


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[edit]

element abstractAlignedSecondaryStructureSequence

code 

<xs:element name="abstractAlignedSecondaryStructureSequence" type="bt:alignedSecondaryStructureSequence" abstract="true" final="restriction" block="restriction"/>

documentation

An abstract aligned secondary structure sequence element for the multiple alignment.


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complexType alignedRnaSecondaryStructureSequence

code 

<xs:complexType name="alignedRnaSecondaryStructureSequence">
  <xs:simpleContent>
    <xs:extension base="bt:gappedRnaSecondaryStructureSequence">
      <xs:attributeGroup ref="bt:alignedSequenceAttrs"/>
    </xs:extension>
  </xs:simpleContent>
</xs:complexType>

documentation

An aligned rna secondary structure sequence.


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element abstractAlignedRnaSecondaryStructureSequence

code 

<xs:element name="abstractAlignedRnaSecondaryStructureSequence" type="bt:alignedRnaSecondaryStructureSequence" abstract="true" final="restriction" block="restriction"/>

documentation

An abstract aligned rna secondary structure sequence element for the multiple alignment.


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complexType alignedAminoAcidSequence

code 


<xs:complexType name="alignedAminoAcidSequence">
  <xs:simpleContent>
    <xs:extension base="bt:gappedAmbiguousAminoAcidOneLetterSequence">
      <xs:attributeGroup ref="bt:alignedSequenceAttrs"/>
    </xs:extension>
  </xs:simpleContent>
</xs:complexType>

documentation

An aligned amino acid sequence.


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[edit]

element abstractAlignedAminoAcidSequence

code 

<xs:element name="abstractAlignedAminoAcidSequence" type="bt:alignedAminoAcidSequence" abstract="true" final="restriction" block="restriction"/>

documentation

An abstract aligned amino acid sequence element for the multiple alignment.


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