Schema BioXSD-1.1.xsd


schema location:  http://bioxsd.org/BioXSD-1.1.xsd
attribute form default:  unqualified
element form default:  qualified
targetNamespace:  http://bioxsd.org/BioXSD-1.1
 
Complex types  Simple types  Attr. groups 
AlignedAminoacidSequence  Accession  WebserviceReference 
AlignedBiosequence  AminoacidSequence 
AlignedGeneralAminoacidSequence  AnyDecimal 
AlignedGeneralNucleotideSequence  AnyInteger 
AlignedNucleotideSequence  BaseQualityString 
AminoacidSequenceAlignment  Biosequence 
AminoacidSequenceRecord  Certainty 
AminoacidTranslationData  ChromosomeName 
BiosequenceAlignment  DatabaseName 
BiosequenceRecord  EmblAccession 
DatabaseReference  ExtendedGenbankAccession 
EntryReference  ExtendedUniprotAccession 
Evidence  GenbankAccession 
ExperimentalEvidence  GenbankMgaAccession 
FeatureOccurrenceData  GenbankNucleotideAccession 
FeatureRecord  GenbankProteinAccession 
FeatureType  GenbankWgsAccession 
FeatureTypeDetails  GeneralAminoacidSequence 
Flag  GeneralNucleotideSequence 
Frameshift  InsertionInteger 
Gap  LocalId 
GeneralAminoacidSequenceAlignment  Name 
GeneralAminoacidSequenceRecord  NcbiGeneticCodeId 
GeneralNucleotideSequenceAlignment  NcbiTaxonomyId 
GeneralNucleotideSequenceRecord  NonnegativeInteger 
GeneralOutsideSequencePoint  NonzeroInteger 
GeneralOutsideSequencePosition  NucleotideSequence 
GeneralOutsideSequenceSegment  OntologyName 
GeneralSequenceInsertionPoint  OutsidePositionCorrespondance 
GeneralSequencePartition  Phase 
GeneralSequencePoint  PositiveInteger 
GeneralSequencePosition  Probability 
GeneralSequenceSegment  PubmedId 
GeneticCode  QualitativeCertainty 
Method  RecommendedDatabaseName 
MethodResult  RecommendedOntologyName 
NucleotideSequenceAlignment  RecommendedReliability 
NucleotideSequenceRecord  RecommendedScoreName 
OntologyReference  RecommendedVerdict 
OutsideSequencePoint  Reliability 
OutsideSequencePosition  ScoreName 
OutsideSequenceSegment  ScoreValue 
PredictionResult  Strand 
Result  Text 
Score  UniprotAccession 
ScoreType  Uri 
SemanticConcept  Verdict 
SequenceInsertionPoint 
SequencePartition 
SequencePoint 
SequencePosition 
SequenceReference 
SequenceSegment 
Species 
TranslationData 


GeneralNucleotideSequence  simpleType
type restriction of xs:string
used by
element GeneralNucleotideSequenceRecord/sequence
simpleTypes Biosequence NucleotideSequence
attribute GeneticCode/codon/@code
facets
Kind Value annotation 
maxLength 1000000000000 
pattern [acgtrykmswbdhvn]+ 
pattern [acgurykmswbdhvn]+ 
documentation Nucleotide sequence, possibly with ambiguous ("degenerate") bases
source <xs:simpleType name="GeneralNucleotideSequence" sawsdl:modelReference="http://edamontology.org/data_2975 http://edamontology.org/format_1210 http://edamontology.org/format_1957">
  <xs:annotation>
    <xs:documentation>Nucleotide sequence, possibly with ambiguous ("degenerate") bases</xs:documentation>
  </xs:annotation>
  <xs:restriction base="xs:string">
    <xs:maxLength value="1000000000000"/>
    <xs:pattern value="[acgtrykmswbdhvn]+"/>
    <xs:pattern value="[acgurykmswbdhvn]+"/>
  </xs:restriction>
</xs:simpleType>

GeneralAminoacidSequence  simpleType
type restriction of xs:string
used by
element GeneralAminoacidSequenceRecord/sequence
simpleTypes AminoacidSequence Biosequence
attribute GeneticCode/codon/@aminoacid
facets
Kind Value annotation 
maxLength 1000000000 
pattern [ACDEFGHIKLMNPQRSTVWYBJZXUO]+ 
documentation Amino-acid sequence, possibly with ambiguous residues (Asx, Xle, Glx, Xaa/Unk) and additional residues (Pyl and Sec)
source <xs:simpleType name="GeneralAminoacidSequence" sawsdl:modelReference="http://edamontology.org/data_2974 http://edamontology.org/format_1219 http://edamontology.org/format_1957">
  <xs:annotation>
    <xs:documentation>Amino-acid sequence, possibly with ambiguous residues (Asx, Xle, Glx, Xaa/Unk) and additional residues (Pyl and Sec)</xs:documentation>
  </xs:annotation>
  <xs:restriction base="xs:string">
    <xs:maxLength value="1000000000"/>
    <xs:pattern value="[ACDEFGHIKLMNPQRSTVWYBJZXUO]+"/>
  </xs:restriction>
</xs:simpleType>

Biosequence  simpleType
type union of (GeneralNucleotideSequence, GeneralAminoacidSequence)
used by
elements FeatureOccurrenceData/variation/canonicalVariant BiosequenceRecord/sequence SequenceReference/supersequence FeatureOccurrenceData/variation/variant
documentation Nucleotide or amino-acid sequence, possibly with ambiguous bases and residues
source <xs:simpleType name="Biosequence" sawsdl:modelReference="http://edamontology.org/data_0848 http://edamontology.org/format_2094 http://edamontology.org/format_1957">
  <xs:annotation>
    <xs:documentation>Nucleotide or amino-acid sequence, possibly with ambiguous bases and residues</xs:documentation>
  </xs:annotation>
  <xs:union memberTypes="GeneralNucleotideSequence GeneralAminoacidSequence"/>
</xs:simpleType>

NucleotideSequence  simpleType
type restriction of GeneralNucleotideSequence
used by
element NucleotideSequenceRecord/sequence
facets
Kind Value annotation 
maxLength 1000000000000 
pattern [acgt]+ 
pattern [acgu]+ 
documentation Nucleotide sequence without ambiguous ("degenerate") bases
source <xs:simpleType name="NucleotideSequence" sawsdl:modelReference="http://edamontology.org/format_2568">
  <xs:annotation>
    <xs:documentation>Nucleotide sequence without ambiguous ("degenerate") bases</xs:documentation>
  </xs:annotation>
  <xs:restriction base="GeneralNucleotideSequence">
    <xs:pattern value="[acgt]+"/>
    <xs:pattern value="[acgu]+"/>
  </xs:restriction>
</xs:simpleType>

AminoacidSequence  simpleType
type restriction of GeneralAminoacidSequence
used by
element AminoacidSequenceRecord/sequence
facets
Kind Value annotation 
maxLength 1000000000 
pattern [ACDEFGHIKLMNPQRSTVWY]+ 
documentation Amino-acid sequence without ambiguous and additional residues (Pyl, Sec)
source <xs:simpleType name="AminoacidSequence" sawsdl:modelReference="http://edamontology.org/format_2607">
  <xs:annotation>
    <xs:documentation>Amino-acid sequence without ambiguous and additional residues (Pyl, Sec)</xs:documentation>
  </xs:annotation>
  <xs:restriction base="GeneralAminoacidSequence">
    <xs:pattern value="[ACDEFGHIKLMNPQRSTVWY]+"/>
  </xs:restriction>
</xs:simpleType>

BaseQualityString  simpleType
type restriction of xs:string
used by
elements BiosequenceRecord/inlineBaseQuality GeneralNucleotideSequenceRecord/inlineBaseQuality NucleotideSequenceRecord/inlineBaseQuality
facets
Kind Value annotation 
maxLength 1000000000000 
pattern [!-~]+ 
source <xs:simpleType name="BaseQualityString">
  <xs:restriction base="xs:string">
    <xs:maxLength value="1000000000000"/>
    <xs:pattern value="[!-~]+"/>
  </xs:restriction>
</xs:simpleType>

BiosequenceRecord  complexType
diagram BioXSD-1.1_p59.png
children sequence species reference name note translationData inlineBaseQuality
used by
elements AlignedBiosequence/sequenceRecord FeatureRecord/referenceSequence/sequenceRecord
complexTypes GeneralAminoacidSequenceRecord GeneralNucleotideSequenceRecord
documentation Nucleotide or amino-acid sequence record including the generic sequence and optional metadata
source <xs:complexType name="BiosequenceRecord" sawsdl:modelReference="http://edamontology.org/data_2043 http://edamontology.org/format_2352">
  <xs:annotation>
    <xs:documentation>Nucleotide or amino-acid sequence record including the generic sequence and optional metadata</xs:documentation>
  </xs:annotation>
  <xs:sequence>
    <xs:element name="sequence" type="Biosequence"/>
    <xs:element name="species" type="Species" minOccurs="0">
      <xs:annotation>
        <xs:documentation>Biological source of the sequence/biopolymer</xs:documentation>
      </xs:annotation>
    </xs:element>
    <xs:element name="reference" type="SequenceReference" minOccurs="0">
      <xs:annotation>
        <xs:documentation>Identification of the sequence record. May refer to data the sequence originates from: a database entry or an explicit super-sequence.
NB. ID/accession is part of the 'reference'</xs:documentation>
      </xs:annotation>
    </xs:element>
    <xs:element name="name" type="Name" minOccurs="0" sawsdl:modelReference="http://www.w3.org/2000/01/rdf-schema#label http://edamontology.org/data_2154"/>
    <!--"Sequence name"(2154)-->
    <xs:element name="note" type="Text" minOccurs="0" sawsdl:modelReference="http://www.w3.org/2000/01/rdf-schema#comment"/>
    <xs:element name="translationData" type="TranslationData" minOccurs="0"/>
    <xs:element name="inlineBaseQuality" type="BaseQualityString" minOccurs="0"/>
  </xs:sequence>
</xs:complexType>
model referencehttp://edamontology.org/data_2043
http://edamontology.org/format_2352

GeneralNucleotideSequenceRecord  complexType
diagram BioXSD-1.1_p182.png
type restriction of BiosequenceRecord
properties
base BiosequenceRecord
children sequence species reference name note translationData inlineBaseQuality
used by
element AlignedGeneralNucleotideSequence/sequenceRecord
complexType NucleotideSequenceRecord
documentation Nucleotide sequence record including the generic nucleotide sequence and optional metadata
source <xs:complexType name="GeneralNucleotideSequenceRecord" sawsdl:modelReference="http://edamontology.org/data_2046 http://edamontology.org/format_2352">
  <xs:annotation>
    <xs:documentation>Nucleotide sequence record including the generic nucleotide sequence and optional metadata</xs:documentation>
  </xs:annotation>
  <xs:complexContent>
    <xs:restriction base="BiosequenceRecord">
      <xs:sequence>
        <xs:element name="sequence" type="GeneralNucleotideSequence"/>
        <xs:element name="species" type="Species" minOccurs="0">
          <xs:annotation>
            <xs:documentation>Biological source of the sequence/biopolymer</xs:documentation>
          </xs:annotation>
        </xs:element>
        <xs:element name="reference" type="SequenceReference" minOccurs="0">
          <xs:annotation>
            <xs:documentation>Identification of the sequence record. May refer to data the sequence originates from: a database entry or an explicit super-sequence.
NB. ID/accession is part of the 'reference'</xs:documentation>
          </xs:annotation>
        </xs:element>
        <xs:element name="name" type="Name" minOccurs="0"/>
        <xs:element name="note" type="Text" minOccurs="0"/>
        <xs:element name="translationData" type="TranslationData" minOccurs="0"/>
        <xs:element name="inlineBaseQuality" type="BaseQualityString" minOccurs="0"/>
      </xs:sequence>
    </xs:restriction>
  </xs:complexContent>
</xs:complexType>
model referencehttp://edamontology.org/data_2046
http://edamontology.org/format_2352

GeneralAminoacidSequenceRecord  complexType
diagram BioXSD-1.1_p171.png
type restriction of BiosequenceRecord
properties
base BiosequenceRecord
children sequence species reference name note translationData
used by
element AlignedGeneralAminoacidSequence/sequenceRecord
complexType AminoacidSequenceRecord
documentation Amino-acid sequence record including the generic amino-acid sequence and optional metadata
source <xs:complexType name="GeneralAminoacidSequenceRecord" sawsdl:modelReference="http://edamontology.org/data_2047 http://edamontology.org/format_2352">
  <xs:annotation>
    <xs:documentation>Amino-acid sequence record including the generic amino-acid sequence and optional metadata</xs:documentation>
  </xs:annotation>
  <xs:complexContent>
    <xs:restriction base="BiosequenceRecord">
      <xs:sequence>
        <xs:element name="sequence" type="GeneralAminoacidSequence"/>
        <xs:element name="species" type="Species" minOccurs="0">
          <xs:annotation>
            <xs:documentation>Biological source of the sequence/biopolymer</xs:documentation>
          </xs:annotation>
        </xs:element>
        <xs:element name="reference" type="SequenceReference" minOccurs="0">
          <xs:annotation>
            <xs:documentation>Identification of the sequence record. May refer to data the sequence originates from: a database entry or an explicit super-sequence.
NB. ID/accession is part of the 'reference'</xs:documentation>
          </xs:annotation>
        </xs:element>
        <xs:element name="name" type="Name" minOccurs="0"/>
        <xs:element name="note" type="Text" minOccurs="0"/>
        <xs:element name="translationData" type="AminoacidTranslationData" minOccurs="0"/>
      </xs:sequence>
    </xs:restriction>
  </xs:complexContent>
</xs:complexType>
model referencehttp://edamontology.org/data_2047
http://edamontology.org/format_2352

NucleotideSequenceRecord  complexType
diagram BioXSD-1.1_p224.png
type restriction of GeneralNucleotideSequenceRecord
properties
base GeneralNucleotideSequenceRecord
children sequence species reference name note translationData inlineBaseQuality
used by
element AlignedNucleotideSequence/sequenceRecord
documentation Nucleotide sequence record including the unambiguous nucleotide sequence and optional metadata
source <xs:complexType name="NucleotideSequenceRecord" sawsdl:modelReference="http://edamontology.org/data_2046 http://edamontology.org/format_2352">
  <xs:annotation>
    <xs:documentation>Nucleotide sequence record including the unambiguous nucleotide sequence and optional metadata</xs:documentation>
  </xs:annotation>
  <xs:complexContent>
    <xs:restriction base="GeneralNucleotideSequenceRecord">
      <xs:sequence>
        <xs:element name="sequence" type="NucleotideSequence"/>
        <xs:element name="species" type="Species" minOccurs="0">
          <xs:annotation>
            <xs:documentation>Biological source of the sequence/biopolymer</xs:documentation>
          </xs:annotation>
        </xs:element>
        <xs:element name="reference" type="SequenceReference" minOccurs="0">
          <xs:annotation>
            <xs:documentation>Identification of the sequence record. May refer to data the sequence originates from: a database entry or an explicit super-sequence.
NB. ID/accession is part of the 'reference'</xs:documentation>
          </xs:annotation>
        </xs:element>
        <xs:element name="name" type="Name" minOccurs="0"/>
        <xs:element name="note" type="Text" minOccurs="0"/>
        <xs:element name="translationData" type="TranslationData" minOccurs="0"/>
        <xs:element name="inlineBaseQuality" type="BaseQualityString" minOccurs="0"/>
      </xs:sequence>
    </xs:restriction>
  </xs:complexContent>
</xs:complexType>
model referencehttp://edamontology.org/data_2046
http://edamontology.org/format_2352

AminoacidSequenceRecord  complexType
diagram BioXSD-1.1_p46.png
type restriction of GeneralAminoacidSequenceRecord
properties
base GeneralAminoacidSequenceRecord
children sequence species reference name note translationData
used by
element AlignedAminoacidSequence/sequenceRecord
documentation Amino-acid sequence record including the unambiguous amino-acid sequence and optional metadata
source <xs:complexType name="AminoacidSequenceRecord" sawsdl:modelReference="http://edamontology.org/data_2047 http://edamontology.org/format_2352">
  <xs:annotation>
    <xs:documentation>Amino-acid sequence record including the unambiguous amino-acid sequence and optional metadata</xs:documentation>
  </xs:annotation>
  <xs:complexContent>
    <xs:restriction base="GeneralAminoacidSequenceRecord">
      <xs:sequence>
        <xs:element name="sequence" type="AminoacidSequence"/>
        <xs:element name="species" type="Species" minOccurs="0">
          <xs:annotation>
            <xs:documentation>Biological source of the sequence/biopolymer</xs:documentation>
          </xs:annotation>
        </xs:element>
        <xs:element name="reference" type="SequenceReference" minOccurs="0">
          <xs:annotation>
            <xs:documentation>Identification of the sequence record. May refer to data the sequence originates from: a database entry or an explicit super-sequence.
NB. ID/accession is part of the 'reference'</xs:documentation>
          </xs:annotation>
        </xs:element>
        <xs:element name="name" type="Name" minOccurs="0"/>
        <xs:element name="note" type="Text" minOccurs="0"/>
        <xs:element name="translationData" type="AminoacidTranslationData" minOccurs="0"/>
      </xs:sequence>
    </xs:restriction>
  </xs:complexContent>
</xs:complexType>
model referencehttp://edamontology.org/data_2047
http://edamontology.org/format_2352

Gap  complexType
diagram BioXSD-1.1_p166.png
used by
elements AlignedBiosequence/gap AlignedGeneralNucleotideSequence/gap AlignedGeneralAminoacidSequence/gap AlignedNucleotideSequence/gap AlignedAminoacidSequence/gap FeatureOccurrenceData/alignment/alignmentOfReference/gap
attributes
Name  Type  Use  Default  Fixed  annotation
posInsertionIntegerrequired      
lenPositiveIntegerrequired      
documentation Single gap in an aligned sequence
source <xs:complexType name="Gap">
  <xs:annotation>
    <xs:documentation>Single gap in an aligned sequence</xs:documentation>
  </xs:annotation>
  <xs:attribute name="pos" type="InsertionInteger" use="required" sawsdl:modelReference="http://edamontology.org/data_1016"/>
  <xs:attribute name="len" type="PositiveInteger" use="required"/>
</xs:complexType>

Frameshift  complexType
diagram BioXSD-1.1_p165.png
used by
elements AlignedBiosequence/frameshift AlignedGeneralAminoacidSequence/frameshift AlignedAminoacidSequence/frameshift FeatureOccurrenceData/alignment/alignmentOfReference/frameshift
attributes
Name  Type  Use  Default  Fixed  annotation
posInsertionIntegerrequired      
basesderived by: NonzeroIntegerrequired      
documentation Frame-shift in an aligned amino-acid sequence
source <xs:complexType name="Frameshift">
  <xs:annotation>
    <xs:documentation>Frame-shift in an aligned amino-acid sequence</xs:documentation>
  </xs:annotation>
  <xs:attribute name="pos" type="InsertionInteger" use="required" sawsdl:modelReference="http://edamontology.org/data_1016"/>
  <xs:attribute name="bases" use="required">
    <xs:simpleType>
      <xs:restriction base="NonzeroInteger">
        <xs:minInclusive value="-2"/>
        <xs:maxInclusive value="2"/>
      </xs:restriction>
    </xs:simpleType>
  </xs:attribute>
</xs:complexType>

AlignedBiosequence  complexType
diagram BioXSD-1.1_p8.png
children localAlignmentPosition sequenceRecord sequenceReference sequenceName species genomeBuild chromosome subsequencePosition variantAccession variantNote gap frameshift reversedDirection sequenceScore
used by
elements BiosequenceAlignment/alignedSequence FeatureOccurrenceData/alignment/alignedSequence
complexTypes AlignedGeneralAminoacidSequence AlignedGeneralNucleotideSequence
source <xs:complexType name="AlignedBiosequence">
  <xs:sequence>
    <xs:element name="localAlignmentPosition" type="SequencePosition" minOccurs="0">
      <xs:annotation>
        <xs:documentation>Coordinates of the locally aligned sub-sequence. (Not present means global alignment)</xs:documentation>
      </xs:annotation>
    </xs:element>
    <xs:choice>
      <xs:element name="sequenceRecord" type="BiosequenceRecord"/>
      <xs:element name="sequenceReference" type="SequenceReference"/>
      <xs:element name="sequenceName" type="Name" sawsdl:modelReference="http://edamontology.org/data_2154"/>
      <xs:sequence>
        <xs:element name="species" type="Species"/>
        <xs:element name="genomeBuild" type="EntryReference" sawsdl:modelReference="http://purl.org/dc/elements/1.1/version http://edamontology.org/data_2041 http://edamontology.org/data_2340"/>
        <!--"Genome build identifier"(2340)-->
        <!--"Genome version information"(2041)-->
        <xs:element name="chromosome" type="ChromosomeName"/>
        <xs:element name="subsequencePosition" type="SequencePosition" minOccurs="0">
          <xs:annotation>
            <xs:documentation>Coordinates of a sub-sequence within the chromosome</xs:documentation>
          </xs:annotation>
        </xs:element>
        <xs:element name="variantAccession" type="Accession" minOccurs="0" sawsdl:modelReference="http://edamontology.org/data_1063 http://edamontology.org/data_2091"/>
        <xs:element name="variantNote" type="Name" minOccurs="0" sawsdl:modelReference="http://edamontology.org/data_1063"/>
      </xs:sequence>
    </xs:choice>
    <xs:element name="gap" type="Gap" minOccurs="0" maxOccurs="unbounded"/>
    <xs:element name="frameshift" type="Frameshift" minOccurs="0" maxOccurs="unbounded"/>
    <xs:element name="reversedDirection" type="Flag" minOccurs="0"/>
    <xs:element name="sequenceScore" type="Result" minOccurs="0" maxOccurs="unbounded"/>
  </xs:sequence>
</xs:complexType>

AlignedGeneralNucleotideSequence  complexType
diagram BioXSD-1.1_p30.png
type restriction of AlignedBiosequence
properties
base AlignedBiosequence
children localAlignmentPosition sequenceRecord gap reversedDirection sequenceScore
used by
element GeneralNucleotideSequenceAlignment/alignedSequence
complexType AlignedNucleotideSequence
source <xs:complexType name="AlignedGeneralNucleotideSequence">
  <xs:complexContent>
    <xs:restriction base="AlignedBiosequence">
      <xs:sequence>
        <xs:element name="localAlignmentPosition" type="SequencePosition" minOccurs="0">
          <xs:annotation>
            <xs:documentation>Coordinates of the locally aligned sub-sequence. (Not present means global alignment)</xs:documentation>
          </xs:annotation>
        </xs:element>
        <xs:element name="sequenceRecord" type="GeneralNucleotideSequenceRecord"/>
        <xs:element name="gap" type="Gap" minOccurs="0" maxOccurs="unbounded"/>
        <xs:element name="reversedDirection" type="Flag" minOccurs="0"/>
        <xs:element name="sequenceScore" type="Result" minOccurs="0" maxOccurs="unbounded"/>
      </xs:sequence>
    </xs:restriction>
  </xs:complexContent>
</xs:complexType>

AlignedGeneralAminoacidSequence  complexType
diagram BioXSD-1.1_p23.png
type restriction of AlignedBiosequence
properties
base AlignedBiosequence
children localAlignmentPosition sequenceRecord gap frameshift reversedDirection sequenceScore
used by
element GeneralAminoacidSequenceAlignment/alignedSequence
complexType AlignedAminoacidSequence
source <xs:complexType name="AlignedGeneralAminoacidSequence">
  <xs:complexContent>
    <xs:restriction base="AlignedBiosequence">
      <xs:sequence>
        <xs:element name="localAlignmentPosition" type="SequencePosition" minOccurs="0">
          <xs:annotation>
            <xs:documentation>Coordinates of the locally aligned sub-sequence. (Not present means global alignment)</xs:documentation>
          </xs:annotation>
        </xs:element>
        <xs:element name="sequenceRecord" type="GeneralAminoacidSequenceRecord"/>
        <xs:element name="gap" type="Gap" minOccurs="0" maxOccurs="unbounded"/>
        <xs:element name="frameshift" type="Frameshift" minOccurs="0" maxOccurs="unbounded"/>
        <xs:element name="reversedDirection" type="Flag" minOccurs="0"/>
        <xs:element name="sequenceScore" type="Result" minOccurs="0" maxOccurs="unbounded"/>
      </xs:sequence>
    </xs:restriction>
  </xs:complexContent>
</xs:complexType>

AlignedNucleotideSequence  complexType
diagram BioXSD-1.1_p36.png
type restriction of AlignedGeneralNucleotideSequence
properties
base AlignedGeneralNucleotideSequence
children localAlignmentPosition sequenceRecord gap reversedDirection sequenceScore
used by
element NucleotideSequenceAlignment/alignedSequence
source <xs:complexType name="AlignedNucleotideSequence">
  <xs:complexContent>
    <xs:restriction base="AlignedGeneralNucleotideSequence">
      <xs:sequence>
        <xs:element name="localAlignmentPosition" type="SequencePosition" minOccurs="0">
          <xs:annotation>
            <xs:documentation>Coordinates of the locally aligned sub-sequence. (Not present means global alignment)</xs:documentation>
          </xs:annotation>
        </xs:element>
        <xs:element name="sequenceRecord" type="NucleotideSequenceRecord"/>
        <xs:element name="gap" type="Gap" minOccurs="0" maxOccurs="unbounded"/>
        <xs:element name="reversedDirection" type="Flag" minOccurs="0"/>
        <xs:element name="sequenceScore" type="Result" minOccurs="0" maxOccurs="unbounded"/>
      </xs:sequence>
    </xs:restriction>
  </xs:complexContent>
</xs:complexType>

AlignedAminoacidSequence  complexType
diagram BioXSD-1.1_p1.png
type restriction of AlignedGeneralAminoacidSequence
properties
base AlignedGeneralAminoacidSequence
children localAlignmentPosition sequenceRecord gap frameshift reversedDirection sequenceScore
used by
element AminoacidSequenceAlignment/alignedSequence
source <xs:complexType name="AlignedAminoacidSequence">
  <xs:complexContent>
    <xs:restriction base="AlignedGeneralAminoacidSequence">
      <xs:sequence>
        <xs:element name="localAlignmentPosition" type="SequencePosition" minOccurs="0">
          <xs:annotation>
            <xs:documentation>Coordinates of the locally aligned sub-sequence. (Not present means global alignment)</xs:documentation>
          </xs:annotation>
        </xs:element>
        <xs:element name="sequenceRecord" type="AminoacidSequenceRecord"/>
        <xs:element name="gap" type="Gap" minOccurs="0" maxOccurs="unbounded"/>
        <xs:element name="frameshift" type="Frameshift" minOccurs="0" maxOccurs="unbounded"/>
        <xs:element name="reversedDirection" type="Flag" minOccurs="0"/>
        <xs:element name="sequenceScore" type="Result" minOccurs="0" maxOccurs="unbounded"/>
      </xs:sequence>
    </xs:restriction>
  </xs:complexContent>
</xs:complexType>

BiosequenceAlignment  complexType
diagram BioXSD-1.1_p55.png
children alignedBy alignedSequence note
used by
complexTypes GeneralAminoacidSequenceAlignment GeneralNucleotideSequenceAlignment
documentation Alignment of 2..n generic nucleotide or amino-acid sequences. A *multiple sequence alignment* in the sense that all sequences are treated equally
source <xs:complexType name="BiosequenceAlignment" sawsdl:modelReference="http://edamontology.org/data_0863 http://edamontology.org/format_2352">
  <xs:annotation>
    <xs:documentation>Alignment of 2..n generic nucleotide or amino-acid sequences. A *multiple sequence alignment* in the sense that all sequences are treated equally</xs:documentation>
  </xs:annotation>
  <xs:sequence>
    <xs:element name="alignedBy" type="MethodResult" minOccurs="0" maxOccurs="unbounded"/>
    <xs:element name="alignedSequence" type="AlignedBiosequence" minOccurs="2" maxOccurs="unbounded">
      <xs:unique name="uniqueGapPos_b">
        <xs:selector xpath="gap"/>
        <xs:field xpath="@pos"/>
      </xs:unique>
      <xs:unique name="uniqueFrameshiftPos_b">
        <xs:selector xpath="frameshift"/>
        <xs:field xpath="@pos"/>
      </xs:unique>
    </xs:element>
    <xs:element name="note" type="Text" minOccurs="0" sawsdl:modelReference="http://www.w3.org/2000/01/rdf-schema#comment"/>
  </xs:sequence>
</xs:complexType>
model referencehttp://edamontology.org/data_0863
http://edamontology.org/format_2352

GeneralNucleotideSequenceAlignment  complexType
diagram BioXSD-1.1_p178.png
type restriction of BiosequenceAlignment
properties
base BiosequenceAlignment
children alignedBy alignedSequence note
used by
complexType NucleotideSequenceAlignment
documentation Alignment of 2..n generic nucleotide sequences. A *multiple sequence alignment* in the sense that all sequences are treated equally
source <xs:complexType name="GeneralNucleotideSequenceAlignment" sawsdl:modelReference="http://edamontology.org/data_1383">
  <xs:annotation>
    <xs:documentation>Alignment of 2..n generic nucleotide sequences. A *multiple sequence alignment* in the sense that all sequences are treated equally</xs:documentation>
  </xs:annotation>
  <xs:complexContent>
    <xs:restriction base="BiosequenceAlignment">
      <xs:sequence>
        <xs:element name="alignedBy" type="MethodResult" minOccurs="0" maxOccurs="unbounded"/>
        <xs:element name="alignedSequence" type="AlignedGeneralNucleotideSequence" minOccurs="2" maxOccurs="unbounded">
          <xs:unique name="uniqueGapPos_gn">
            <xs:selector xpath="gap"/>
            <xs:field xpath="@pos"/>
          </xs:unique>
        </xs:element>
        <xs:element name="note" type="Text" minOccurs="0"/>
      </xs:sequence>
    </xs:restriction>
  </xs:complexContent>
</xs:complexType>
model referencehttp://edamontology.org/data_1383

GeneralAminoacidSequenceAlignment  complexType
diagram BioXSD-1.1_p167.png
type restriction of BiosequenceAlignment
properties
base BiosequenceAlignment
children alignedBy alignedSequence note
used by
complexType AminoacidSequenceAlignment
documentation Alignment of 2..n generic amino-acid sequences. A *multiple sequence alignment* in the sense that all sequences are treated equally
source <xs:complexType name="GeneralAminoacidSequenceAlignment" sawsdl:modelReference="http://edamontology.org/data_1384">
  <xs:annotation>
    <xs:documentation>Alignment of 2..n generic amino-acid sequences. A *multiple sequence alignment* in the sense that all sequences are treated equally</xs:documentation>
  </xs:annotation>
  <xs:complexContent>
    <xs:restriction base="BiosequenceAlignment">
      <xs:sequence>
        <xs:element name="alignedBy" type="MethodResult" minOccurs="0" maxOccurs="unbounded"/>
        <xs:element name="alignedSequence" type="AlignedGeneralAminoacidSequence" minOccurs="2" maxOccurs="unbounded">
          <xs:unique name="uniqueGapPos_ga">
            <xs:selector xpath="gap"/>
            <xs:field xpath="@pos"/>
          </xs:unique>
          <xs:unique name="uniqueFrameshiftPos_ga">
            <xs:selector xpath="frameshift"/>
            <xs:field xpath="@pos"/>
          </xs:unique>
        </xs:element>
        <xs:element name="note" type="Text" minOccurs="0"/>
      </xs:sequence>
    </xs:restriction>
  </xs:complexContent>
</xs:complexType>
model referencehttp://edamontology.org/data_1384

NucleotideSequenceAlignment  complexType
diagram BioXSD-1.1_p220.png
type restriction of GeneralNucleotideSequenceAlignment
properties
base GeneralNucleotideSequenceAlignment
children alignedBy alignedSequence note
documentation Alignment of 2..n nucleotide sequences. A *multiple sequence alignment* in the sense that all sequences are treated equally
source <xs:complexType name="NucleotideSequenceAlignment">
  <xs:annotation>
    <xs:documentation>Alignment of 2..n nucleotide sequences. A *multiple sequence alignment* in the sense that all sequences are treated equally</xs:documentation>
  </xs:annotation>
  <xs:complexContent>
    <xs:restriction base="GeneralNucleotideSequenceAlignment">
      <xs:sequence>
        <xs:element name="alignedBy" type="MethodResult" minOccurs="0" maxOccurs="unbounded"/>
        <xs:element name="alignedSequence" type="AlignedNucleotideSequence" minOccurs="2" maxOccurs="unbounded">
          <xs:unique name="uniqueGapPos_n">
            <xs:selector xpath="gap"/>
            <xs:field xpath="@pos"/>
          </xs:unique>
        </xs:element>
        <xs:element name="note" type="Text" minOccurs="0"/>
      </xs:sequence>
    </xs:restriction>
  </xs:complexContent>
</xs:complexType>

AminoacidSequenceAlignment  complexType
diagram BioXSD-1.1_p42.png
type restriction of GeneralAminoacidSequenceAlignment
properties
base GeneralAminoacidSequenceAlignment
children alignedBy alignedSequence note
documentation Alignment of 2..n amino-acid sequences. A *multiple sequence alignment* in the sense that all sequences are treated equally
source <xs:complexType name="AminoacidSequenceAlignment">
  <xs:annotation>
    <xs:documentation>Alignment of 2..n amino-acid sequences. A *multiple sequence alignment* in the sense that all sequences are treated equally</xs:documentation>
  </xs:annotation>
  <xs:complexContent>
    <xs:restriction base="GeneralAminoacidSequenceAlignment">
      <xs:sequence>
        <xs:element name="alignedBy" type="MethodResult" minOccurs="0" maxOccurs="unbounded"/>
        <xs:element name="alignedSequence" type="AlignedAminoacidSequence" minOccurs="2" maxOccurs="unbounded">
          <xs:unique name="uniqueGapPos_a">
            <xs:selector xpath="gap"/>
            <xs:field xpath="@pos"/>
          </xs:unique>
          <xs:unique name="uniqueFrameshiftPos_a">
            <xs:selector xpath="frameshift"/>
            <xs:field xpath="@pos"/>
          </xs:unique>
        </xs:element>
        <xs:element name="note" type="Text" minOccurs="0"/>
      </xs:sequence>
    </xs:restriction>
  </xs:complexContent>
</xs:complexType>

FeatureType  complexType
diagram BioXSD-1.1_p143.png
children name equalConcept equalConcept equalAlias className classConcept properties
used by
elements FeatureTypeDetails/association/associatedFeature FeatureRecord/annotation/feature FeatureRecord/blockWithOccurrenceReferences/annotation/feature
documentation Annotation by a particular feature. That is, a single-feature sequence annotation track for one particular reference sequence
source <xs:complexType name="FeatureType" sawsdl:modelReference="http://edamontology.org/data_1015 http://edamontology.org/format_2352">
  <xs:annotation>
    <xs:documentation>Annotation by a particular feature. That is, a single-feature sequence annotation track for one particular reference sequence</xs:documentation>
  </xs:annotation>
  <xs:sequence>
    <xs:choice>
      <xs:sequence>
        <xs:element name="name" type="Name" sawsdl:modelReference="http://edamontology.org/data_1015">
          <xs:annotation>
            <xs:documentation>Human-readable display name of the feature</xs:documentation>
          </xs:annotation>
          <!--"Sequence feature identifier"(1015)-->
        </xs:element>
        <xs:element name="equalConcept" type="SemanticConcept" minOccurs="0" maxOccurs="unbounded" sawsdl:modelReference="http://edamontology.org/data_1015"/>
        <!--"Sequence feature identifier"(1015)-->
      </xs:sequence>
      <xs:element name="equalConcept" type="SemanticConcept" maxOccurs="unbounded" sawsdl:modelReference="http://edamontology.org/data_1015"/>
      <!--"Sequence feature identifier"(1015)-->
    </xs:choice>
    <xs:element name="equalAlias" type="Name" minOccurs="0" maxOccurs="unbounded" sawsdl:modelReference="http://edamontology.org/data_1015">
      <xs:annotation>
        <xs:documentation>Alternative human-readable display name of the feature</xs:documentation>
      </xs:annotation>
      <!--"Sequence feature identifier"(1015)-->
    </xs:element>
    <xs:element name="className" type="Name" minOccurs="0">
      <xs:annotation>
        <xs:documentation>More generic class of features containing this feature (human-readable display name of the class)</xs:documentation>
      </xs:annotation>
    </xs:element>
    <xs:element name="classConcept" type="SemanticConcept" minOccurs="0" maxOccurs="unbounded"/>
    <xs:element name="properties" type="FeatureTypeDetails" minOccurs="0"/>
  </xs:sequence>
  <!--"Sequence feature identifier"(1015)-->
  <!--"BioXSD"(2352)-->
</xs:complexType>
model referencehttp://edamontology.org/data_1015
http://edamontology.org/format_2352

FeatureTypeDetails  complexType
diagram BioXSD-1.1_p151.png
children specificFeatureName specificFeatureConcept specificFeatureAlias databaseEntry note association
used by
elements FeatureOccurrenceData/featureTypeDetails FeatureType/properties
documentation Specific properties of a feature
source <xs:complexType name="FeatureTypeDetails" sawsdl:modelReference="http://edamontology.org/data_1021 http://edamontology.org/format_2352">
  <xs:annotation>
    <xs:documentation>Specific properties of a feature</xs:documentation>
  </xs:annotation>
  <xs:sequence>
    <xs:element name="specificFeatureName" type="Name" minOccurs="0" sawsdl:modelReference="http://edamontology.org/data_1020"/>
    <!--"Sequence feature qualifier"(1021)-->
    <xs:element name="specificFeatureConcept" type="SemanticConcept" minOccurs="0" maxOccurs="unbounded"/>
    <!--"Sequence feature qualifier"(1021)-->
    <xs:element name="specificFeatureAlias" type="Name" minOccurs="0" maxOccurs="unbounded" sawsdl:modelReference="http://edamontology.org/data_1020"/>
    <!--"Sequence feature qualifier"(1021)-->
    <xs:element name="databaseEntry" type="EntryReference" minOccurs="0" maxOccurs="unbounded">
      <xs:annotation>
        <xs:documentation>Pointer to a database entry specifying the feature-type details</xs:documentation>
      </xs:annotation>
    </xs:element>
    <xs:element name="note" type="Text" minOccurs="0" sawsdl:modelReference="http://www.w3.org/2000/01/rdf-schema#comment"/>
    <xs:element name="association" minOccurs="0" maxOccurs="unbounded" sawsdl:modelReference="http://edamontology.org/data_2093 http://edamontology.org/format_2352">
      <xs:complexType>
        <xs:sequence>
          <xs:element name="relationName" type="Name" minOccurs="0"/>
          <xs:element name="relationConcept" type="SemanticConcept" minOccurs="0" maxOccurs="unbounded"/>
          <xs:choice>
            <xs:element name="associatedConcept" type="SemanticConcept" maxOccurs="unbounded"/>
            <xs:element name="associatedDatabaseEntry" type="EntryReference" maxOccurs="unbounded"/>
            <xs:element name="associatedDatabase" type="DatabaseReference" maxOccurs="unbounded"/>
            <xs:element name="associatedFeature" type="FeatureType" maxOccurs="unbounded"/>
          </xs:choice>
        </xs:sequence>
      </xs:complexType>
    </xs:element>
  </xs:sequence>
  <!--"Sequence feature qualifier"(1021)-->
  <!--"BioXSD"(2352)-->
</xs:complexType>
model referencehttp://edamontology.org/data_1021
http://edamontology.org/format_2352

FeatureOccurrenceData  complexType
diagram BioXSD-1.1_p77.png
children appliesToWholeSequence position occurrenceEntryReference occurrenceName occurrenceNote featureTypeDetails score evidence frame phase variation alignment
used by
elements FeatureRecord/annotation/occurrence FeatureRecord/blockWithOccurrenceReferences/annotation/occurrence
documentation Occurrence of a feature in a reference sequence. Positioned or non-positioned (non-positioned means applied to the whole sequence)
source <xs:complexType name="FeatureOccurrenceData" sawsdl:modelReference="http://edamontology.org/data_1021 http://edamontology.org/format_2352">
  <xs:annotation>
    <xs:documentation>Occurrence of a feature in a reference sequence. Positioned or non-positioned (non-positioned means applied to the whole sequence)</xs:documentation>
  </xs:annotation>
  <xs:sequence>
    <xs:choice>
      <xs:element name="appliesToWholeSequence" type="Flag"/>
      <xs:element name="position" type="GeneralSequencePosition"/>
    </xs:choice>
    <xs:element name="occurrenceEntryReference" type="EntryReference" minOccurs="0" maxOccurs="unbounded"/>
    <xs:element name="occurrenceName" type="Name" minOccurs="0"/>
    <xs:element name="occurrenceNote" type="Text" minOccurs="0"/>
    <xs:element name="featureTypeDetails" type="FeatureTypeDetails" minOccurs="0"/>
    <xs:element name="score" type="Score" minOccurs="0" maxOccurs="unbounded"/>
    <xs:element name="evidence" type="Evidence" minOccurs="0" maxOccurs="unbounded"/>
    <xs:element name="frame" minOccurs="0" sawsdl:modelReference="http://edamontology.org/data_2126">
      <xs:annotation>
        <xs:documentation>NB. Should be 0 for non-translated but transcribed features. Should be 'strand'*(('min'-1) mod 3 + 1) for translated features within a whole-chromosome annotation</xs:documentation>
      </xs:annotation>
      <xs:simpleType>
        <xs:restriction base="AnyInteger">
          <xs:minInclusive value="-3"/>
          <xs:maxInclusive value="3"/>
        </xs:restriction>
      </xs:simpleType>
    </xs:element>
    <xs:element name="phase" type="Phase" minOccurs="0"/>
    <xs:element name="variation" minOccurs="0" maxOccurs="unbounded" sawsdl:modelReference="http://edamontology.org/data_0918 http://edamontology.org/format_2352">
      <xs:complexType>
        <xs:sequence>
          <xs:element name="canonicalVariant" type="Biosequence" minOccurs="0"/>
          <xs:choice>
            <xs:element name="variant" type="Biosequence" maxOccurs="unbounded"/>
            <xs:element name="missing" type="Flag"/>
          </xs:choice>
          <xs:element name="score" type="Score" minOccurs="0" maxOccurs="unbounded"/>
          <xs:element name="position" type="SequencePosition" minOccurs="0">
            <xs:annotation>
              <xs:documentation>NB. Corresponds to a position within the feature occurrence</xs:documentation>
            </xs:annotation>
          </xs:element>
        </xs:sequence>
      </xs:complexType>
    </xs:element>
    <xs:element name="alignment" minOccurs="0" sawsdl:modelReference="http://edamontology.org/data_1381 http://edamontology.org/format_2352">
      <xs:complexType>
        <xs:sequence>
          <xs:element name="alignmentOfReference" minOccurs="0">
            <xs:complexType>
              <xs:sequence>
                <xs:element name="gap" type="Gap" minOccurs="0" maxOccurs="unbounded"/>
                <xs:element name="frameshift" type="Frameshift" minOccurs="0" maxOccurs="unbounded"/>
                <xs:element name="sequenceScore" type="Result" minOccurs="0" maxOccurs="unbounded"/>
              </xs:sequence>
            </xs:complexType>
            <xs:unique name="uniqueGapPos_ar">
              <xs:selector xpath="gap"/>
              <xs:field xpath="@pos"/>
            </xs:unique>
            <xs:unique name="uniqueFrameshiftPos_ar">
              <xs:selector xpath="frameshift"/>
              <xs:field xpath="@pos"/>
            </xs:unique>
          </xs:element>
          <xs:element name="alignedSequence" type="AlignedBiosequence">
            <xs:unique name="uniqueGapPos_as">
              <xs:selector xpath="gap"/>
              <xs:field xpath="@pos"/>
            </xs:unique>
            <xs:unique name="uniqueFrameshiftPos_as">
              <xs:selector xpath="frameshift"/>
              <xs:field xpath="@pos"/>
            </xs:unique>
          </xs:element>
        </xs:sequence>
      </xs:complexType>
    </xs:element>
  </xs:sequence>
</xs:complexType>
model referencehttp://edamontology.org/data_1021
http://edamontology.org/format_2352

FeatureRecord  complexType
diagram BioXSD-1.1_p100.png
children referenceSequence annotation blockWithOccurrenceReferences
documentation Features of a sequence/biopolymer (or a genome/metagenome).The reference sequence may me included explicitly, referred to remotely, or implicit
source <xs:complexType name="FeatureRecord" sawsdl:modelReference="http://edamontology.org/data_2044 http://edamontology.org/data_0867 http://edamontology.org/data_1381 http://edamontology.org/data_0855 http://edamontology.org/data_2201 http://edamontology.org/data_0924 http://edamontology.org/data_0857 http://edamontology.org/data_0916 http://edamontology.org/data_2084 http://edamontology.org/data_0896 http://edamontology.org/data_2081 http://edamontology.org/format_2352">
  <xs:annotation>
    <xs:documentation>Features of a sequence/biopolymer (or a genome/metagenome).
The reference sequence may me included explicitly, referred to remotely, or implicit</xs:documentation>
  </xs:annotation>
  <xs:sequence>
    <!--= Reference sequence =-->
    <xs:element name="referenceSequence">
      <xs:annotation>
        <xs:documentation>The *reference* sequence that is annotated</xs:documentation>
      </xs:annotation>
      <xs:complexType>
        <xs:choice>
          <xs:element name="sequenceRecord" type="BiosequenceRecord"/>
          <xs:element name="sequenceReference" type="SequenceReference"/>
          <xs:element name="sequenceName" type="Name" sawsdl:modelReference="http://edamontology.org/data_2154"/>
          <xs:sequence>
            <xs:element name="species" type="Species"/>
            <xs:element name="genomeBuild" type="EntryReference" sawsdl:modelReference="http://edamontology.org/data_2340"/>
            <xs:element name="chromosome" type="ChromosomeName"/>
            <xs:element name="subsequencePosition" type="SequencePosition" minOccurs="0">
              <xs:annotation>
                <xs:documentation>Coordinates of a sub-sequence within the chromosome</xs:documentation>
              </xs:annotation>
            </xs:element>
            <xs:element name="variantAccession" type="Accession" minOccurs="0" sawsdl:modelReference="http://edamontology.org/data_1063 http://edamontology.org/data_2091"/>
            <xs:element name="variantNote" type="Name" minOccurs="0" sawsdl:modelReference="http://edamontology.org/data_1063"/>
          </xs:sequence>
        </xs:choice>
      </xs:complexType>
    </xs:element>
    <xs:choice maxOccurs="unbounded">
      <!--= Annotation by a feature (a track) =-->
      <xs:element name="annotation" sawsdl:modelReference="http://edamontology.org/data_3002 http://edamontology.org/format_2352">
        <xs:annotation>
          <xs:documentation>Annotation by a particular feature or property. Corresponds to one sequence annotation track.</xs:documentation>
        </xs:annotation>
        <!--"Sequence annotation track"(3002)-->
        <!--"BioXSD format"(2352)-->
        <xs:complexType>
          <xs:sequence>
            <!--= Feature type =-->
            <xs:element name="feature" type="FeatureType"/>
            <!--= Condensed references for feature occurrence(s) =-->
            <xs:element name="condensedReferences" minOccurs="0">
              <xs:complexType>
                <xs:sequence>
                  <xs:element name="method" type="Method" minOccurs="0"/>
                  <xs:element name="ontology" type="OntologyReference" minOccurs="0"/>
                  <xs:element name="database" type="DatabaseReference" minOccurs="0"/>
                  <xs:element name="scoreType" type="ScoreType" minOccurs="0"/>
                </xs:sequence>
              </xs:complexType>
            </xs:element>
            <!--= Feature occurrence(s) (instance(s)) =-->
            <xs:element name="occurrence" type="FeatureOccurrenceData" minOccurs="0" maxOccurs="unbounded"/>
          </xs:sequence>
        </xs:complexType>
      </xs:element>
      <!--= Annotation by a block of inter-related features =-->
      <xs:element name="blockWithOccurrenceReferences">
        <xs:complexType>
          <xs:sequence>
            <!--= Sources (globally declared) =-->
            <xs:element name="database" minOccurs="0" maxOccurs="unbounded" sawsdl:modelReference="http://edamontology.org/data_0856">
              <xs:complexType>
                <xs:complexContent>
                  <xs:extension base="DatabaseReference">
                    <xs:attribute name="localId" type="LocalId" use="required"/>
                  </xs:extension>
                </xs:complexContent>
              </xs:complexType>
            </xs:element>
            <xs:element name="ontology" minOccurs="0" maxOccurs="unbounded">
              <xs:complexType>
                <xs:complexContent>
                  <xs:extension base="OntologyReference">
                    <xs:attribute name="localId" type="LocalId" use="required"/>
                  </xs:extension>
                </xs:complexContent>
              </xs:complexType>
            </xs:element>
            <xs:element name="semanticConcept" minOccurs="0" maxOccurs="unbounded">
              <xs:complexType>
                <xs:complexContent>
                  <xs:extension base="SemanticConcept">
                    <xs:attribute name="localId" type="LocalId" use="required"/>
                  </xs:extension>
                </xs:complexContent>
              </xs:complexType>
            </xs:element>
            <xs:element name="method" minOccurs="0" maxOccurs="unbounded" sawsdl:modelReference="http://edamontology.org/data_0856">
              <xs:complexType>
                <xs:complexContent>
                  <xs:extension base="Method">
                    <xs:attribute name="localId" type="LocalId" use="required"/>
                  </xs:extension>
                </xs:complexContent>
              </xs:complexType>
            </xs:element>
            <xs:element name="scoreType" minOccurs="0" maxOccurs="unbounded">
              <xs:complexType>
                <xs:complexContent>
                  <xs:extension base="ScoreType">
                    <xs:attribute name="localId" type="LocalId" use="required"/>
                  </xs:extension>
                </xs:complexContent>
              </xs:complexType>
            </xs:element>
            <!--= Annotation by a feature (in a block) =-->
            <xs:element name="annotation" maxOccurs="unbounded" sawsdl:modelReference="http://edamontology.org/data_3002 http://edamontology.org/format_2352">
              <xs:annotation>
                <xs:documentation>Annotation by a particular feature or property. Corresponds to one sequence annotation track.</xs:documentation>
              </xs:annotation>
              <!--"Sequence annotation track"(3002)-->
              <!--"BioXSD format"(2352)-->
              <xs:complexType>
                <xs:sequence>
                  <!--= Feature type (in a block) =-->
                  <xs:element name="feature" type="FeatureType"/>
                  <!--= Condensed references for feature occurrence(s) =-->
                  <xs:element name="condensedReferences" minOccurs="0">
                    <xs:complexType>
                      <xs:sequence>
                        <xs:choice>
                          <xs:element name="method" type="Method" minOccurs="0"/>
                          <xs:element name="methodIdRef" type="LocalId" minOccurs="0"/>
                        </xs:choice>
                        <xs:choice>
                          <xs:element name="ontology" type="OntologyReference" minOccurs="0"/>
                          <xs:element name="ontologyIdRef" type="LocalId" minOccurs="0"/>
                        </xs:choice>
                        <xs:choice>
                          <xs:element name="database" type="DatabaseReference" minOccurs="0"/>
                          <xs:element name="databaseIdRef" type="LocalId" minOccurs="0"/>
                        </xs:choice>
                        <xs:choice>
                          <xs:element name="scoreType" type="ScoreType" minOccurs="0"/>
                          <xs:element name="scoreTypeIdRef" type="LocalId" minOccurs="0"/>
                        </xs:choice>
                      </xs:sequence>
                    </xs:complexType>
                  </xs:element>
                  <!--= Feature occurrence(s) (instance(s)) (in a block) =-->
                  <xs:element name="occurrence" minOccurs="0" maxOccurs="unbounded">
                    <xs:complexType>
                      <xs:complexContent>
                        <xs:extension base="FeatureOccurrenceData">
                          <xs:sequence>
                            <xs:element name="association" minOccurs="0" maxOccurs="unbounded">
                              <xs:complexType>
                                <xs:sequence>
                                  <xs:element name="relationName" type="Name" minOccurs="0"/>
                                  <xs:element name="relationConcept" type="SemanticConcept" minOccurs="0" maxOccurs="unbounded"/>
                                  <xs:element name="relationConceptIdRef" type="LocalId" minOccurs="0" maxOccurs="unbounded"/>
                                  <xs:element name="associatedFeatureOccurrence" maxOccurs="unbounded">
                                    <xs:complexType>
                                      <xs:sequence>
                                        <xs:element name="score" type="Score" minOccurs="0" maxOccurs="unbounded"/>
                                      </xs:sequence>
                                      <xs:attribute name="localIdRef" use="required"/>
                                    </xs:complexType>
                                  </xs:element>
                                </xs:sequence>
                              </xs:complexType>
                            </xs:element>
                          </xs:sequence>
                          <xs:attribute name="localId" type="LocalId"/>
                        </xs:extension>
                      </xs:complexContent>
                    </xs:complexType>
                  </xs:element>
                </xs:sequence>
              </xs:complexType>
            </xs:element>
          </xs:sequence>
        </xs:complexType>
        <xs:unique name="uniqueLocalId_occ">
          <xs:selector xpath="annotation/occurrence"/>
          <xs:field xpath="@localId"/>
        </xs:unique>
      </xs:element>
    </xs:choice>
  </xs:sequence>
  <!--"Sequence data"(2044)-->
  <!--"Sequence alignment annotation"(0867)-->
  <!--"Sequence alignment (pairwise)"(1381)-->
  <!--"Sequence annotation"(0855)-->
  <!--"Sequence record full"(2201)-->
  <!--"Sequence trace"(0924)-->
  <!--"Sequence database hits"(0857)-->
  <!--"Gene annotation"(0916)-->
  <!--"Nucleic acid annotation"(2084)-->
  <!--"Protein annotation"(0896)-->
  <!--"Secondary structure"(2081)-->
  <!--"BioXSD format"(2352)-->
</xs:complexType>
model referencehttp://edamontology.org/data_2044
http://edamontology.org/data_0867
http://edamontology.org/data_1381
http://edamontology.org/data_0855
http://edamontology.org/data_2201
http://edamontology.org/data_0924
http://edamontology.org/data_0857
http://edamontology.org/data_0916
http://edamontology.org/data_2084
http://edamontology.org/data_0896
http://edamontology.org/data_2081
http://edamontology.org/format_2352

Evidence  complexType
diagram BioXSD-1.1_p69.png
children predicted experimental
used by
element FeatureOccurrenceData/evidence
source <xs:complexType name="Evidence" sawsdl:modelReference="http://edamontology.org/data_2042 http://edamontology.org/format_2352">
  <xs:choice>
    <xs:element name="predicted" type="PredictionResult"/>
    <xs:element name="experimental" type="ExperimentalEvidence"/>
  </xs:choice>
</xs:complexType>
model referencehttp://edamontology.org/data_2042
http://edamontology.org/format_2352

MethodResult  complexType
diagram BioXSD-1.1_p217.png
children method score
used by
elements BiosequenceAlignment/alignedBy GeneralNucleotideSequenceAlignment/alignedBy GeneralAminoacidSequenceAlignment/alignedBy NucleotideSequenceAlignment/alignedBy AminoacidSequenceAlignment/alignedBy
source <xs:complexType name="MethodResult">
  <xs:sequence>
    <xs:element name="method">
      <xs:complexType>
        <xs:complexContent>
          <xs:extension base="Method">
            <xs:attribute name="localId" type="LocalId"/>
          </xs:extension>
        </xs:complexContent>
      </xs:complexType>
    </xs:element>
    <xs:element name="score" type="Score" minOccurs="0" maxOccurs="unbounded"/>
  </xs:sequence>
</xs:complexType>

Result  complexType
diagram BioXSD-1.1_p246.png
children methodIdRef score
used by
elements AlignedBiosequence/sequenceScore AlignedGeneralNucleotideSequence/sequenceScore AlignedGeneralAminoacidSequence/sequenceScore AlignedNucleotideSequence/sequenceScore AlignedAminoacidSequence/sequenceScore FeatureOccurrenceData/alignment/alignmentOfReference/sequenceScore
source <xs:complexType name="Result">
  <xs:sequence>
    <xs:element name="methodIdRef" type="LocalId" sawsdl:modelReference="http://edamontology.org/data_0007 http://edamontology.org/data_2337 http://edamontology.org/data_0977 http://edamontology.org/format_2352"/>
    <xs:element name="score" type="Score" minOccurs="0" maxOccurs="unbounded"/>
  </xs:sequence>
</xs:complexType>

PredictionResult  complexType
diagram BioXSD-1.1_p241.png
children method methodIdRef score verdict
used by
element Evidence/predicted
source <xs:complexType name="PredictionResult">
  <xs:sequence>
    <xs:choice>
      <xs:element name="method" type="Method" sawsdl:modelReference="http://edamontology.org/data_0856"/>
      <xs:element name="methodIdRef" type="LocalId" sawsdl:modelReference="http://edamontology.org/data_0007 http://edamontology.org/data_2337 http://edamontology.org/data_0977 http://edamontology.org/format_2352 http://edamontology.org/data_0856"/>
    </xs:choice>
    <xs:element name="score" type="Score" minOccurs="0" maxOccurs="unbounded"/>
    <xs:element name="verdict" type="Verdict" minOccurs="0"/>
  </xs:sequence>
</xs:complexType>

ExperimentalEvidence  complexType
diagram BioXSD-1.1_p72.png
children dataReference citation verdict reliability
used by
element Evidence/experimental
source <xs:complexType name="ExperimentalEvidence">
  <xs:sequence>
    <xs:element name="dataReference" type="EntryReference" sawsdl:modelReference="http://edamontology.org/data_0856"/>
    <xs:element name="citation" type="EntryReference" minOccurs="0" maxOccurs="unbounded" sawsdl:modelReference="http://edamontology.org/data_0970 "/>
    <xs:element name="verdict" type="Verdict" minOccurs="0"/>
    <xs:element name="reliability" type="Reliability" minOccurs="0"/>
  </xs:sequence>
</xs:complexType>

ScoreType  complexType
diagram BioXSD-1.1_p251.png
children concept method methodIdRef
used by
elements FeatureRecord/annotation/condensedReferences/scoreType FeatureRecord/blockWithOccurrenceReferences/scoreType FeatureRecord/blockWithOccurrenceReferences/annotation/condensedReferences/scoreType
complexType Score
attributes
Name  Type  Use  Default  Fixed  annotation
nameScoreName      
indexName      
unitName      
noteText      
documentation Type of score of an experiment or computation
source <xs:complexType name="ScoreType" sawsdl:modelReference="http://edamontology.org/data_1772 http://edamontology.org/format_2352">
  <xs:annotation>
    <xs:documentation>Type of score of an experiment or computation</xs:documentation>
  </xs:annotation>
  <xs:sequence>
    <xs:element name="concept" type="SemanticConcept" minOccurs="0" maxOccurs="unbounded"/>
    <xs:element name="method" type="Method" minOccurs="0" maxOccurs="unbounded" sawsdl:modelReference="http://edamontology.org/data_0856"/>
    <xs:element name="methodIdRef" type="LocalId" minOccurs="0" maxOccurs="unbounded" sawsdl:modelReference="http://edamontology.org/data_0007 http://edamontology.org/data_2337 http://edamontology.org/data_0977 http://edamontology.org/format_2352 http://edamontology.org/data_0856"/>
  </xs:sequence>
  <xs:attribute name="name" type="ScoreName"/>
  <xs:attribute name="index" type="Name"/>
  <xs:attribute name="unit" type="Name"/>
  <xs:attribute name="note" type="Text" sawsdl:modelReference="http://www.w3.org/2000/01/rdf-schema#comment"/>
</xs:complexType>
model referencehttp://edamontology.org/data_1772
http://edamontology.org/format_2352

Score  complexType
diagram BioXSD-1.1_p249.png
type extension of ScoreType
properties
base ScoreType
children concept method methodIdRef position
used by
elements FeatureOccurrenceData/score FeatureOccurrenceData/variation/score FeatureRecord/blockWithOccurrenceReferences/annotation/occurrence/association/associatedFeatureOccurrence/score MethodResult/score Result/score PredictionResult/score
attributes
Name  Type  Use  Default  Fixed  annotation
nameScoreName      
indexName      
unitName      
noteText      
valueScoreValuerequired      
scoreTypeIdRefLocalId      
documentation Score of an experiment or computation
source <xs:complexType name="Score" sawsdl:modelReference="http://edamontology.org/data_1772 http://edamontology.org/format_2352">
  <xs:annotation>
    <xs:documentation>Score of an experiment or computation</xs:documentation>
  </xs:annotation>
  <xs:complexContent>
    <xs:extension base="ScoreType">
      <xs:sequence>
        <xs:element name="position" type="SequencePosition" minOccurs="0">
          <xs:annotation>
            <xs:documentation>NB. Corresponds to a position in the (sub)sequence the score belongs to</xs:documentation>
          </xs:annotation>
        </xs:element>
      </xs:sequence>
      <xs:attribute name="value" type="ScoreValue" use="required"/>
      <xs:attribute name="scoreTypeIdRef" type="LocalId"/>
    </xs:extension>
  </xs:complexContent>
</xs:complexType>
model referencehttp://edamontology.org/data_1772
http://edamontology.org/format_2352

GeneralSequencePoint  complexType
diagram BioXSD-1.1_p200.png
used by
element GeneralSequencePosition/point
complexType SequencePoint
attributes
Name  Type  Use  Default  Fixed  annotation
posPositiveInteger      
documentation
NB. Omit 'pos' attribute only if 'certainty'="Unknown"
strandStrand      
certaintyCertainty  Certain    
documentation Position in the sequence, referring to a single point (base, residue, or C-alpha atom), possibly with a certain level of uncertainty
source <xs:complexType name="GeneralSequencePoint" sawsdl:modelReference="http://edamontology.org/data_1016 http://edamontology.org/format_2352">
  <xs:annotation>
    <xs:documentation>Position in the sequence, referring to a single point (base, residue, or C-alpha atom), possibly with a certain level of uncertainty</xs:documentation>
  </xs:annotation>
  <xs:attribute name="pos" type="PositiveInteger">
    <xs:annotation>
      <xs:documentation>NB. Omit 'pos' attribute only if 'certainty'="Unknown"</xs:documentation>
    </xs:annotation>
  </xs:attribute>
  <xs:attribute name="strand" type="Strand"/>
  <xs:attribute name="certainty" type="Certainty" default="Certain"/>
</xs:complexType>
model referencehttp://edamontology.org/data_1016
http://edamontology.org/format_2352

SequencePoint  complexType
diagram BioXSD-1.1_p258.png
type restriction of GeneralSequencePoint
properties
base GeneralSequencePoint
used by
element SequencePosition/point
attributes
Name  Type  Use  Default  Fixed  annotation
posPositiveIntegerrequired      
strandStrand      
certaintyCertaintyprohibited    Certain  
documentation Certain position in the sequence, referring to a single point (base, residue, or C-alpha atom)
source <xs:complexType name="SequencePoint">
  <xs:annotation>
    <xs:documentation>Certain position in the sequence, referring to a single point (base, residue, or C-alpha atom)</xs:documentation>
  </xs:annotation>
  <xs:complexContent>
    <xs:restriction base="GeneralSequencePoint">
      <xs:attribute name="pos" type="PositiveInteger" use="required"/>
      <xs:attribute name="certainty" type="Certainty" use="prohibited" fixed="Certain"/>
    </xs:restriction>
  </xs:complexContent>
</xs:complexType>

GeneralSequenceInsertionPoint  complexType
diagram BioXSD-1.1_p198.png
used by
element GeneralSequencePosition/insertion
complexType SequenceInsertionPoint
attributes
Name  Type  Use  Default  Fixed  annotation
posInsertionInteger      
documentation
NB. Omit 'pos' attribute only if 'certainty'="Unknown"
strandStrand      
certaintyCertainty  Certain    
documentation Position of an insertion into the sequence, possibly with a certain level of uncertainty.
NB. Insertion *behind* (to the right of) the given point in the direction of the sequence; *-1* for preceeding the sequence
source <xs:complexType name="GeneralSequenceInsertionPoint" sawsdl:modelReference="http://edamontology.org/data_1016">
  <xs:annotation>
    <xs:documentation>Position of an insertion into the sequence, possibly with a certain level of uncertainty.
NB. Insertion *behind* (to the right of) the given point in the direction of the sequence; *-1* for preceeding the sequence.</xs:documentation>
  </xs:annotation>
  <xs:attribute name="pos" type="InsertionInteger">
    <xs:annotation>
      <xs:documentation>NB. Omit 'pos' attribute only if 'certainty'="Unknown"</xs:documentation>
    </xs:annotation>
  </xs:attribute>
  <xs:attribute name="strand" type="Strand"/>
  <xs:attribute name="certainty" type="Certainty" default="Certain"/>
</xs:complexType>
model referencehttp://edamontology.org/data_1016

SequenceInsertionPoint  complexType
diagram BioXSD-1.1_p256.png
type restriction of GeneralSequenceInsertionPoint
properties
base GeneralSequenceInsertionPoint
used by
element SequencePosition/insertion
attributes
Name  Type  Use  Default  Fixed  annotation
posInsertionIntegerrequired      
strandStrand      
certaintyCertaintyprohibited    Certain  
documentation Certain position of an insertion into the sequence.
NB. Insertion *behind* (to the right of) the given point in the direction of the sequence; *-1* for preceeding the sequence
source <xs:complexType name="SequenceInsertionPoint">
  <xs:annotation>
    <xs:documentation>Certain position of an insertion into the sequence.
NB. Insertion *behind* (to the right of) the given point in the direction of the sequence; *-1* for preceeding the sequence.</xs:documentation>
  </xs:annotation>
  <xs:complexContent>
    <xs:restriction base="GeneralSequenceInsertionPoint">
      <xs:attribute name="pos" type="InsertionInteger" use="required"/>
      <xs:attribute name="certainty" type="Certainty" use="prohibited" fixed="Certain"/>
    </xs:restriction>
  </xs:complexContent>
</