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 
AlignedAminoacidSequence  Accession   
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 
Insert  RecommendedDatabaseName 
Method  RecommendedOntologyName 
MethodResult  RecommendedReliability 
NucleotideSequenceAlignment  RecommendedScoreName 
NucleotideSequenceRecord  RecommendedVerdict 
OntologyReference  Reliability 
OutsideSequencePoint  ScoreName 
OutsideSequencePosition  ScoreValue 
OutsideSequenceSegment  Strand 
PredictionResult  Text 
Result  UniprotAccession 
Score  Uri 
ScoreType  Verdict 
SemanticConcept 
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 
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: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 
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 
pattern [!-~]+ 
source <xs:simpleType name="BaseQualityString">
 
<xs:restriction base="xs:string">
   
<xs:pattern value="[!-~]+"/>
 
</xs:restriction>
</xs:simpleType>

BiosequenceRecord  complexType
diagram BioXSD-1.1_p64.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_p188.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_p177.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_p233.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_p51.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

BiosequenceAlignment  complexType
diagram BioXSD-1.1_p60.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="uniqueInsertPos_b">
       
<xs:selector xpath="insert"/>
       
<xs:field xpath="@min"/>
       
<xs:field xpath="@max"/>
     
</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_p184.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: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_p173.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: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_p229.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:element name="note" type="Text" minOccurs="0"/>
     
</xs:sequence>
   
</xs:restriction>
 
</xs:complexContent>
</xs:complexType>

AminoacidSequenceAlignment  complexType
diagram BioXSD-1.1_p47.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:element name="note" type="Text" minOccurs="0"/>
     
</xs:sequence>
   
</xs:restriction>
 
</xs:complexContent>
</xs:complexType>

Gap  complexType
diagram BioXSD-1.1_p172.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>

Insert  complexType
diagram BioXSD-1.1_p220.png
type restriction of SequenceSegment
properties
base SequenceSegment
used by
elements AlignedBiosequence/insert AlignedGeneralNucleotideSequence/insert AlignedGeneralAminoacidSequence/insert AlignedNucleotideSequence/insert AlignedAminoacidSequence/insert FeatureOccurrenceData/alignment/alignmentOfReference/insert
attributes
Name  Type  Use  Default  Fixed  annotation
strandStrandprohibited      
minPositiveIntegerrequired      
documentation
NB. Keep 'min' &lt; 'max', use 'strand' if necessary
maxPositiveIntegerrequired      
documentation
NB. Keep 'max' > 'min', use 'strand' if necessary
documentation Single insert in an aligned sequence
source <xs:complexType name="Insert">
 
<xs:annotation>
   
<xs:documentation>Single insert in an aligned sequence</xs:documentation>
 
</xs:annotation>
 
<xs:complexContent>
   
<xs:restriction base="SequenceSegment">
     
<xs:attribute name="strand" type="Strand" use="prohibited"/>
   
</xs:restriction>
 
</xs:complexContent>
</xs:complexType>

Frameshift  complexType
diagram BioXSD-1.1_p171.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_p9.png
children localAlignmentPosition sequenceRecord sequenceReference sequenceName species genomeBuild chromosome subsequencePosition variantAccession variantNote gap insert 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="insert" type="Insert" 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_p33.png
type restriction of AlignedBiosequence
properties
base AlignedBiosequence
children localAlignmentPosition sequenceRecord gap insert 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="insert" type="Insert" 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_p25.png
type restriction of AlignedBiosequence
properties
base AlignedBiosequence
children localAlignmentPosition sequenceRecord gap insert 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="insert" type="Insert" 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_p40.png
type restriction of AlignedGeneralNucleotideSequence
properties
base AlignedGeneralNucleotideSequence
children localAlignmentPosition sequenceRecord gap insert 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="insert" type="Insert" 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 insert 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="insert" type="Insert" 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>

FeatureType  complexType
diagram BioXSD-1.1_p149.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_p157.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_p82.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="insert" type="Insert" 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="uniqueInsertPos_ar">
             
<xs:selector xpath="insert"/>
             
<xs:field xpath="@min"/>
             
<xs:field xpath="@max"/>
           
</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="uniqueInsertPos_as">
             
<xs:selector xpath="insert"/>
             
<xs:field xpath="@min"/>
             
<xs:field xpath="@max"/>
           
</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_p106.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" type="LocalId" 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_p74.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_p226.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_p255.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_p250.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_p77.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_p260.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_p258.png
type extension of ScoreType
properties
base ScoreType
children concept method methodIdRef position
used by
elements Method/inputParameter Method/outputParameter 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_p206.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_p267.png
type restriction of GeneralSequencePoint
properties
base GeneralSequencePoint
used by
element SequencePosition/point
attributes
Name  Type  Use  Default  Fixed  annotation
posPositiveIntegerrequired      
strandStrand      
certaintyCertaintyprohibited      
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"/>
   
</xs:restriction>
 
</xs:complexContent>
</xs:complexType>

GeneralSequenceInsertionPoint  complexType
diagram BioXSD-1.1_p204.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 preceding 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 preceding 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_p265.png
type restriction of GeneralSequenceInsertionPoint
properties
base GeneralSequenceInsertionPoint
used by
element SequencePosition/insertion
attributes
Name  Type  Use  Default  Fixed  annotation
posInsertionIntegerrequired      
strandStrand      
certaintyCertaintyprohibited      
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 preceding 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 preceding 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"/>
   
</xs:restriction>
 
</xs:complexContent>
</xs:complexType>

GeneralOutsideSequencePoint  complexType
diagram BioXSD-1.1_p196.png
used by
elements GeneralOutsideSequencePosition/insertion GeneralOutsideSequencePosition/point
complexType OutsideSequencePoint
attributes
Name  Type  Use  Default  Fixed  annotation
posNonzeroInteger      
documentation
NB. Omit 'pos' attribute only if 'certainty'="Unknown"
strandStrand      
certaintyCertainty  Certain    
documentation Position outside of the reference sequence, referring to a single point (a nucleotide, residue, or C-alpha atom), possibly uncertain
source <xs:complexType name="GeneralOutsideSequencePoint" sawsdl:modelReference="http://edamontology.org/data_1016">
 
<xs:annotation>
   
<xs:documentation>Position outside of the reference sequence, referring to a single point (a nucleotide, residue, or C-alpha atom), possibly uncertain</xs:documentation>
 
</xs:annotation>
 
<xs:attribute name="pos" type="NonzeroInteger">
   
<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

OutsideSequencePoint  complexType
diagram BioXSD-1.1_p242.png
type restriction of GeneralOutsideSequencePoint
properties
base GeneralOutsideSequencePoint
used by
elements OutsideSequencePosition/insertion OutsideSequencePosition/point
attributes
Name  Type  Use  Default  Fixed  annotation
posNonzeroIntegerrequired      
strandStrand      
certaintyCertaintyprohibited      
documentation Certain position outside of the reference sequence, referring to a single point (a nucleotide, residue, or C-alpha atom)
source <xs:complexType name="OutsideSequencePoint">
 
<xs:annotation>
   
<xs:documentation>Certain position outside of the reference sequence, referring to a single point (a nucleotide, residue, or C-alpha atom)</xs:documentation>
 
</xs:annotation>
 
<xs:complexContent>
   
<xs:restriction base="GeneralOutsideSequencePoint">
     
<xs:attribute name="pos" type="NonzeroInteger" use="required"/>
     
<xs:attribute name="certainty" type="Certainty" use="prohibited"/>
   
</xs:restriction>
 
</xs:complexContent>
</xs:complexType>

GeneralSequenceSegment  complexType
diagram BioXSD-1.1_p216.png
used by
element GeneralSequencePosition/segment
complexType SequenceSegment
attributes
Name  Type  Use  Default  Fixed  annotation
minPositiveInteger      
documentation
NB. Keep 'min' &lt; 'max', use 'strand' if necessary. Omit 'min' attribute only if 'minCertainty'="Unknown"
maxPositiveInteger      
documentation
NB. Keep 'max' > 'min', use 'strand' if necessary. Omit 'max' attribute only if 'maxCertainty'="Unknown"
strandStrand      
minCertaintyCertainty  Certain    
maxCertaintyCertainty  Certain    
documentation Position in the sequence referring to a continuous segment of the sequence, possibly uncertain
source <xs:complexType name="GeneralSequenceSegment" sawsdl:modelReference="http://edamontology.org/data_1017">
 
<xs:annotation>
   
<xs:documentation>Position in the sequence referring to a continuous segment of the sequence, possibly uncertain</xs:documentation>
 
</xs:annotation>
 
<xs:attribute name="min" type="PositiveInteger">
   
<xs:annotation>
     
<xs:documentation>NB. Keep 'min' &lt; 'max', use 'strand' if necessary. Omit 'min' attribute only if 'minCertainty'="Unknown"</xs:documentation>
   
</xs:annotation>
 
</xs:attribute>
 
<xs:attribute name="max" type="PositiveInteger">
   
<xs:annotation>
     
<xs:documentation>NB. Keep 'max' > 'min', use 'strand' if necessary. Omit 'max' attribute only if 'maxCertainty'="Unknown"</xs:documentation>
   
</xs:annotation>
 
</xs:attribute>
 
<xs:attribute name="strand" type="Strand"/>
 
<xs:attribute name="minCertainty" type="Certainty" default="Certain"/>
 
<xs:attribute name="maxCertainty" type="Certainty" default="Certain"/>
 
<!--"Sequence range"(1017)-->
</xs:complexType>
model referencehttp://edamontology.org/data_1017

SequenceSegment  complexType
diagram BioXSD-1.1_p281.png
type restriction of GeneralSequenceSegment
properties
base GeneralSequenceSegment
used by
element SequencePosition/segment
complexType Insert
attributes
Name  Type  Use  Default  Fixed  annotation
minPositiveIntegerrequired      
documentation
NB. Keep 'min' &lt; 'max', use 'strand' if necessary
maxPositiveIntegerrequired      
documentation
NB. Keep 'max' > 'min', use 'strand' if necessary
strandStrand      
minCertaintyCertaintyprohibited      
maxCertaintyCertaintyprohibited      
documentation Certain position in the sequence referring to a continuous segment of the sequence
source <xs:complexType name="SequenceSegment">
 
<xs:annotation>
   
<xs:documentation>Certain position in the sequence referring to a continuous segment of the sequence</xs:documentation>
 
</xs:annotation>
 
<xs:complexContent>
   
<xs:restriction base="GeneralSequenceSegment">
     
<xs:attribute name="min" type="PositiveInteger" use="required">
       
<xs:annotation>
         
<xs:documentation>NB. Keep 'min' &lt; 'max', use 'strand' if necessary</xs:documentation>
       
</xs:annotation>
     
</xs:attribute>
     
<xs:attribute name="max" type="PositiveInteger" use="required">
       
<xs:annotation>
         
<xs:documentation>NB. Keep 'max' > 'min', use 'strand' if necessary</xs:documentation>
       
</xs:annotation>
     
</xs:attribute>
     
<xs:attribute name="minCertainty" type="Certainty" use="prohibited"/>
     
<xs:attribute name="maxCertainty" type="Certainty" use="prohibited"/>
   
</xs:restriction>
 
</xs:complexContent>
</xs:complexType>

GeneralOutsideSequenceSegment  complexType
diagram BioXSD-1.1_p203.png
used by
element GeneralOutsideSequencePosition/segment
complexType OutsideSequenceSegment
attributes
Name  Type  Use  Default  Fixed  annotation
minNonzeroInteger      
documentation
NB. Keep 'min' &lt; 'max', use 'strand' if necessary. Omit 'min' attribute only if 'minCertainty'="Unknown"
maxNonzeroInteger      
documentation
NB. Keep 'max' > 'min', use 'strand' if necessary. Omit 'max' attribute only if 'maxCertainty'="Unknown"
strandStrand      
minCertaintyCertainty  Certain    
maxCertaintyCertainty  Certain    
documentation Position outside of the reference sequence, referring to a continuous segment, possibly uncertain
source <xs:complexType name="GeneralOutsideSequenceSegment" sawsdl:modelReference="http://edamontology.org/data_1017">
 
<xs:annotation>
   
<xs:documentation>Position outside of the reference sequence, referring to a continuous segment, possibly uncertain</xs:documentation>
 
</xs:annotation>
 
<xs:attribute name="min" type="NonzeroInteger">
   
<xs:annotation>
     
<xs:documentation>NB. Keep 'min' &lt; 'max', use 'strand' if necessary. Omit 'min' attribute only if 'minCertainty'="Unknown"</xs:documentation>
   
</xs:annotation>
 
</xs:attribute>
 
<xs:attribute name="max" type="NonzeroInteger">
   
<xs:annotation>
     
<xs:documentation>NB. Keep 'max' > 'min', use 'strand' if necessary. Omit 'max' attribute only if 'maxCertainty'="Unknown"</xs:documentation>
   
</xs:annotation>
 
</xs:attribute>
 
<xs:attribute name="strand" type="Strand"/>
 
<xs:attribute name="minCertainty" type="Certainty" default="Certain"/>
 
<xs:attribute name="maxCertainty" type="Certainty" default="Certain"/>
</xs:complexType>
model referencehttp://edamontology.org/data_1017

OutsideSequenceSegment  complexType
diagram BioXSD-1.1_p249.png
type restriction of GeneralOutsideSequenceSegment
properties
base GeneralOutsideSequenceSegment
used by
element OutsideSequencePosition/segment
attributes
Name  Type  Use  Default  Fixed  annotation
minNonzeroIntegerrequired      
documentation
NB. Keep 'min' &lt; 'max', use 'strand' if necessary
maxNonzeroIntegerrequired      
documentation
NB. Keep 'max' > 'min', use 'strand' if necessary
strandStrand      
minCertaintyCertaintyprohibited      
maxCertaintyCertaintyprohibited      
documentation Certain position outside of the reference sequence, referring to a continuous segment
source <xs:complexType name="OutsideSequenceSegment">
 
<xs:annotation>
   
<xs:documentation>Certain position outside of the reference sequence, referring to a continuous segment</xs:documentation>
 
</xs:annotation>
 
<xs:complexContent>
   
<xs:restriction base="GeneralOutsideSequenceSegment">
     
<xs:attribute name="min" type="NonzeroInteger" use="required">
       
<xs:annotation>
         
<xs:documentation>NB. Keep 'min' &lt; 'max', use 'strand' if necessary</xs:documentation>
       
</xs:annotation>
     
</xs:attribute>
     
<xs:attribute name="max" type="NonzeroInteger" use="required">
       
<xs:annotation>
         
<xs:documentation>NB. Keep 'max' > 'min', use 'strand' if necessary</xs:documentation>
       
</xs:annotation>
     
</xs:attribute>
     
<xs:attribute name="minCertainty" type="Certainty" use="prohibited"/>
     
<xs:attribute name="maxCertainty" type="Certainty" use="prohibited"/>
   
</xs:restriction>
 
</xs:complexContent>
</xs:complexType>

GeneralSequencePartition  complexType
diagram BioXSD-1.1_p205.png
used by
element GeneralSequencePosition/nextPartition
complexType SequencePartition
attributes
Name  Type  Use  Default  Fixed  annotation
maxPositiveInteger      
documentation
NB. Omit 'max' attribute only if 'certainty'="Unknown"
certaintyCertainty  Certain    
source <xs:complexType name="GeneralSequencePartition">
 
<xs:attribute name="max" type="PositiveInteger">
   
<xs:annotation>
     
<xs:documentation>NB. Omit 'max' attribute only if 'certainty'="Unknown"</xs:documentation>
   
</xs:annotation>
 
</xs:attribute>
 
<xs:attribute name="certainty" type="Certainty" default="Certain"/>
</xs:complexType>

SequencePartition  complexType
diagram BioXSD-1.1_p266.png
type restriction of GeneralSequencePartition
properties
base GeneralSequencePartition
used by
element SequencePosition/nextPartition
attributes
Name  Type  Use  Default  Fixed  annotation
maxPositiveIntegerrequired      
certaintyCertaintyprohibited      
source <xs:complexType name="SequencePartition">
 
<xs:complexContent>
   
<xs:restriction base="GeneralSequencePartition">
     
<xs:attribute name="max" type="PositiveInteger" use="required"/>
     
<xs:attribute name="certainty" type="Certainty" use="prohibited"/>
   
</xs:restriction>
 
</xs:complexContent>
</xs:complexType>

GeneralSequencePosition  complexType
diagram BioXSD-1.1_p207.png
children point insertion segment nextPoint nextPartition samePoint samePartition outside
used by
element FeatureOccurrenceData/position
complexType SequencePosition
documentation Position in the sequence, referring either to a subsequence, a single point, an insertion, or outside of the sequence, possibly uncertain
source <xs:complexType name="GeneralSequencePosition" sawsdl:modelReference="http://edamontology.org/data_1014">
 
<xs:annotation>
   
<xs:documentation>Position in the sequence, referring either to a subsequence, a single point, an insertion, or outside of the sequence, possibly uncertain</xs:documentation>
 
</xs:annotation>
 
<xs:choice>
   
<xs:element name="point" type="GeneralSequencePoint" maxOccurs="unbounded"/>
   
<xs:element name="insertion" type="GeneralSequenceInsertionPoint"/>
   
<xs:element name="segment" type="GeneralSequenceSegment" maxOccurs="unbounded"/>
   
<xs:element name="nextPoint" type="Flag"/>
   
<xs:element name="nextPartition" type="GeneralSequencePartition"/>
   
<xs:element name="samePoint" type="Flag"/>
   
<xs:element name="samePartition" type="Flag"/>
   
<xs:element name="outside" type="GeneralOutsideSequencePosition"/>
 
</xs:choice>
 
<!--"Sequence position specification"(1014)-->
</xs:complexType>
model referencehttp://edamontology.org/data_1014

SequencePosition  complexType
diagram BioXSD-1.1_p268.png
type restriction of GeneralSequencePosition
properties
base GeneralSequencePosition
children point insertion segment nextPoint nextPartition samePoint samePartition outside
used by
elements AlignedBiosequence/localAlignmentPosition AlignedGeneralNucleotideSequence/localAlignmentPosition AlignedGeneralAminoacidSequence/localAlignmentPosition AlignedNucleotideSequence/localAlignmentPosition AlignedAminoacidSequence/localAlignmentPosition FeatureOccurrenceData/variation/position Score/position AlignedBiosequence/subsequencePosition FeatureRecord/referenceSequence/subsequencePosition SequenceReference/subsequencePosition
documentation Certain position in the sequence, referring either to a subsequence, a single point, an insertion, or outside of the sequence
source <xs:complexType name="SequencePosition">
 
<xs:annotation>
   
<xs:documentation>Certain position in the sequence, referring either to a subsequence, a single point, an insertion, or outside of the sequence</xs:documentation>
 
</xs:annotation>
 
<xs:complexContent>
   
<xs:restriction base="GeneralSequencePosition">
     
<xs:choice>
       
<xs:element name="point" type="SequencePoint" maxOccurs="unbounded"/>
       
<xs:element name="insertion" type="SequenceInsertionPoint"/>
       
<xs:element name="segment" type="SequenceSegment" maxOccurs="unbounded"/>
       
<xs:element name="nextPoint" type="Flag"/>
       
<xs:element name="nextPartition" type="SequencePartition"/>
       
<xs:element name="samePoint" type="Flag"/>
       
<xs:element name="samePartition" type="Flag"/>
       
<xs:element name="outside" type="OutsideSequencePosition"/>
     
</xs:choice>
   
</xs:restriction>
 
</xs:complexContent>
</xs:complexType>

GeneralOutsideSequencePosition  complexType
diagram BioXSD-1.1_p197.png
children correspondance point insertion segment explicitSequenceReference
used by
element GeneralSequencePosition/outside
complexType OutsideSequencePosition
documentation Position outside of the sequence, possibly uncertain
source <xs:complexType name="GeneralOutsideSequencePosition" sawsdl:modelReference="http://edamontology.org/data_1014">
 
<xs:annotation>
   
<xs:documentation>Position outside of the sequence, possibly uncertain</xs:documentation>
 
</xs:annotation>
 
<xs:sequence>
   
<xs:sequence minOccurs="0">
     
<xs:element name="correspondance" type="OutsidePositionCorrespondance"/>
     
<xs:choice>
       
<xs:element name="point" type="GeneralOutsideSequencePoint" maxOccurs="unbounded"/>
       
<xs:element name="insertion" type="GeneralOutsideSequencePoint"/>
       
<xs:element name="segment" type="GeneralOutsideSequenceSegment" maxOccurs="unbounded"/>
     
</xs:choice>
   
</xs:sequence>
   
<xs:element name="explicitSequenceReference" type="SequenceReference" minOccurs="0"/>
 
</xs:sequence>
</xs:complexType>
model referencehttp://edamontology.org/data_1014

OutsideSequencePosition  complexType
diagram BioXSD-1.1_p243.png
type restriction of GeneralOutsideSequencePosition
properties
base GeneralOutsideSequencePosition
children correspondance point insertion segment explicitSequenceReference
used by
element SequencePosition/outside
documentation Certain position outside of the sequence
source <xs:complexType name="OutsideSequencePosition">
 
<xs:annotation>
   
<xs:documentation>Certain position outside of the sequence</xs:documentation>
 
</xs:annotation>
 
<xs:complexContent>
   
<xs:restriction base="GeneralOutsideSequencePosition">
     
<xs:sequence>
       
<xs:sequence minOccurs="0">
         
<xs:element name="correspondance" type="OutsidePositionCorrespondance"/>
         
<xs:choice>
           
<xs:element name="point" type="OutsideSequencePoint" maxOccurs="unbounded"/>
           
<xs:element name="insertion" type="OutsideSequencePoint"/>
           
<xs:element name="segment" type="OutsideSequenceSegment" maxOccurs="unbounded"/>
         
</xs:choice>
       
</xs:sequence>
       
<xs:element name="explicitSequenceReference" type="SequenceReference" minOccurs="0"/>
     
</xs:sequence>
   
</xs:restriction>
 
</xs:complexContent>
</xs:complexType>

GeneticCode  complexType
diagram BioXSD-1.1_p217.png
children reference codon
used by
elements TranslationData/geneticCode AminoacidTranslationData/geneticCode
documentation Particular genetic code (codon encoding)
source <xs:complexType name="GeneticCode" sawsdl:modelReference="http://edamontology.org/data_1598 http://edamontology.org/format_2352">
 
<xs:annotation>
   
<xs:documentation>Particular genetic code (codon encoding)</xs:documentation>
 
</xs:annotation>
 
<xs:sequence>
   
<xs:element name="reference" type="EntryReference" minOccurs="0" sawsdl:modelReference="http://edamontology.org/data_2127"/>
   
<xs:element name="codon" minOccurs="0" maxOccurs="unbounded" sawsdl:modelReference="http://edamontology.org/data_2116 http://edamontology.org/format_2352">
     
<xs:complexType>
       
<xs:attribute name="code" use="required">
         
<xs:annotation>
           
<xs:documentation>Codon code consisting of 3 bases (possibly ambiguous, "degenerate")</xs:documentation>
         
</xs:annotation>
         
<xs:simpleType>
           
<xs:restriction base="GeneralNucleotideSequence">
             
<xs:length value="3"/>
           
</xs:restriction>
         
</xs:simpleType>
       
</xs:attribute>
       
<xs:attribute name="start" type="xs:boolean" default="false"/>
       
<xs:attribute name="end" type="xs:boolean" default="false"/>
       
<xs:attribute name="aminoacid" sawsdl:modelReference="http://edamontology.org/data_0994">
         
<xs:annotation>
           
<xs:documentation>One amino-acid (possibly ambiguous). NB. If the same codon codes for multiple amino-acids, use multiple 'codon' elements and fill in the 'note' attribute</xs:documentation>
         
</xs:annotation>
         
<xs:simpleType>
           
<xs:restriction base="GeneralAminoacidSequence">
             
<xs:length value="1"/>
           
</xs:restriction>
         
</xs:simpleType>
       
</xs:attribute>
       
<xs:attribute name="veryRare" type="xs:boolean" default="false"/>
       
<xs:attribute name="note" type="Text" sawsdl:modelReference="http://www.w3.org/2000/01/rdf-schema#comment"/>
     
</xs:complexType>
   
</xs:element>
 
</xs:sequence>
</xs:complexType>
model referencehttp://edamontology.org/data_1598
http://edamontology.org/format_2352

TranslationData  complexType
diagram BioXSD-1.1_p283.png
children geneticCode phase reversedTranslationDirection
used by
elements BiosequenceRecord/translationData GeneralNucleotideSequenceRecord/translationData NucleotideSequenceRecord/translationData
complexType AminoacidTranslationData
source <xs:complexType name="TranslationData" sawsdl:modelReference="http://edamontology.org/data_1317 http://edamontology.org/format_2352">
 
<xs:sequence>
   
<xs:element name="geneticCode" type="GeneticCode" minOccurs="0"/>
   
<xs:element name="phase" type="Phase" minOccurs="0"/>
   
<xs:element name="reversedTranslationDirection" type="Flag" minOccurs="0"/>
 
</xs:sequence>
</xs:complexType>
model referencehttp://edamontology.org/data_1317
http://edamontology.org/format_2352

AminoacidTranslationData  complexType
diagram BioXSD-1.1_p58.png
type restriction of TranslationData
properties
base TranslationData
children geneticCode
used by
elements GeneralAminoacidSequenceRecord/translationData AminoacidSequenceRecord/translationData
source <xs:complexType name="AminoacidTranslationData">
 
<xs:complexContent>
   
<xs:restriction base="TranslationData">
     
<xs:sequence>
       
<xs:element name="geneticCode" type="GeneticCode" minOccurs="0"/>
     
</xs:sequence>
   
</xs:restriction>
 
</xs:complexContent>
</xs:complexType>

DatabaseReference  complexType
diagram BioXSD-1.1_p72.png
used by
elements FeatureTypeDetails/association/associatedDatabase FeatureRecord/annotation/condensedReferences/database FeatureRecord/blockWithOccurrenceReferences/database FeatureRecord/blockWithOccurrenceReferences/annotation/condensedReferences/database
complexType EntryReference
attributes
Name  Type  Use  Default  Fixed  annotation
dbNameDatabaseName      
dbUriUri      
documentation
General URI of the database
dbVersionName      
localCopyOfDbxs:boolean  false    
wsdlUri      
documentation
URL of a WSDL file describing the referenced Web service (can be WSDL version 1.0, 1.1, 2.0)
wsdlServicexs:NMTOKEN      
documentation
A 'wsdl:service' 'name' in the WSDL file referenced in 'wsdl'
wsdlPortxs:NMTOKEN      
documentation
A 'wsdl:port' 'name' (WSDL 1.0/1.1) or 'wsdl:endpoint' 'name' (WSDL 2.0) in the WSDL file referenced in 'wsdl'
webserviceEndpointAddressUri      
documentation
URI of the referenced Web service endpoint
webserviceOperationxs:NMTOKEN      
documentation
Identifier of an operation of the Web service referenced in 'wsdl' or 'webserviceEnpointAddress'. Can be a 'wsdl:operation' 'name' in a WSDL file, or another operation handle
webserviceInputParametersderived by: Name      
documentation
Space-separated list of input-parameter identifiers of the Web-service operation referenced in 'webserviceOperation'. Used together with the 'webserviceInputValues' attribute in order to define a list of necessary parameter-value pairs for obtaining the referenced data entry or resource. NB. Space characters will be interpreted as delimiters. An item in the 'webserviceInputParameters' list can be a parameter handle without whitespace characters such as an XPath or JSONPath expression, an 'xs:element' or 'wsdl:part' 'name', or another placeholder, name, or label without whitespace characters
webserviceInputValuesderived by: Name      
documentation
Space-separated list of input values of the Web-service operation referenced in 'webserviceOperation'. Used together with the 'webserviceInputParameters' attribute in order to define a list of necessary parameter-value pairs for obtaining the referenced data entry or resource. NB. Space characters will be interpreted as delimiters. n-th item in the 'webserviceInputValues' list corresponds to the n-th item in the 'webserviceInputParameters' list. An empty 'webserviceInputParameters' with a single item in 'webserviceInputValues' is usable for unary operations. An item of the 'webserviceInputValues' list can be a simple value without whitespace characters. Cannot be used for complex input values. If complex input values are required as part of a reference to a Web service, use 'bx:Method' complex type instead
webserviceVersionName      
documentation
Version of the Web service referenced in 'wsdl' or 'webserviceEnpointAddress'
webserviceDatexs:date      
documentation
The date when this Web-service reference was valid (created or last time updated)
documentation Reference to a database
source <xs:complexType name="DatabaseReference" sawsdl:modelReference="http://edamontology.org/format_2352">
 
<xs:annotation>
   
<xs:documentation>Reference to a database</xs:documentation>
 
</xs:annotation>
 
<xs:attribute name="dbName" type="DatabaseName"/>
 
<xs:attribute name="dbUri" type="Uri" sawsdl:modelReference="http://purl.org/dc/elements/1.1/identifier http://edamontology.org/data_1048">
   
<xs:annotation>
     
<xs:documentation>General URI of the database</xs:documentation>
   
</xs:annotation>
   
<!--"Database identifier"(1048)-->
   
<!--"Identifier"(0842)-->
 
</xs:attribute>
 
<xs:attribute name="dbVersion" type="Name" sawsdl:modelReference="http://purl.org/dc/elements/1.1/version http://edamontology.org/data_1670"/>
 
<xs:attribute name="localCopyOfDb" type="xs:boolean" default="false"/>
 
<xs:attributeGroup ref="WebserviceReference"/>
 
<!--"Database identifier"(1048)-->
 
<!--"Identifier"(0842)-->
 
<!--"BioXSD"(2352)-->
 
<!--"Database version information"(1670)-->
</xs:complexType>
model referencehttp://edamontology.org/format_2352

EntryReference  complexType
diagram BioXSD-1.1_p73.png
type extension of DatabaseReference
properties
base DatabaseReference
used by
elements FeatureTypeDetails/association/associatedDatabaseEntry ExperimentalEvidence/citation Method/citation FeatureTypeDetails/databaseEntry ExperimentalEvidence/dataReference AlignedBiosequence/genomeBuild FeatureRecord/referenceSequence/genomeBuild FeatureOccurrenceData/occurrenceEntryReference GeneticCode/reference
complexTypes SequenceReference Species
attributes
Name  Type  Use  Default  Fixed  annotation
dbNameDatabaseName      
dbUriUri      
documentation
General URI of the database
dbVersionName      
localCopyOfDbxs:boolean  false    
wsdlUri      
documentation
URL of a WSDL file describing the referenced Web service (can be WSDL version 1.0, 1.1, 2.0)
wsdlServicexs:NMTOKEN      
documentation
A 'wsdl:service' 'name' in the WSDL file referenced in 'wsdl'
wsdlPortxs:NMTOKEN      
documentation
A 'wsdl:port' 'name' (WSDL 1.0/1.1) or 'wsdl:endpoint' 'name' (WSDL 2.0) in the WSDL file referenced in 'wsdl'
webserviceEndpointAddressUri      
documentation
URI of the referenced Web service endpoint
webserviceOperationxs:NMTOKEN      
documentation
Identifier of an operation of the Web service referenced in 'wsdl' or 'webserviceEnpointAddress'. Can be a 'wsdl:operation' 'name' in a WSDL file, or another operation handle
webserviceInputParametersderived by: Name      
documentation
Space-separated list of input-parameter identifiers of the Web-service operation referenced in 'webserviceOperation'. Used together with the 'webserviceInputValues' attribute in order to define a list of necessary parameter-value pairs for obtaining the referenced data entry or resource. NB. Space characters will be interpreted as delimiters. An item in the 'webserviceInputParameters' list can be a parameter handle without whitespace characters such as an XPath or JSONPath expression, an 'xs:element' or 'wsdl:part' 'name', or another placeholder, name, or label without whitespace characters
webserviceInputValuesderived by: Name      
documentation
Space-separated list of input values of the Web-service operation referenced in 'webserviceOperation'. Used together with the 'webserviceInputParameters' attribute in order to define a list of necessary parameter-value pairs for obtaining the referenced data entry or resource. NB. Space characters will be interpreted as delimiters. n-th item in the 'webserviceInputValues' list corresponds to the n-th item in the 'webserviceInputParameters' list. An empty 'webserviceInputParameters' with a single item in 'webserviceInputValues' is usable for unary operations. An item of the 'webserviceInputValues' list can be a simple value without whitespace characters. Cannot be used for complex input values. If complex input values are required as part of a reference to a Web service, use 'bx:Method' complex type instead
webserviceVersionName      
documentation
Version of the Web service referenced in 'wsdl' or 'webserviceEnpointAddress'
webserviceDatexs:date      
documentation
The date when this Web-service reference was valid (created or last time updated)
accessionAccession      
entryUriUri      
entryVersionName      
datexs:date      
documentation
Date when this reference was fully valid: created or last time updated
documentation Reference to an entry in a database
source <xs:complexType name="EntryReference">
 
<xs:annotation>
   
<xs:documentation>Reference to an entry in a database</xs:documentation>
 
</xs:annotation>
 
<xs:complexContent>
   
<xs:extension base="DatabaseReference">
     
<xs:attribute name="accession" type="Accession"/>
     
<xs:attribute name="entryUri" type="Uri" sawsdl:modelReference="http://purl.org/dc/elements/1.1/identifier http://edamontology.org/data_2091"/>
     
<xs:attribute name="entryVersion" type="Name" sawsdl:modelReference="http://edamontology.org/data_2090 http://purl.org/dc/elements/1.1/version"/>
     
<xs:attribute name="date" type="xs:date" sawsdl:modelReference="http://edamontology.org/data_2156 http://edamontology.org/data_2337">
       
<xs:annotation>
         
<xs:documentation>Date when this reference was fully valid: created or last time updated</xs:documentation>
       
</xs:annotation>
     
</xs:attribute>
   
</xs:extension>
   
<!--"Accession"(2091)-->
   
<!--"Identifier"(0842)-->
   
<!--"Database entry version information"(2090)-->
 
</xs:complexContent>
 
<!--"Identifier"(0842)-->
</xs:complexType>

OntologyReference  complexType
diagram BioXSD-1.1_p241.png
used by
elements FeatureRecord/annotation/condensedReferences/ontology FeatureRecord/blockWithOccurrenceReferences/ontology FeatureRecord/blockWithOccurrenceReferences/annotation/condensedReferences/ontology
complexType SemanticConcept
attributes
Name  Type  Use  Default  Fixed  annotation
ontologyNameOntologyName      
ontologyUriUri      
documentation
General URI of the controlled vocabulary (ontology)
ontologyVersionName      
localCopyOfOntologyxs:boolean  false    
documentation Reference to an ontology, controlled vocabulary, or a collection of semantic concepts
source <xs:complexType name="OntologyReference" sawsdl:modelReference="http://edamontology.org/data_2338 http://edamontology.org/data_2352">
 
<xs:annotation>
   
<xs:documentation>Reference to an ontology, controlled vocabulary, or a collection of semantic concepts</xs:documentation>
 
</xs:annotation>
 
<xs:attribute name="ontologyName" type="OntologyName" sawsdl:modelReference="http://edamontology.org/data_1051"/>
 
<xs:attribute name="ontologyUri" type="Uri" sawsdl:modelReference="http://edamontology.org/data_2338">
   
<xs:annotation>
     
<xs:documentation>General URI of the controlled vocabulary (ontology)</xs:documentation>
   
</xs:annotation>
 
</xs:attribute>
 
<xs:attribute name="ontologyVersion" type="Name" sawsdl:modelReference="http://purl.org/dc/elements/1.1/version http://edamontology.org/data_0953"/>
 
<xs:attribute name="localCopyOfOntology" type="xs:boolean" default="false"/>
 
<!--"Version information"(0953)-->
</xs:complexType>
model referencehttp://edamontology.org/data_2338
http://edamontology.org/data_2352

SemanticConcept  complexType
diagram BioXSD-1.1_p264.png
type extension of OntologyReference
properties
base OntologyReference
used by
elements FeatureTypeDetails/association/associatedConcept Method/categoryConcept FeatureType/classConcept ScoreType/concept FeatureType/equalConcept FeatureType/equalConcept FeatureTypeDetails/association/relationConcept FeatureRecord/blockWithOccurrenceReferences/annotation/occurrence/association/relationConcept FeatureRecord/blockWithOccurrenceReferences/semanticConcept FeatureTypeDetails/specificFeatureConcept
attributes
Name  Type  Use  Default  Fixed  annotation
ontologyNameOntologyName      
ontologyUriUri      
documentation
General URI of the controlled vocabulary (ontology)
ontologyVersionName      
localCopyOfOntologyxs:boolean  false    
accessionAccession      
documentation
The local ID of the semantic concept within an ontology, vocabulary, or a collection of concepts. Note: The local ID is supposed to be persistent (an accession)
conceptUriUri      
termName      
documentation
Human-readable term, or a name of an ontology concept. NB. Does not have to be always up to date and canonical.
(Use also 'conceptUri' or 'accession': up-to-date name and other properties of the concept should be downloadable given the 'conceptUri' or 'accession')
documentation Reference to a concept from an ontology or the Semantic Web, or a term from a controlled vocabulary
source <xs:complexType name="SemanticConcept" sawsdl:modelReference="http://edamontology.org/data_0966 http://edamontology.org/data_1087 http://edamontology.org/data_2352">
 
<xs:annotation>
   
<xs:documentation>Reference to a concept from an ontology or the Semantic Web, or a term from a controlled vocabulary</xs:documentation>
 
</xs:annotation>
 
<xs:complexContent>
   
<xs:extension base="OntologyReference">
     
<xs:attribute name="accession" type="Accession" sawsdl:modelReference="http://edamontology.org/data_1087">
       
<xs:annotation>
         
<xs:documentation>The local ID of the semantic concept within an ontology, vocabulary, or a collection of concepts. Note: The local ID is supposed to be persistent (an accession)</xs:documentation>
       
</xs:annotation>
     
</xs:attribute>
     
<xs:attribute name="conceptUri" type="Uri" sawsdl:modelReference="http://edamontology.org/data_1087"/>
     
<xs:attribute name="term" type="Name" sawsdl:modelReference="http://edamontology.org/data_2339">
       
<xs:annotation>
         
<xs:documentation>Human-readable term, or a name of an ontology concept. NB. Does not have to be always up to date and canonical.
(Use also 'conceptUri' or 'accession': up-to-date name and other properties of the concept should be downloadable given the 'conceptUri' or 'accession')
</xs:documentation>
       
</xs:annotation>
     
</xs:attribute>
   
</xs:extension>
 
</xs:complexContent>
</xs:complexType>
model referencehttp://edamontology.org/data_0966
http://edamontology.org/data_1087
http://edamontology.org/data_2352

Species  complexType
diagram BioXSD-1.1_p282.png
type extension of EntryReference
properties
base EntryReference
used by
elements BiosequenceRecord/species GeneralNucleotideSequenceRecord/species GeneralAminoacidSequenceRecord/species NucleotideSequenceRecord/species AminoacidSequenceRecord/species AlignedBiosequence/species FeatureRecord/referenceSequence/species
attributes
Name  Type  Use  Default  Fixed  annotation
dbNameDatabaseName      
dbUriUri      
documentation
General URI of the database
dbVersionName      
localCopyOfDbxs:boolean  false    
wsdlUri      
documentation
URL of a WSDL file describing the referenced Web service (can be WSDL version 1.0, 1.1, 2.0)
wsdlServicexs:NMTOKEN      
documentation
A 'wsdl:service' 'name' in the WSDL file referenced in 'wsdl'
wsdlPortxs:NMTOKEN      
documentation
A 'wsdl:port' 'name' (WSDL 1.0/1.1) or 'wsdl:endpoint' 'name' (WSDL 2.0) in the WSDL file referenced in 'wsdl'
webserviceEndpointAddressUri      
documentation
URI of the referenced Web service endpoint
webserviceOperationxs:NMTOKEN      
documentation
Identifier of an operation of the Web service referenced in 'wsdl' or 'webserviceEnpointAddress'. Can be a 'wsdl:operation' 'name' in a WSDL file, or another operation handle
webserviceInputParametersderived by: Name      
documentation
Space-separated list of input-parameter identifiers of the Web-service operation referenced in 'webserviceOperation'. Used together with the 'webserviceInputValues' attribute in order to define a list of necessary parameter-value pairs for obtaining the referenced data entry or resource. NB. Space characters will be interpreted as delimiters. An item in the 'webserviceInputParameters' list can be a parameter handle without whitespace characters such as an XPath or JSONPath expression, an 'xs:element' or 'wsdl:part' 'name', or another placeholder, name, or label without whitespace characters
webserviceInputValuesderived by: Name      
documentation
Space-separated list of input values of the Web-service operation referenced in 'webserviceOperation'. Used together with the 'webserviceInputParameters' attribute in order to define a list of necessary parameter-value pairs for obtaining the referenced data entry or resource. NB. Space characters will be interpreted as delimiters. n-th item in the 'webserviceInputValues' list corresponds to the n-th item in the 'webserviceInputParameters' list. An empty 'webserviceInputParameters' with a single item in 'webserviceInputValues' is usable for unary operations. An item of the 'webserviceInputValues' list can be a simple value without whitespace characters. Cannot be used for complex input values. If complex input values are required as part of a reference to a Web service, use 'bx:Method' complex type instead
webserviceVersionName      
documentation
Version of the Web service referenced in 'wsdl' or 'webserviceEnpointAddress'
webserviceDatexs:date      
documentation
The date when this Web-service reference was valid (created or last time updated)
accessionAccession      
entryUriUri      
entryVersionName      
datexs:date      
documentation
Date when this reference was fully valid: created or last time updated
speciesNameName      
documentation
Custom human-readable name of the species. NB. Does not have to be always up to date and canonical. Use also entryUri or accession if possible
speciesNoteText      
documentation Reference to a species (can be used also for a phenotype, cell line, tissue, sample, geo location, ...)
source <xs:complexType name="Species">
 
<xs:annotation>
   
<xs:documentation>Reference to a species (can be used also for a phenotype, cell line, tissue, sample, geo location, ...)</xs:documentation>
 
</xs:annotation>
 
<xs:complexContent>
   
<xs:extension base="EntryReference">
     
<xs:attribute name="speciesName" type="Name" sawsdl:modelReference="http://www.w3.org/2000/01/rdf-schema#label http://edamontology.org/data_1045">
       
<xs:annotation>
         
<xs:documentation>Custom human-readable name of the species. NB. Does not have to be always up to date and canonical. Use also entryUri or accession if possible</xs:documentation>
       
</xs:annotation>
       
<!--"Species name"(1045)-->
     
</xs:attribute>
     
<xs:attribute name="speciesNote" type="Text" sawsdl:modelReference="http://www.w3.org/2000/01/rdf-schema#comment"/>
   
</xs:extension>
 
</xs:complexContent>
 
<!--"Organism identifier"(1869)-->
</xs:complexType>

SequenceReference  complexType
diagram BioXSD-1.1_p277.png
type extension of EntryReference
properties
base EntryReference
children subsequencePosition supersequence supersequenceName
used by
elements GeneralOutsideSequencePosition/explicitSequenceReference OutsideSequencePosition/explicitSequenceReference BiosequenceRecord/reference GeneralNucleotideSequenceRecord/reference GeneralAminoacidSequenceRecord/reference NucleotideSequenceRecord/reference AminoacidSequenceRecord/reference AlignedBiosequence/sequenceReference FeatureRecord/referenceSequence/sequenceReference
attributes
Name  Type  Use  Default  Fixed  annotation
dbNameDatabaseName      
dbUriUri      
documentation
General URI of the database
dbVersionName      
localCopyOfDbxs:boolean  false    
wsdlUri      
documentation
URL of a WSDL file describing the referenced Web service (can be WSDL version 1.0, 1.1, 2.0)
wsdlServicexs:NMTOKEN      
documentation
A 'wsdl:service' 'name' in the WSDL file referenced in 'wsdl'
wsdlPortxs:NMTOKEN      
documentation
A 'wsdl:port' 'name' (WSDL 1.0/1.1) or 'wsdl:endpoint' 'name' (WSDL 2.0) in the WSDL file referenced in 'wsdl'
webserviceEndpointAddressUri      
documentation
URI of the referenced Web service endpoint
webserviceOperationxs:NMTOKEN      
documentation
Identifier of an operation of the Web service referenced in 'wsdl' or 'webserviceEnpointAddress'. Can be a 'wsdl:operation' 'name' in a WSDL file, or another operation handle
webserviceInputParametersderived by: Name      
documentation
Space-separated list of input-parameter identifiers of the Web-service operation referenced in 'webserviceOperation'. Used together with the 'webserviceInputValues' attribute in order to define a list of necessary parameter-value pairs for obtaining the referenced data entry or resource. NB. Space characters will be interpreted as delimiters. An item in the 'webserviceInputParameters' list can be a parameter handle without whitespace characters such as an XPath or JSONPath expression, an 'xs:element' or 'wsdl:part' 'name', or another placeholder, name, or label without whitespace characters
webserviceInputValuesderived by: Name      
documentation
Space-separated list of input values of the Web-service operation referenced in 'webserviceOperation'. Used together with the 'webserviceInputParameters' attribute in order to define a list of necessary parameter-value pairs for obtaining the referenced data entry or resource. NB. Space characters will be interpreted as delimiters. n-th item in the 'webserviceInputValues' list corresponds to the n-th item in the 'webserviceInputParameters' list. An empty 'webserviceInputParameters' with a single item in 'webserviceInputValues' is usable for unary operations. An item of the 'webserviceInputValues' list can be a simple value without whitespace characters. Cannot be used for complex input values. If complex input values are required as part of a reference to a Web service, use 'bx:Method' complex type instead
webserviceVersionName      
documentation
Version of the Web service referenced in 'wsdl' or 'webserviceEnpointAddress'
webserviceDatexs:date      
documentation
The date when this Web-service reference was valid (created or last time updated)
accessionAccession      
entryUriUri      
entryVersionName      
datexs:date      
documentation
Date when this reference was fully valid: created or last time updated
sequenceVersionName      
variantAccessionAccession      
variantNoteName      
documentation Formal reference to a sequence in a database or an explicit super-sequence
source <xs:complexType name="SequenceReference">
 
<xs:annotation>
   
<xs:documentation>Formal reference to a sequence in a database or an explicit super-sequence</xs:documentation>
 
</xs:annotation>
 
<xs:complexContent>
   
<xs:extension base="EntryReference">
     
<xs:sequence>
       
<xs:element name="subsequencePosition" type="SequencePosition" minOccurs="0">
         
<xs:annotation>
           
<xs:documentation>Coordinates of the sub-sequence within the referenced sequence</xs:documentation>
         
</xs:annotation>
       
</xs:element>
       
<xs:element name="supersequence" type="Biosequence" minOccurs="0">
         
<xs:annotation>
           
<xs:documentation>Explicit super-sequence, in case it is not desired or not possible to point to a database entry</xs:documentation>
         
</xs:annotation>
       
</xs:element>
       
<xs:element name="supersequenceName" type="Name" minOccurs="0" sawsdl:modelReference="http://edamontology.org/data_2154">
         
<xs:annotation>
           
<xs:documentation>Custom name of the super-sequence, in case it is not desired or not possible to point to a database entry</xs:documentation>
         
</xs:annotation>
       
</xs:element>
     
</xs:sequence>
     
<xs:attribute name="sequenceVersion" type="Name" sawsdl:modelReference="http://edamontology.org/data_1771 http://purl.org/dc/elements/1.1/version"/>
     
<xs:attribute name="variantAccession" type="Accession" sawsdl:modelReference="http://purl.org/dc/elements/1.1/identifier http://edamontology.org/data_1063"/>
     
<xs:attribute name="variantNote" type="Name" sawsdl:modelReference="http://www.w3.org/2000/01/rdf-schema#comment http://edamontology.org/data_1063"/>
   
</xs:extension>
   
<!--"Sequence version information"(1771)-->
   
<!--"Sequence identifier"(1063)-->
 
</xs:complexContent>
 
<!--"Sequence identifier"(1063)-->
</xs:complexType>

Method  complexType
diagram BioXSD-1.1_p221.png
children categoryConcept citation inputParameter outputParameter
used by
elements FeatureRecord/annotation/condensedReferences/method FeatureRecord/blockWithOccurrenceReferences/method FeatureRecord/blockWithOccurrenceReferences/annotation/condensedReferences/method MethodResult/method PredictionResult/method ScoreType/method
attributes
Name  Type  Use  Default  Fixed  annotation
nameNamerequired      
uriUri      
versionName      
datexs:date      
wsdlUri      
documentation
URL of a WSDL file describing the referenced Web service (can be WSDL version 1.0, 1.1, 2.0)
wsdlServicexs:NMTOKEN      
documentation
A 'wsdl:service' 'name' in the WSDL file referenced in 'wsdl'
wsdlPortxs:NMTOKEN      
documentation
A 'wsdl:port' 'name' (WSDL 1.0/1.1) or 'wsdl:endpoint' 'name' (WSDL 2.0) in the WSDL file referenced in 'wsdl'
webserviceEndpointAddressUri      
documentation
URI of the referenced Web service endpoint
webserviceOperationxs:NMTOKEN      
documentation
Identifier of an operation of the Web service referenced in 'wsdl' or 'webserviceEnpointAddress'. Can be a 'wsdl:operation' 'name' in a WSDL file, or another operation handle
webserviceInputParametersderived by: Name      
documentation
Space-separated list of input-parameter identifiers of the Web-service operation referenced in 'webserviceOperation'. Used together with the 'webserviceInputValues' attribute in order to define a list of necessary parameter-value pairs for obtaining the referenced data entry or resource. NB. Space characters will be interpreted as delimiters. An item in the 'webserviceInputParameters' list can be a parameter handle without whitespace characters such as an XPath or JSONPath expression, an 'xs:element' or 'wsdl:part' 'name', or another placeholder, name, or label without whitespace characters
webserviceInputValuesderived by: Name      
documentation
Space-separated list of input values of the Web-service operation referenced in 'webserviceOperation'. Used together with the 'webserviceInputParameters' attribute in order to define a list of necessary parameter-value pairs for obtaining the referenced data entry or resource. NB. Space characters will be interpreted as delimiters. n-th item in the 'webserviceInputValues' list corresponds to the n-th item in the 'webserviceInputParameters' list. An empty 'webserviceInputParameters' with a single item in 'webserviceInputValues' is usable for unary operations. An item of the 'webserviceInputValues' list can be a simple value without whitespace characters. Cannot be used for complex input values. If complex input values are required as part of a reference to a Web service, use 'bx:Method' complex type instead
webserviceVersionName      
documentation
Version of the Web service referenced in 'wsdl' or 'webserviceEnpointAddress'
webserviceDatexs:date      
documentation
The date when this Web-service reference was valid (created or last time updated)
source <xs:complexType name="Method" sawsdl:modelReference="http://edamontology.org/data_0007 http://edamontology.org/data_2337 http://edamontology.org/data_0977 http://edamontology.org/format_2352">
 
<xs:sequence>
   
<xs:element name="categoryConcept" type="SemanticConcept" minOccurs="0" maxOccurs="unbounded" sawsdl:modelReference="http://edamontology.org/data_0958 http://edamontology.org/operation_0004"/>
   
<xs:element name="citation" type="EntryReference" minOccurs="0" maxOccurs="unbounded" sawsdl:modelReference="http://edamontology.org/data_0958 http://edamontology.org/data_0970 "/>
   
<xs:element name="inputParameter" type="Score" minOccurs="0" maxOccurs="unbounded" sawsdl:modelReference="http://edamontology.org/data_2527"/>
   
<!--"Parameter"(2527)-->
   
<xs:element name="outputParameter" type="Score" minOccurs="0" maxOccurs="unbounded" sawsdl:modelReference="http://edamontology.org/data_2527"/>
   
<!--"Parameter"(2527)-->
 
</xs:sequence>
 
<xs:attribute name="name" type="Name" use="required" sawsdl:modelReference="http://edamontology.org/data_1190"/>
 
<xs:attribute name="uri" type="Uri" sawsdl:modelReference="http://edamontology.org/data_0977"/>
 
<xs:attribute name="version" type="Name" sawsdl:modelReference="http://purl.org/dc/elements/1.1/version http://edamontology.org/data_1671">
   
<!--"Tool version information"(1671)-->
 
</xs:attribute>
 
<xs:attribute name="date" type="xs:date" sawsdl:modelReference="http://edamontology.org/data_2156 http://edamontology.org/data_2337"/>
 
<xs:attributeGroup ref="WebserviceReference"/>
</xs:complexType>
model referencehttp://edamontology.org/data_0007
http://edamontology.org/data_2337
http://edamontology.org/data_0977
http://edamontology.org/format_2352

LocalId  simpleType
type restriction of xs:string
used by
elements FeatureRecord/blockWithOccurrenceReferences/annotation/condensedReferences/databaseIdRef FeatureRecord/blockWithOccurrenceReferences/annotation/condensedReferences/methodIdRef Result/methodIdRef PredictionResult/methodIdRef ScoreType/methodIdRef FeatureRecord/blockWithOccurrenceReferences/annotation/condensedReferences/ontologyIdRef FeatureRecord/blockWithOccurrenceReferences/annotation/occurrence/association/relationConceptIdRef FeatureRecord/blockWithOccurrenceReferences/annotation/condensedReferences/scoreTypeIdRef
attributes FeatureRecord/blockWithOccurrenceReferences/database/@localId FeatureRecord/blockWithOccurrenceReferences/ontology/@localId FeatureRecord/blockWithOccurrenceReferences/semanticConcept/@localId FeatureRecord/blockWithOccurrenceReferences/method/@localId FeatureRecord/blockWithOccurrenceReferences/scoreType/@localId FeatureRecord/blockWithOccurrenceReferences/annotation/occurrence/@localId MethodResult/method/@localId FeatureRecord/blockWithOccurrenceReferences/annotation/occurrence/association/associatedFeatureOccurrence/@localIdRef Score/@scoreTypeIdRef
facets
Kind Value annotation 
pattern [A-Za-z0-9#]{1,4} 
documentation Identifier for local references within a data record. NB. Objects define their local identifier always in their 'localId' attribute
source <xs:simpleType name="LocalId" sawsdl:modelReference="http://purl.org/dc/elements/1.1/identifier http://edamontology.org/data_0842">
 
<xs:annotation>
   
<xs:documentation>Identifier for local references within a data record. NB. Objects define their local identifier always in their 'localId' attribute</xs:documentation>
 
</xs:annotation>
 
<xs:restriction base="xs:string">
   
<xs:pattern value="[A-Za-z0-9#]{1,4}"/>
 
</xs:restriction>
 
<!--"Identifier"(0842)-->
</xs:simpleType>

Accession  simpleType
type restriction of xs:string
used by
elements AlignedBiosequence/variantAccession FeatureRecord/referenceSequence/variantAccession
simpleTypes EmblAccession ExtendedGenbankAccession ExtendedUniprotAccession NcbiGeneticCodeId NcbiTaxonomyId PubmedId
attributes EntryReference/@accession SemanticConcept/@accession SequenceReference/@variantAccession
facets
Kind Value annotation 
maxLength 1000 
pattern [A-Za-z0-9\-._~]+ 
documentation Generalisation of bioinformatics accession numbers (stable primary keys/stable unique identifiers), or bioinformatics primary keys/unique identifiers (where no stable accessions)
source <xs:simpleType name="Accession" sawsdl:modelReference="http://purl.org/dc/elements/1.1/identifier http://edamontology.org/data_0842 http://edamontology.org/data_2091">
 
<xs:annotation>
   
<xs:documentation>Generalisation of bioinformatics accession numbers (stable primary keys/stable unique identifiers), or bioinformatics primary keys/unique identifiers (where no stable accessions)</xs:documentation>
 
</xs:annotation>
 
<xs:restriction base="xs:string">
   
<xs:maxLength value="1000"/>
   
<xs:pattern value="[A-Za-z0-9\-._~]+"/>
 
</xs:restriction>
 
<!--"Identifier"(0842)-->
 
<!--"Accession"(2091)-->
</xs:simpleType>

EmblAccession  simpleType
type Accession
facets
Kind Value annotation 
maxLength 1000 
pattern [A-Za-z0-9\-._~]+ 
source <xs:simpleType name="EmblAccession" sawsdl:modelReference="http://edamontology.org/data_1107">
 
<xs:restriction base="Accession"/>
</xs:simpleType>

ExtendedUniprotAccession  simpleType
type restriction of Accession
used by
simpleType UniprotAccession
facets
Kind Value annotation 
maxLength 1000 
pattern [OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9] 
pattern [A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9] 
pattern [A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9][A-Z][A-Z0-9][A-Z0-9][0-9] 
pattern [OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9][.-][0-9]+ 
pattern [A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9][.-][0-9]+ 
pattern [A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9][A-Z][A-Z0-9][A-Z0-9][0-9][.-][0-9]+ 
documentation UniProt accession number, optionally with version after a dot (.) or the variant (isoform) suffix after a hyphen (-)
source <xs:simpleType name="ExtendedUniprotAccession">
 
<xs:annotation>
   
<xs:documentation>UniProt accession number, optionally with version after a dot (.) or the variant (isoform) suffix after a hyphen (-)</xs:documentation>
 
</xs:annotation>
 
<xs:restriction base="Accession">
   
<xs:pattern value="[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]"/>
   
<xs:pattern value="[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]"/>
   
<xs:pattern value="[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]"/>
   
<xs:pattern value="[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9][.-][0-9]+"/>
   
<xs:pattern value="[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9][.-][0-9]+"/>
   
<xs:pattern value="[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9][A-Z][A-Z0-9][A-Z0-9][0-9][.-][0-9]+"/>
 
</xs:restriction>
</xs:simpleType>

UniprotAccession  simpleType
type restriction of ExtendedUniprotAccession
facets
Kind Value annotation 
maxLength 1000 
pattern [OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9] 
pattern [A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9] 
pattern [A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9][A-Z][A-Z0-9][A-Z0-9][0-9] 
documentation UniProt accession number, without the sequence version and splice-variant suffix
source <xs:simpleType name="UniprotAccession" sawsdl:modelReference="http://edamontology.org/data_1099">
 
<xs:annotation>
   
<xs:documentation>UniProt accession number, without the sequence version and splice-variant suffix</xs:documentation>
 
</xs:annotation>
 
<xs:restriction base="ExtendedUniprotAccession">
   
<xs:pattern value="[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]"/>
   
<xs:pattern value="[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]"/>
   
<xs:pattern value="[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]"/>
 
</xs:restriction>
</xs:simpleType>

ExtendedGenbankAccession  simpleType
type restriction of Accession
used by
simpleType GenbankAccession
facets
Kind Value annotation 
maxLength 1000 
pattern [A-Z][0-9]{5}(.[0-9]+)? 
pattern [A-Z]{2}[0-9]{6}(.[0-9]+)? 
pattern [A-Z]{3}[0-9]{5}(.[0-9]+)? 
pattern [A-Z]{4}[0-9]{8,10}(.[0-9]+)? 
pattern [A-Z]{5}[0-9]{7}(.[0-9]+)? 
pattern [A-Z]{2}_[0-9]{6}(.[0-9]+)? 
pattern [A-Z]{2}_[0-9]{9}(.[0-9]+)? 
pattern [A-Z]{2}_[A-Z]{4}[0-9]{8,10}(.[0-9]+)? 
source <xs:simpleType name="ExtendedGenbankAccession">
 
<xs:restriction base="Accession">
   
<xs:pattern value="[A-Z][0-9]{5}(.[0-9]+)?"/>
   
<xs:pattern value="[A-Z]{2}[0-9]{6}(.[0-9]+)?"/>
   
<xs:pattern value="[A-Z]{3}[0-9]{5}(.[0-9]+)?"/>
   
<xs:pattern value="[A-Z]{4}[0-9]{8,10}(.[0-9]+)?"/>
   
<xs:pattern value="[A-Z]{5}[0-9]{7}(.[0-9]+)?"/>
   
<xs:pattern value="[A-Z]{2}_[0-9]{6}(.[0-9]+)?"/>
   
<xs:pattern value="[A-Z]{2}_[0-9]{9}(.[0-9]+)?"/>
   
<xs:pattern value="[A-Z]{2}_[A-Z]{4}[0-9]{8,10}(.[0-9]+)?"/>
 
</xs:restriction>
</xs:simpleType>

GenbankAccession  simpleType
type restriction of ExtendedGenbankAccession
used by
simpleTypes GenbankMgaAccession GenbankNucleotideAccession GenbankProteinAccession GenbankWgsAccession
facets
Kind Value annotation 
maxLength 1000 
pattern [A-Z][0-9]{5} 
pattern [A-Z]{2}[0-9]{6} 
pattern [A-Z]{3}[0-9]{5} 
pattern [A-Z]{4}[0-9]{8,10} 
pattern [A-Z]{5}[0-9]{7} 
pattern [A-Z]{2}_[0-9]{6} 
pattern [A-Z]{2}_[0-9]{9} 
pattern [A-Z]{2}_[A-Z]{4}[0-9]{8,10} 
source <xs:simpleType name="GenbankAccession">
 
<xs:restriction base="ExtendedGenbankAccession">
   
<xs:pattern value="[A-Z][0-9]{5}"/>
   
<xs:pattern value="[A-Z]{2}[0-9]{6}"/>
   
<xs:pattern value="[A-Z]{3}[0-9]{5}"/>
   
<xs:pattern value="[A-Z]{4}[0-9]{8,10}"/>
   
<xs:pattern value="[A-Z]{5}[0-9]{7}"/>
   
<xs:pattern value="[A-Z]{2}_[0-9]{6}"/>
   
<xs:pattern value="[A-Z]{2}_[0-9]{9}"/>
   
<xs:pattern value="[A-Z]{2}_[A-Z]{4}[0-9]{8,10}"/>
 
</xs:restriction>
</xs:simpleType>

GenbankNucleotideAccession  simpleType
type restriction of GenbankAccession
facets
Kind Value annotation 
maxLength 1000 
pattern [A-Z][0-9]{5} 
pattern [A-Z]{2}[0-9]{6} 
pattern [A-Z]{2}_[0-9]{6} 
pattern [A-Z]{2}_[0-9]{9} 
documentation GenBank/EMBL/DDBJ nucleotide accession number
source <xs:simpleType name="GenbankNucleotideAccession" sawsdl:modelReference="http://edamontology.org/data_1108">
 
<xs:annotation>
   
<xs:documentation>GenBank/EMBL/DDBJ nucleotide accession number</xs:documentation>
 
</xs:annotation>
 
<xs:restriction base="GenbankAccession">
   
<xs:pattern value="[A-Z][0-9]{5}"/>
   
<xs:pattern value="[A-Z]{2}[0-9]{6}"/>
   
<xs:pattern value="[A-Z]{2}_[0-9]{6}"/>
   
<xs:pattern value="[A-Z]{2}_[0-9]{9}"/>
 
</xs:restriction>
</xs:simpleType>

GenbankProteinAccession  simpleType
type restriction of GenbankAccession
facets
Kind Value annotation 
maxLength 1000 
pattern [A-Z]{3}[0-9]{5} 
documentation GenBank/EMBL/DDBJ protein accession number
source <xs:simpleType name="GenbankProteinAccession">
 
<xs:annotation>
   
<xs:documentation>GenBank/EMBL/DDBJ protein accession number</xs:documentation>
 
</xs:annotation>
 
<xs:restriction base="GenbankAccession">
   
<xs:pattern value="[A-Z]{3}[0-9]{5}"/>
 
</xs:restriction>
</xs:simpleType>

GenbankWgsAccession  simpleType
type restriction of GenbankAccession
facets
Kind Value annotation 
maxLength 1000 
pattern [A-Z]{4}[0-9]{8,10} 
pattern [A-Z]{2}_[A-Z]{4}[0-9]{8,10} 
documentation GenBank/EMBL/DDBJ WGS accession number
source <xs:simpleType name="GenbankWgsAccession">
 
<xs:annotation>
   
<xs:documentation>GenBank/EMBL/DDBJ WGS accession number</xs:documentation>
 
</xs:annotation>
 
<xs:restriction base="GenbankAccession">
   
<xs:pattern value="[A-Z]{4}[0-9]{8,10}"/>
   
<xs:pattern value="[A-Z]{2}_[A-Z]{4}[0-9]{8,10}"/>
 
</xs:restriction>
</xs:simpleType>

GenbankMgaAccession  simpleType
type restriction of GenbankAccession
facets
Kind Value annotation 
maxLength 1000 
pattern [A-Z]{5}[0-9]{7} 
documentation GenBank/EMBL/DDBJ MGA accession number
source <xs:simpleType name="GenbankMgaAccession">
 
<xs:annotation>
   
<xs:documentation>GenBank/EMBL/DDBJ MGA accession number</xs:documentation>
 
</xs:annotation>
 
<xs:restriction base="GenbankAccession">
   
<xs:pattern value="[A-Z]{5}[0-9]{7}"/>
 
</xs:restriction>
</xs:simpleType>

PubmedId  simpleType
type restriction of Accession
facets
Kind Value annotation 
maxLength 1000 
pattern [1-9][0-9]{0,8} 
source <xs:simpleType name="PubmedId">
 
<xs:restriction base="Accession">
   
<xs:pattern value="[1-9][0-9]{0,8}"/>
 
</xs:restriction>
</xs:simpleType>

NcbiTaxonomyId  simpleType
type restriction of Accession
facets
Kind Value annotation 
maxLength 1000 
pattern [1-9][0-9]{0,8} 
documentation NCBI Taxonomy ID (0 ... 999999999; i.e. a subset of 32-bit (4B) signed int)
source <xs:simpleType name="NcbiTaxonomyId" sawsdl:modelReference="http://edamontology.org/data_1179">
 
<xs:annotation>
   
<xs:documentation>NCBI Taxonomy ID (0 ... 999999999; i.e. a subset of 32-bit (4B) signed int)</xs:documentation>
 
</xs:annotation>
 
<xs:restriction base="Accession">
   
<xs:pattern value="[1-9][0-9]{0,8}"/>
 
</xs:restriction>
</xs:simpleType>

NcbiGeneticCodeId  simpleType
type restriction of Accession
facets
Kind Value annotation 
maxLength 1000 
pattern [1-9][0-9]? 
documentation NCBI ID of a genetic code (1 ... 99)
source <xs:simpleType name="NcbiGeneticCodeId">
 
<xs:annotation>
   
<xs:documentation>NCBI ID of a genetic code (1 ... 99)</xs:documentation>
 
</xs:annotation>
 
<xs:restriction base="Accession">
   
<xs:pattern value="[1-9][0-9]?"/>
 
</xs:restriction>
</xs:simpleType>

RecommendedScoreName  simpleType
type restriction of Name
used by
simpleType ScoreName
facets
Kind Value annotation 
maxLength 1000 
pattern \S(\S|\s\S)* 
enumeration p-value 
enumeration E-value 
enumeration Standard deviation 
enumeration Bit 
enumeration Z-score 
enumeration Probability 
enumeration Q3 
enumeration SOV 
source <xs:simpleType name="RecommendedScoreName">
 
<xs:restriction base="Name">
   
<xs:enumeration value="p-value" sawsdl:modelReference="http://edamontology.org/data_1669"/>
   
<xs:enumeration value="E-value" sawsdl:modelReference="http://edamontology.org/data_1667"/>
   
<xs:enumeration value="Standard deviation"/>
   
<xs:enumeration value="Bit" sawsdl:modelReference="http://edamontology.org/data_2335"/>
   
<xs:enumeration value="Z-score"/>
   
<xs:enumeration value="Probability"/>
   
<xs:enumeration value="Q3" sawsdl:modelReference="http://edamontology.org/NumberOfBlahblah"/>
   
<xs:enumeration value="SOV" sawsdl:modelReference="http://edamontology.org/SegmentOverlap"/>
 
</xs:restriction>
</xs:simpleType>

RecommendedVerdict  simpleType
type restriction of Name
used by
simpleTypes ScoreValue Verdict
facets
Kind Value annotation 
maxLength 1000 
pattern \S(\S|\s\S)* 
enumeration Present 
enumeration Putative 
enumeration Improbable 
enumeration Not present 
documentation Predefined, recommended verdict of a predicted or experimental evidence
source <xs:simpleType name="RecommendedVerdict">
 
<xs:annotation>
   
<xs:documentation>Predefined, recommended verdict of a predicted or experimental evidence</xs:documentation>
 
</xs:annotation>
 
<xs:restriction base="Name">
   
<xs:enumeration value="Present"/>
   
<xs:enumeration value="Putative"/>
   
<xs:enumeration value="Improbable"/>
   
<xs:enumeration value="Not present"/>
 
</xs:restriction>
</xs:simpleType>

RecommendedReliability  simpleType
type restriction of Name
used by
simpleTypes Reliability ScoreValue
facets
Kind Value annotation 
maxLength 1000 
pattern \S(\S|\s\S)* 
enumeration Reliable 
enumeration Disputable 
documentation Predefined, recommended reliability of an experimental evidence
source <xs:simpleType name="RecommendedReliability">
 
<xs:annotation>
   
<xs:documentation>Predefined, recommended reliability of an experimental evidence</xs:documentation>
 
</xs:annotation>
 
<xs:restriction base="Name">
   
<xs:enumeration value="Reliable"/>
   
<xs:enumeration value="Disputable"/>
 
</xs:restriction>
</xs:simpleType>

QualitativeCertainty  simpleType
type restriction of Name
used by
simpleType Certainty
facets
Kind Value annotation 
maxLength 1000 
pattern \S(\S|\s\S)* 
enumeration Certain 
enumeration Uncertain 
enumeration Value unknown 
documentation
The referred value completely unknown, not the certainty unknown
enumeration Certainly greater or equal 
enumeration Certainly less or equal 
documentation Qualitative certainty tag
source <xs:simpleType name="QualitativeCertainty" sawsdl:modelReference="http://edamontology.org/format_2352">
 
<xs:annotation>
   
<xs:documentation>Qualitative certainty tag</xs:documentation>
 
</xs:annotation>
 
<xs:restriction base="Name">
   
<xs:enumeration value="Certain"/>
   
<xs:enumeration value="Uncertain"/>
   
<xs:enumeration value="Value unknown">
     
<xs:annotation>
       
<xs:documentation>The referred value completely unknown, not the certainty unknown</xs:documentation>
     
</xs:annotation>
   
</xs:enumeration>
   
<xs:enumeration value="Certainly greater or equal"/>
   
<xs:enumeration value="Certainly less or equal"/>
 
</xs:restriction>
</xs:simpleType>

Strand  simpleType
type restriction of Name
used by
attributes Insert/@strand GeneralSequencePoint/@strand GeneralSequenceInsertionPoint/@strand GeneralOutsideSequencePoint/@strand GeneralSequenceSegment/@strand GeneralOutsideSequenceSegment/@strand
facets
Kind Value annotation 
maxLength 1000 
pattern \S(\S|\s\S)* 
enumeration 
enumeration 
enumeration + over start 
enumeration - over start 
enumeration Unknown 
source <xs:simpleType name="Strand" sawsdl:modelReference="http://edamontology.org/data_0853 http://edamontology.org/format_2352">
 
<xs:restriction base="Name">
   
<xs:enumeration value="+"/>
   
<xs:enumeration value="-"/>
   
<xs:enumeration value="+ over start"/>
   
<xs:enumeration value="- over start"/>
   
<xs:enumeration value="Unknown"/>
 
</xs:restriction>
</xs:simpleType>

OutsidePositionCorrespondance  simpleType
type restriction of Name
used by
elements GeneralOutsideSequencePosition/correspondance OutsideSequencePosition/correspondance
facets
Kind Value annotation 
maxLength 1000 
pattern \S(\S|\s\S)* 
enumeration In chromosome/scaffold/contig 
documentation
The outside position is in the nucleotide sequence of the either explicitly given chromosome or scaffold/contig, or the chromosome/scaffold/contig of the reference sequence.
Outside-positions 1..m are positions in the chromosome
enumeration In explicit sequence 
documentation
The outside position is in an explicitly referenced nucleotide or amino-acid sequence. Can but does not have to be a supersequence of the reference sequence.
Outside-positions 1..m are in the explicitly referenced supersequence. Fill in the 'explicitSequenceReference' element
enumeration In implicit supersequence 
documentation
The outside position is in a nucleotide or amino-acid supersequence (respectively) of the reference subsequence.
Positions 1..n correspond, position -1 is the preceding (next point to the left) from 1
enumeration Relative to 1st translated base 
documentation
The outside position is in a nucleotide sequence.
Position 1 corresponds to the 1st base of the 1st translated codon within the reference isoform, position -1 is the next to the left from 1
(NB. CDSs include the start and stop codons: do not use this correspondence option for outside features of CDSs)
enumeration Relative to 1st transcribed base 
documentation
The outside position is in a nucleotide sequence.
Position 1 corresponds to the 1st base transcribed within the reference isoform, position -1 is the next to the left from 1
documentation Correspondence of the outside positions to the reference sequence
source <xs:simpleType name="OutsidePositionCorrespondance" sawsdl:modelReference="http://edamontology.org/format_2352">
 
<xs:annotation>
   
<xs:documentation>Correspondence of the outside positions to the reference sequence</xs:documentation>
 
</xs:annotation>
 
<xs:restriction base="Name">
   
<xs:enumeration value="In chromosome/scaffold/contig">
     
<xs:annotation>
       
<xs:documentation>The outside position is in the nucleotide sequence of the either explicitly given chromosome or scaffold/contig, or the chromosome/scaffold/contig of the reference sequence.
Outside-positions 1..m are positions in the chromosome
</xs:documentation>
     
</xs:annotation>
   
</xs:enumeration>
   
<xs:enumeration value="In explicit sequence">
     
<xs:annotation>
       
<xs:documentation>The outside position is in an explicitly referenced nucleotide or amino-acid sequence. Can but does not have to be a supersequence of the reference sequence.
Outside-positions 1..m are in the explicitly referenced supersequence. Fill in the 'explicitSequenceReference' element
</xs:documentation>
     
</xs:annotation>
   
</xs:enumeration>
   
<xs:enumeration value="In implicit supersequence">
     
<xs:annotation>
       
<xs:documentation>The outside position is in a nucleotide or amino-acid supersequence (respectively) of the reference subsequence.
Positions 1..n correspond, position -1 is the preceding (next point to the left) from 1
</xs:documentation>
     
</xs:annotation>
   
</xs:enumeration>
   
<xs:enumeration value="Relative to 1st translated base">
     
<xs:annotation>
       
<xs:documentation>The outside position is in a nucleotide sequence.
Position 1 corresponds to the 1st base of the 1st translated codon within the reference isoform, position -1 is the next to the left from 1
(NB. CDSs include the start and stop codons: do not use this correspondence option for outside features of CDSs)
</xs:documentation>
     
</xs:annotation>
   
</xs:enumeration>
   
<xs:enumeration value="Relative to 1st transcribed base">
     
<xs:annotation>