Schema BioXSD-1.0.xsd


schema location:  http://bioxsd.org/BioXSD-1.0.xsd
attribute form default:  unqualified
element form default:  qualified
targetNamespace:  http://bioxsd.org/BioXSD-1.0
 
Complex types  Simple types 
AlignedAminoacidSequence  Accession 
AlignedBiosequence  AminoacidSequence 
AlignedGeneralAminoacidSequence  AnyDecimal 
AlignedGeneralNucleotideSequence  AnyInteger 
AlignedNucleotideSequence  Biosequence 
AminoacidSequenceAlignment  Certainty 
AminoacidSequenceRecord  ChromosomeName 
AminoacidTranslationData  DatabaseName 
AnnotatedSequence  EmblAccession 
BiosequenceAlignment  ExtendedGenbankAccession 
BiosequenceRecord  ExtendedUniprotAccession 
DatabaseReference  FreeText 
Empty  GenbankAccession 
EntryReference  GenbankMgaAccession 
Evidence  GenbankNucleotideAccession 
ExperimentalEvidence  GenbankProteinAccession 
Feature  GenbankWgsAccession 
FeatureData  GeneralAminoacidSequence 
FeatureOccurence  GeneralNucleotideSequence 
Frameshift  InsertionInteger 
Gap  LocalReference 
GeneralAminoacidSequenceAlignment  Name 
GeneralAminoacidSequenceRecord  NcbiGeneticCodeId 
GeneralNucleotideSequenceAlignment  NcbiTaxonomyId 
GeneralNucleotideSequenceRecord  NonnegativeInteger 
GeneralOutsideSequencePoint  NonzeroInteger 
GeneralOutsideSequencePosition  NucleotideSequence 
GeneralOutsideSequenceSegment  OboTermId 
GeneralSequenceInsertionPoint  OntologyName 
GeneralSequencePoint  OutsidePositionCorrespondance 
GeneralSequencePosition  Phase 
GeneralSequenceSegment  PositiveInteger 
GeneticCode  Probability 
Method  PubmedId 
MethodResult  QualitativeCertainty 
NucleotideSequenceAlignment  RecommendedDatabaseName 
NucleotideSequenceRecord  RecommendedOntologyName 
OntologyReference  RecommendedReliability 
OntologyTerm  RecommendedScoreName 
OutsideSequencePoint  RecommendedVerdict 
OutsideSequencePosition  Reliability 
OutsideSequenceSegment  ScoreName 
PredictionResult  Strand 
Result  UniprotAccession 
Score  Uri 
SequenceInsertionPoint  Verdict 
SequencePoint 
SequencePosition 
SequenceReference 
SequenceSegment 
Species 
TranslationData 
WebserviceReference 


Empty  complexType
diagram BioXSD-1.0_p87.png
properties
final #all
used by
elements FeatureOccurence/appliesToWholeSequence FeatureOccurence/variation/missing AlignedBiosequence/reversedDirection AlignedGeneralNucleotideSequence/reversedDirection AlignedGeneralAminoacidSequence/reversedDirection AlignedNucleotideSequence/reversedDirection AlignedAminoacidSequence/reversedDirection TranslationData/reversedTranslationDirection
source <xs:complexType name="Empty" final="#all"/>

AnyInteger  simpleType
type xs:long
used by
element FeatureOccurence/frame
simpleTypes NonnegativeInteger NonzeroInteger
Documentation Any integer number (~-9.2x10^18 ... ~9.2x10^18). Represented by a 64-bit (8B) signed long integer (long, long long, int64, same as xs:long, different from xs:integer)
source <xs:simpleType name="AnyInteger">
  <xs:annotation>
    <xs:documentation>
Any integer number (~-9.2x10^18 ... ~9.2x10^18). Represented by a 64-bit (8B) signed long integer (long, long long, int64, same as xs:long, different from xs:integer)
</xs:documentation>
  </xs:annotation>
  <xs:restriction base="xs:long"/>
</xs:simpleType>

NonnegativeInteger  simpleType
type restriction of AnyInteger
used by
simpleType Phase
facets
Kind Value annotation 
minInclusive 0 
Documentation Non-negative integer number (0 ... ~9.2x10^18). Represented by a 64-bit (8B) signed long integer
source <xs:simpleType name="NonnegativeInteger">
  <xs:annotation>
    <xs:documentation>Non-negative integer number (0 ... ~9.2x10^18). Represented by a 64-bit (8B) signed long integer</xs:documentation>
  </xs:annotation>
  <xs:restriction base="AnyInteger">
    <xs:minInclusive value="0"/>
  </xs:restriction>
</xs:simpleType>

NonzeroInteger  simpleType
type restriction of AnyInteger
used by
complexType GeneralOutsideSequencePoint
simpleTypes InsertionInteger PositiveInteger
attribute Frameshift/@bases
facets
Kind Value annotation 
pattern [\-+]?[1-9][0-9]* 
Documentation Non-zero integer number (~-9.2x10^18 ... -1, 1 ... ~9.2x10^18). Represented by a 64-bit (8B) signed long integer
source <xs:simpleType name="NonzeroInteger">
  <xs:annotation>
    <xs:documentation>Non-zero integer number (~-9.2x10^18 ... -1, 1 ... ~9.2x10^18). Represented by a 64-bit (8B) signed long integer</xs:documentation>
  </xs:annotation>
  <xs:restriction base="AnyInteger">
    <xs:pattern value="[\-+]?[1-9][0-9]*"/>
  </xs:restriction>
</xs:simpleType>

InsertionInteger  simpleType
type restriction of NonzeroInteger
used by
complexType GeneralSequenceInsertionPoint
attributes Frameshift/@pos Gap/@start
facets
Kind Value annotation 
minInclusive -1 
pattern [\-+]?[1-9][0-9]* 
Documentation Insertion-point specific integer number (-1, 1 ... ~9.2x10^18). Represented by a 64-bit (8B) signed long integer
source <xs:simpleType name="InsertionInteger">
  <xs:annotation>
    <xs:documentation>Insertion-point specific integer number (-1, 1 ... ~9.2x10^18). Represented by a 64-bit (8B) signed long integer</xs:documentation>
  </xs:annotation>
  <xs:restriction base="NonzeroInteger">
    <xs:minInclusive value="-1"/>
  </xs:restriction>
</xs:simpleType>

PositiveInteger  simpleType
type restriction of NonzeroInteger
used by
complexType GeneralSequencePoint
attribute Gap/@len
facets
Kind Value annotation 
minInclusive 1 
pattern [\-+]?[1-9][0-9]* 
Documentation Positive integer number (1 ... ~9.2x10^18). Represented by a 64-bit (8B) signed long integer
source <xs:simpleType name="PositiveInteger">
  <xs:annotation>
    <xs:documentation>Positive integer number (1 ... ~9.2x10^18). Represented by a 64-bit (8B) signed long integer</xs:documentation>
  </xs:annotation>
  <xs:restriction base="NonzeroInteger">
    <xs:minInclusive value="1"/>
  </xs:restriction>
</xs:simpleType>

AnyDecimal  simpleType
type xs:double
used by
element Score/value
simpleType Probability
Documentation Any decimal number with double precision (-INF, ~-1.7E308 ... 0, ~5E-324 subnormal ... ~2.3E-308 ... ~1.7E308, INF; +NaN). Represented by a 64-bit (8B) signed floating point number (double, long double, same as xs:double, different from xs:decimal)
source <xs:simpleType name="AnyDecimal">
  <xs:annotation>
    <xs:documentation>
Any decimal number with double precision (-INF, ~-1.7E308 ... 0, ~5E-324 subnormal ... ~2.3E-308 ... ~1.7E308, INF; +NaN). Represented by a 64-bit (8B) signed floating point number (double, long double, same as xs:double, different from xs:decimal)
</xs:documentation>
  </xs:annotation>
  <xs:restriction base="xs:double"/>
</xs:simpleType>

Probability  simpleType
type restriction of AnyDecimal
used by
simpleType Certainty
facets
Kind Value annotation 
minInclusive 0 
maxInclusive 1 
Documentation Probability with double precision (0 ... 1). Represented by a 64-bit (8B) signed floating point number
source <xs:simpleType name="Probability">
  <xs:annotation>
    <xs:documentation>Probability with double precision (0 ... 1). Represented by a 64-bit (8B) signed floating point number</xs:documentation>
  </xs:annotation>
  <xs:restriction base="AnyDecimal">
    <xs:minInclusive value="0"/>
    <xs:maxInclusive value="1"/>
  </xs:restriction>
</xs:simpleType>

Certainty  simpleType
type union of (Probability, QualitativeCertainty)
used by
attributes GeneralSequencePoint/@certainty SequencePoint/@certainty GeneralSequenceInsertionPoint/@certainty SequenceInsertionPoint/@certainty GeneralOutsideSequencePoint/@certainty OutsideSequencePoint/@certainty
Documentation Quantitave or qualitative certainty
source <xs:simpleType name="Certainty">
  <xs:annotation>
    <xs:documentation>Quantitave or qualitative certainty</xs:documentation>
  </xs:annotation>
  <xs:union memberTypes="Probability QualitativeCertainty"/>
</xs:simpleType>

Uri  simpleType
type restriction of xs:string
used by
elements DatabaseReference/databaseUri EntryReference/entryUri OntologyReference/ontologyUri OntologyTerm/termUri Method/uri WebserviceReference/wsdl
facets
Kind Value annotation 
pattern http://[a-z0-9]([a-z0-9]|\-[a-z0-9])*(\.[a-z0-9]([a-z0-9]|\-[a-z0-9])*)*(:[2-9][0-9]{3,})?(/([A-Za-z0-9\-._~!$'()*+,;=]|%[0-9A-F]{2})+)*(\?([A-Za-z0-9\-._~!$'()*+,;=/\?]|%[0-9A-F]{2})*)?(#([A-Za-z0-9\-._~!$'()*+,;=/\?]|%[0-9A-F]{2})*)? 
pattern https://[a-z0-9]([a-z0-9]|\-[a-z0-9])*(\.[a-z0-9]([a-z0-9]|\-[a-z0-9])*)*(:[2-9][0-9]{3,})?(/([A-Za-z0-9\-._~!$'()*+,;=]|%[0-9A-F]{2})+)*(\?([A-Za-z0-9\-._~!$'()*+,;=/\?]|%[0-9A-F]{2})*)?(#([A-Za-z0-9\-._~!$'()*+,;=/\?]|%[0-9A-F]{2})*)? 
pattern ftp://[a-z0-9]([a-z0-9]|\-[a-z0-9])*(\.[a-z0-9]([a-z0-9]|\-[a-z0-9])*)*(:[2-9][0-9]{3,})?(/([A-Za-z0-9\-._~!$'()*+,;=]|%[0-9A-F]{2})+)*(\?([A-Za-z0-9\-._~!$'()*+,;=/\?]|%[0-9A-F]{2})*)?(#([A-Za-z0-9\-._~!$'()*+,;=/\?]|%[0-9A-F]{2})*)? 
pattern urn:lsid:[a-z0-9]([a-z0-9]|\-[a-z0-9])*(\.[a-z0-9]([a-z0-9]|\-[a-z0-9])*)*:[A-Za-z0-9\-._~]+:[A-Za-z0-9\-._~]+(:[A-Za-z0-9\-._~]+)? 
Documentation An absolute Unified Resource Identifier (URI), possibly a Web link.NB. Supports a subset of RFC 3986 generic syntax (selected schemes, DNS only, no user info, constrained port and characters)
source <xs:simpleType name="Uri" sawsdl:modelReference="http://purl.org/edam/data/0001047">
  <xs:annotation>
    <xs:documentation>
An absolute Unified Resource Identifier (URI), possibly a Web link.
NB. Supports a subset of RFC 3986 generic syntax (selected schemes, DNS only, no user info, constrained port and characters)
</xs:documentation>
  </xs:annotation>
  <xs:restriction base="xs:string">
    <xs:pattern value="http://[a-z0-9]([a-z0-9]|\-[a-z0-9])*(\.[a-z0-9]([a-z0-9]|\-[a-z0-9])*)*(:[2-9][0-9]{3,})?(/([A-Za-z0-9\-._~!$'()*+,;=]|%[0-9A-F]{2})+)*(\?([A-Za-z0-9\-._~!$'()*+,;=/\?]|%[0-9A-F]{2})*)?(#([A-Za-z0-9\-._~!$'()*+,;=/\?]|%[0-9A-F]{2})*)?"/>
    <xs:pattern value="https://[a-z0-9]([a-z0-9]|\-[a-z0-9])*(\.[a-z0-9]([a-z0-9]|\-[a-z0-9])*)*(:[2-9][0-9]{3,})?(/([A-Za-z0-9\-._~!$'()*+,;=]|%[0-9A-F]{2})+)*(\?([A-Za-z0-9\-._~!$'()*+,;=/\?]|%[0-9A-F]{2})*)?(#([A-Za-z0-9\-._~!$'()*+,;=/\?]|%[0-9A-F]{2})*)?"/>
    <xs:pattern value="ftp://[a-z0-9]([a-z0-9]|\-[a-z0-9])*(\.[a-z0-9]([a-z0-9]|\-[a-z0-9])*)*(:[2-9][0-9]{3,})?(/([A-Za-z0-9\-._~!$'()*+,;=]|%[0-9A-F]{2})+)*(\?([A-Za-z0-9\-._~!$'()*+,;=/\?]|%[0-9A-F]{2})*)?(#([A-Za-z0-9\-._~!$'()*+,;=/\?]|%[0-9A-F]{2})*)?"/>
    <xs:pattern value="urn:lsid:[a-z0-9]([a-z0-9]|\-[a-z0-9])*(\.[a-z0-9]([a-z0-9]|\-[a-z0-9])*)*:[A-Za-z0-9\-._~]+:[A-Za-z0-9\-._~]+(:[A-Za-z0-9\-._~]+)?"/>
  </xs:restriction>
</xs:simpleType>

FreeText  simpleType
type restriction of xs:string
used by
elements BiosequenceRecord/customNote GeneralNucleotideSequenceRecord/customNote GeneralAminoacidSequenceRecord/customNote NucleotideSequenceRecord/customNote AminoacidSequenceRecord/customNote FeatureData/customNote BiosequenceAlignment/customNote GeneralNucleotideSequenceAlignment/customNote GeneralAminoacidSequenceAlignment/customNote NucleotideSequenceAlignment/customNote AminoacidSequenceAlignment/customNote Species/note
attribute GeneticCode/codon/@note
facets
Kind Value annotation 
minLength 1 
whiteSpace preserve 
Documentation Any plain text (possibly formatted)
source <xs:simpleType name="FreeText" sawsdl:modelReference="http://purl.org/edam/data/0000969">
  <xs:annotation>
    <xs:documentation>Any plain text (possibly formatted)</xs:documentation>
  </xs:annotation>
  <xs:restriction base="xs:string">
    <xs:minLength value="1"/>
    <xs:whiteSpace value="preserve"/>
  </xs:restriction>
</xs:simpleType>

Name  simpleType
type restriction of xs:string
used by
elements Feature/className BiosequenceRecord/customName GeneralNucleotideSequenceRecord/customName GeneralAminoacidSequenceRecord/customName NucleotideSequenceRecord/customName AminoacidSequenceRecord/customName AlignedBiosequence/customSequenceName AnnotatedSequence/customSequenceName DatabaseReference/databaseVersion EntryReference/entryVersion Feature/equalAlias Score/index SequenceReference/isoformNote Method/name Feature/name Species/name OntologyReference/ontologyVersion FeatureData/association/relationName AnnotatedSequence/blockWithOccurenceReferences/annotation/occurence/association/relationName SequenceReference/sequenceVersion FeatureData/specificFeatureAlias FeatureData/specificFeatureName SequenceReference/supersequenceCustomName OntologyTerm/termName Score/unit Method/version WebserviceReference/webserviceVersion
simpleTypes ChromosomeName DatabaseName OntologyName OutsidePositionCorrespondance QualitativeCertainty RecommendedDatabaseName RecommendedOntologyName RecommendedReliability RecommendedScoreName RecommendedVerdict Reliability ScoreName Strand Verdict
facets
Kind Value annotation 
pattern \S(\S|\s\S)* 
source <xs:simpleType name="Name">
  <xs:restriction base="xs:string">
    <xs:pattern value="\S(\S|\s\S)*"/>
  </xs:restriction>
</xs:simpleType>

ChromosomeName  simpleType
type restriction of Name
used by
elements AnnotatedSequence/chromosome GeneralSequencePosition/chromosome SequencePosition/chromosome GeneralOutsideSequencePosition/chromosome OutsideSequencePosition/chromosome AlignedBiosequence/chromosome
facets
Kind Value annotation 
pattern [A-Z][A-Za-z]* 
pattern [0-9]+[A-Za-z]* 
source <xs:simpleType name="ChromosomeName">
  <xs:restriction base="Name">
    <xs:pattern value="[A-Z][A-Za-z]*"/>
    <xs:pattern value="[0-9]+[A-Za-z]*"/>
  </xs:restriction>
</xs:simpleType>

DatabaseName  simpleType
type union of (Name, RecommendedDatabaseName)
used by
element DatabaseReference/databaseName
Documentation Name of a public or private database (predefined or arbitrary name)
source <xs:simpleType name="DatabaseName" sawsdl:modelReference="http://purl.org/edam/data/0001056">
  <xs:annotation>
    <xs:documentation>Name of a public or private database (predefined or arbitrary name)</xs:documentation>
  </xs:annotation>
  <xs:union memberTypes="Name RecommendedDatabaseName"/>
</xs:simpleType>

OntologyName  simpleType
type union of (Name, RecommendedOntologyName)
used by
element OntologyReference/ontologyName
Documentation Name of a public or private controlled vocabulary/ontology (predefined or arbitrary name)
source <xs:simpleType name="OntologyName" sawsdl:modelReference="http://purl.org/edam/data/0001051">
  <xs:annotation>
    <xs:documentation>Name of a public or private controlled vocabulary/ontology (predefined or arbitrary name)</xs:documentation>
  </xs:annotation>
  <xs:union memberTypes="Name RecommendedOntologyName"/>
</xs:simpleType>

ScoreName  simpleType
type union of (Name, RecommendedScoreName)
used by
element Score/type
source <xs:simpleType name="ScoreName">
  <xs:union memberTypes="Name RecommendedScoreName"/>
</xs:simpleType>

Verdict  simpleType
type union of (Name, RecommendedVerdict)
used by
elements PredictionResult/verdict ExperimentalEvidence/verdict
source <xs:simpleType name="Verdict">
  <xs:union memberTypes="Name RecommendedVerdict"/>
</xs:simpleType>

Reliability  simpleType
type union of (Name, RecommendedReliability)
used by
element ExperimentalEvidence/reliability
source <xs:simpleType name="Reliability">
  <xs:union memberTypes="Name RecommendedReliability"/>
</xs:simpleType>

Phase  simpleType
type restriction of NonnegativeInteger
used by
element TranslationData/phase
facets
Kind Value annotation 
minInclusive 0 
maxInclusive 2 
Documentation Phase of an incomplete peptide-coding nucleotide sequence, in the direction of translation
source <xs:simpleType name="Phase">
  <xs:annotation>
    <xs:documentation>Phase of an incomplete peptide-coding nucleotide sequence, in the direction of translation</xs:documentation>
  </xs:annotation>
  <xs:restriction base="NonnegativeInteger">
    <xs:maxInclusive value="2"/>
  </xs:restriction>
</xs:simpleType>

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 in any letter case, possibly with ambiguous ("degenerate") bases
source <xs:simpleType name="GeneralNucleotideSequence" sawsdl:modelReference="http://purl.org/edam/data/0001210">
  <xs:annotation>
    <xs:documentation>Nucleotide sequence in any letter case, 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 
pattern [ACDEFGHIKLMNPQRSTVWYBJZXUO]+ 
Documentation Amino-acid sequence in capital letters, possibly with ambiguous residues (Asx, Xle, Glx, Xaa/Unk) and additional residues (Pyl and Sec)
source <xs:simpleType name="GeneralAminoacidSequence" sawsdl:modelReference="http://purl.org/edam/data/0001219">
  <xs:annotation>
    <xs:documentation>
Amino-acid sequence in capital letters, 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:pattern value="[ACDEFGHIKLMNPQRSTVWYBJZXUO]+"/>
  </xs:restriction>
</xs:simpleType>

Biosequence  simpleType
type union of (GeneralNucleotideSequence, GeneralAminoacidSequence)
used by
elements FeatureOccurence/variation/original BiosequenceRecord/sequence SequenceReference/supersequence FeatureOccurence/variation/variant
Documentation Nucleotide or amino-acid sequence in any letter case, possibly with ambiguous bases and residues
source <xs:simpleType name="Biosequence">
  <xs:annotation>
    <xs:documentation>
Nucleotide or amino-acid sequence in any letter case, 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 in any letter case, without ambiguous ("degenerate") bases
source <xs:simpleType name="NucleotideSequence" sawsdl:modelReference="http://purl.org/edam/data/0001211">
  <xs:annotation>
    <xs:documentation>Nucleotide sequence in any letter case, 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 
pattern [ACDEFGHIKLMNPQRSTVWY]+ 
Documentation Amino-acid sequence in capital letters, without ambiguous and additional residues (Pyl, Sec)
source <xs:simpleType name="AminoacidSequence" sawsdl:modelReference="http://purl.org/edam/data/0001218">
  <xs:annotation>
    <xs:documentation>Amino-acid sequence in capital letters, without ambiguous and additional residues (Pyl, Sec)</xs:documentation>
  </xs:annotation>
  <xs:restriction base="GeneralAminoacidSequence">
    <xs:pattern value="[ACDEFGHIKLMNPQRSTVWY]+"/>
  </xs:restriction>
</xs:simpleType>

BiosequenceRecord  complexType
diagram BioXSD-1.0_p75.png
children sequence species customName customNote formalReference translationData
used by
elements AnnotatedSequence/sequenceRecord AlignedBiosequence/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://purl.org/edam/data/0000849">
  <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:element name="customName" type="Name" minOccurs="0"/>
    <xs:element name="customNote" type="FreeText" minOccurs="0"/>
    <xs:element name="formalReference" type="SequenceReference" minOccurs="0">
      <xs:annotation>
        <xs:documentation>Reference to where the sequence originates from: a database entry or an explicit super-sequence</xs:documentation>
      </xs:annotation>
    </xs:element>
    <xs:element name="translationData" type="TranslationData" minOccurs="0"/>
  </xs:sequence>
</xs:complexType>
Model Referencehttp://purl.org/edam/data/0000849

GeneralNucleotideSequenceRecord  complexType
diagram BioXSD-1.0_p155.png
type restriction of BiosequenceRecord
properties
base BiosequenceRecord
children sequence species customName customNote formalReference translationData
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://purl.org/edam/data/0000849">
  <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:element name="customName" type="Name" minOccurs="0"/>
        <xs:element name="customNote" type="FreeText" minOccurs="0"/>
        <xs:element name="formalReference" type="SequenceReference" minOccurs="0">
          <xs:annotation>
            <xs:documentation>Reference to where the sequence originates from: a database entry or an explicit super-sequence</xs:documentation>
          </xs:annotation>
        </xs:element>
        <xs:element name="translationData" type="TranslationData" minOccurs="0"/>
      </xs:sequence>
    </xs:restriction>
  </xs:complexContent>
</xs:complexType>
Model Referencehttp://purl.org/edam/data/0000849

GeneralAminoacidSequenceRecord  complexType
diagram BioXSD-1.0_p144.png
type restriction of BiosequenceRecord
properties
base BiosequenceRecord
children sequence species customName customNote formalReference 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://purl.org/edam/data/0000849">
  <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:element name="customName" type="Name" minOccurs="0"/>
        <xs:element name="customNote" type="FreeText" minOccurs="0"/>
        <xs:element name="formalReference" type="SequenceReference" minOccurs="0">
          <xs:annotation>
            <xs:documentation>Reference to where the sequence originates from: a database entry or an explicit super-sequence</xs:documentation>
          </xs:annotation>
        </xs:element>
        <xs:element name="translationData" type="AminoacidTranslationData" minOccurs="0"/>
      </xs:sequence>
    </xs:restriction>
  </xs:complexContent>
</xs:complexType>
Model Referencehttp://purl.org/edam/data/0000849

NucleotideSequenceRecord  complexType
diagram BioXSD-1.0_p201.png
type restriction of GeneralNucleotideSequenceRecord
properties
base GeneralNucleotideSequenceRecord
children sequence species customName customNote formalReference translationData
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://purl.org/edam/data/0000849">
  <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:element name="customName" type="Name" minOccurs="0"/>
        <xs:element name="customNote" type="FreeText" minOccurs="0"/>
        <xs:element name="formalReference" type="SequenceReference" minOccurs="0">
          <xs:annotation>
            <xs:documentation>Reference to where the sequence originates from: a database entry or an explicit super-sequence</xs:documentation>
          </xs:annotation>
        </xs:element>
        <xs:element name="translationData" type="TranslationData" minOccurs="0"/>
      </xs:sequence>
    </xs:restriction>
  </xs:complexContent>
</xs:complexType>
Model Referencehttp://purl.org/edam/data/0000849

AminoacidSequenceRecord  complexType
diagram BioXSD-1.0_p43.png
type restriction of GeneralAminoacidSequenceRecord
properties
base GeneralAminoacidSequenceRecord
children sequence species customName customNote formalReference 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://purl.org/edam/data/0000849">
  <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:element name="customName" type="Name" minOccurs="0"/>
        <xs:element name="customNote" type="FreeText" minOccurs="0"/>
        <xs:element name="formalReference" type="SequenceReference" minOccurs="0">
          <xs:annotation>
            <xs:documentation>Reference to where the sequence originates from: a database entry or an explicit super-sequence</xs:documentation>
          </xs:annotation>
        </xs:element>
        <xs:element name="translationData" type="AminoacidTranslationData" minOccurs="0"/>
      </xs:sequence>
    </xs:restriction>
  </xs:complexContent>
</xs:complexType>
Model Referencehttp://purl.org/edam/data/0000849

GeneticCode  complexType
diagram BioXSD-1.0_p183.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://purl.org/edam/data/0001598">
  <xs:annotation>
    <xs:documentation>Particular genetic code (codon encoding)</xs:documentation>
  </xs:annotation>
  <xs:sequence>
    <xs:element name="reference" type="EntryReference" minOccurs="0"/>
    <xs:element name="codon" minOccurs="0" maxOccurs="unbounded">
      <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">
          <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="note" type="FreeText"/>
      </xs:complexType>
    </xs:element>
  </xs:sequence>
</xs:complexType>
Model Referencehttp://purl.org/edam/data/0001598

TranslationData  complexType
diagram BioXSD-1.0_p262.png
children geneticCode phase reversedTranslationDirection
used by
elements BiosequenceRecord/translationData GeneralNucleotideSequenceRecord/translationData NucleotideSequenceRecord/translationData FeatureOccurence/translationData
complexType AminoacidTranslationData
source <xs:complexType name="TranslationData">
  <xs:sequence>
    <xs:element name="geneticCode" type="GeneticCode" minOccurs="0"/>
    <xs:element name="phase" type="Phase" minOccurs="0"/>
    <xs:element name="reversedTranslationDirection" type="Empty" minOccurs="0"/>
  </xs:sequence>
</xs:complexType>

AminoacidTranslationData  complexType
diagram BioXSD-1.0_p50.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-1.0_p82.png
children databaseName databaseUri databaseVersion webserviceReference
used by
complexType EntryReference
Documentation Reference to a database
source <xs:complexType name="DatabaseReference">
  <xs:annotation>
    <xs:documentation>Reference to a database</xs:documentation>
  </xs:annotation>
  <xs:sequence>
    <xs:element name="databaseName" type="DatabaseName" minOccurs="0"/>
    <xs:element name="databaseUri" type="Uri" minOccurs="0">
      <xs:annotation>
        <xs:documentation>General URI of the database</xs:documentation>
      </xs:annotation>
    </xs:element>
    <xs:element name="databaseVersion" type="Name" minOccurs="0" sawsdl:modelReference="http://purl.org/edam/data/0001670"/>
    <xs:element name="webserviceReference" type="WebserviceReference" minOccurs="0"/>
  </xs:sequence>
</xs:complexType>

EntryReference  complexType
diagram BioXSD-1.0_p88.png
type extension of DatabaseReference
properties
base DatabaseReference
children databaseName databaseUri databaseVersion webserviceReference accession entryUri entryVersion date
used by
elements FeatureData/association/associatedDatabaseEntry Method/citation ExperimentalEvidence/citation FeatureData/databaseEntry ExperimentalEvidence/dataReference AnnotatedSequence/genomeBuild AlignedBiosequence/genomeBuild GeneticCode/reference
complexTypes SequenceReference Species
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:sequence>
        <xs:element name="accession" type="Accession" minOccurs="0"/>
        <xs:element name="entryUri" type="Uri" minOccurs="0" sawsdl:modelReference="http://purl.org/edam/data/0001054"/>
        <xs:element name="entryVersion" type="Name" minOccurs="0"/>
        <xs:element name="date" type="xs:date" minOccurs="0">
          <xs:annotation>
            <xs:documentation>Date when this reference was fully valid: created or last time updated</xs:documentation>
          </xs:annotation>
        </xs:element>
      </xs:sequence>
    </xs:extension>
  </xs:complexContent>
</xs:complexType>

OntologyReference  complexType
diagram BioXSD-1.0_p208.png
children ontologyName ontologyUri ontologyVersion
used by
complexType OntologyTerm
Documentation Reference to a controlled vocabulary (ontology)
source <xs:complexType name="OntologyReference">
  <xs:annotation>
    <xs:documentation>Reference to a controlled vocabulary (ontology)</xs:documentation>
  </xs:annotation>
  <xs:sequence>
    <xs:element name="ontologyName" type="OntologyName" minOccurs="0"/>
    <xs:element name="ontologyUri" type="Uri" minOccurs="0">
      <xs:annotation>
        <xs:documentation>General URI of the controlled vocabulary (ontology)</xs:documentation>
      </xs:annotation>
    </xs:element>
    <xs:element name="ontologyVersion" type="Name" minOccurs="0"/>
  </xs:sequence>
</xs:complexType>

OntologyTerm  complexType
diagram BioXSD-1.0_p212.png
type extension of OntologyReference
properties
base OntologyReference
children ontologyName ontologyUri ontologyVersion accession termUri termName
used by
elements FeatureData/association/associatedTerm Method/categoryTerm Feature/classTerm Feature/equalTerm FeatureData/association/relationTerm AnnotatedSequence/blockWithOccurenceReferences/annotation/occurence/association/relationTerm FeatureData/specificFeatureTerm Score/typeTerm
Documentation Reference to a term from a controlled vocabulary (ontology)
source <xs:complexType name="OntologyTerm">
  <xs:annotation>
    <xs:documentation>Reference to a term from a controlled vocabulary (ontology)</xs:documentation>
  </xs:annotation>
  <xs:complexContent>
    <xs:extension base="OntologyReference">
      <xs:sequence>
        <xs:element name="accession" type="Accession" minOccurs="0" sawsdl:modelReference="http://purl.org/edam/data/0001087"/>
        <xs:element name="termUri" type="Uri" minOccurs="0" sawsdl:modelReference="http://purl.org/edam/data/0001087"/>
        <xs:element name="termName" type="Name" minOccurs="0">
          <xs:annotation>
            <xs:documentation>
Human-readable name of the term. NB. Does not have to be always up to date and canonical.
(Use also termUri or accession: up-to-date name and other properties of the term should be downloadable given the termUri or accession)</xs:documentation>
          </xs:annotation>
        </xs:element>
      </xs:sequence>
    </xs:extension>
  </xs:complexContent>
</xs:complexType>

Species  complexType
diagram BioXSD-1.0_p259.png
type extension of EntryReference
properties
base EntryReference
children databaseName databaseUri databaseVersion webserviceReference accession entryUri entryVersion date name note
used by
elements BiosequenceRecord/species GeneralNucleotideSequenceRecord/species GeneralAminoacidSequenceRecord/species NucleotideSequenceRecord/species AminoacidSequenceRecord/species AnnotatedSequence/species AlignedBiosequence/species
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:sequence>
        <xs:element name="name" type="Name" minOccurs="0" sawsdl:modelReference="http://purl.org/edam/data/0001045">
          <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>
        </xs:element>
        <xs:element name="note" type="FreeText" minOccurs="0"/>
      </xs:sequence>
    </xs:extension>
  </xs:complexContent>
</xs:complexType>

SequenceReference  complexType
diagram BioXSD-1.0_p249.png
type extension of EntryReference
properties
base EntryReference
children databaseName databaseUri databaseVersion webserviceReference accession entryUri entryVersion date sequenceVersion isoformAccession isoformNote subsequencePosition supersequence supersequenceCustomName
used by
elements BiosequenceRecord/formalReference GeneralNucleotideSequenceRecord/formalReference GeneralAminoacidSequenceRecord/formalReference NucleotideSequenceRecord/formalReference AminoacidSequenceRecord/formalReference AnnotatedSequence/sequenceReference AlignedBiosequence/sequenceReference
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="sequenceVersion" type="Name" minOccurs="0" sawsdl:modelReference="http://purl.org/edam/data/0001771"/>
        <xs:element name="isoformAccession" type="Accession" minOccurs="0"/>
        <xs:element name="isoformNote" type="Name" minOccurs="0"/>
        <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="supersequenceCustomName" type="Name" minOccurs="0">
          <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:extension>
  </xs:complexContent>
</xs:complexType>

Method  complexType
diagram BioXSD-1.0_p186.png
children name uri version date categoryTerm citation webserviceReference
used by
elements AnnotatedSequence/method MethodResult/method PredictionResult/method
attributes
Name  Type  Use  Default  Fixed  annotation
localIdLocalReference      
source <xs:complexType name="Method">
  <xs:sequence>
    <xs:element name="name" type="Name"/>
    <xs:element name="uri" type="Uri" minOccurs="0" sawsdl:modelReference="http://purl.org/edam/data/0000977"/>
    <xs:element name="version" type="Name" minOccurs="0" sawsdl:modelReference="http://purl.org/edam/data/0001671"/>
    <xs:element name="date" type="xs:date" minOccurs="0"/>
    <xs:element name="categoryTerm" type="OntologyTerm" minOccurs="0" maxOccurs="unbounded"/>
    <xs:element name="citation" type="EntryReference" minOccurs="0" maxOccurs="unbounded" sawsdl:modelReference="http://purl.org/edam/data/0000970"/>
    <xs:element name="webserviceReference" type="WebserviceReference" minOccurs="0"/>
  </xs:sequence>
  <xs:attribute name="localId" type="LocalReference"/>
</xs:complexType>

WebserviceReference  complexType
diagram BioXSD-1.0_p266.png
children wsdl wsdlService wsdlPort operation webserviceVersion date
used by
elements DatabaseReference/webserviceReference Method/webserviceReference
Documentation A reference to a SOAP Web service
source <xs:complexType name="WebserviceReference">
  <xs:annotation>
    <xs:documentation>A reference to a SOAP Web service</xs:documentation>
  </xs:annotation>
  <xs:sequence>
    <xs:element name="wsdl" type="Uri"/>
    <xs:element name="wsdlService" type="xs:NMTOKEN" minOccurs="0"/>
    <xs:element name="wsdlPort" type="xs:NMTOKEN" minOccurs="0"/>
    <xs:element name="operation" type="xs:NMTOKEN" minOccurs="0"/>
    <xs:element name="webserviceVersion" type="Name" minOccurs="0"/>
    <xs:element name="date" type="xs:date" minOccurs="0">
      <xs:annotation>
        <xs:documentation>Date when this Web-service reference was fully valid: created or last time updated</xs:documentation>
      </xs:annotation>
    </xs:element>
  </xs:sequence>
</xs:complexType>

LocalReference  simpleType
type restriction of xs:string
used by
elements AnnotatedSequence/blockWithOccurenceReferences/annotation/occurence/association/associatedFeatureOccurence Result/methodId PredictionResult/methodId
attributes Method/@localId AnnotatedSequence/blockWithOccurenceReferences/annotation/occurence/@localId
facets
Kind Value annotation 
pattern [A-Za-z0-9\-._~]+ 
Documentation Identifier for local references within a data record
source <xs:simpleType name="LocalReference">
  <xs:annotation>
    <xs:documentation>Identifier for local references within a data record</xs:documentation>
  </xs:annotation>
  <xs:restriction base="xs:string">
    <xs:pattern value="[A-Za-z0-9\-._~]+"/>
  </xs:restriction>
</xs:simpleType>

Accession  simpleType
type restriction of xs:string
used by
elements EntryReference/accession OntologyTerm/accession SequenceReference/isoformAccession
simpleTypes EmblAccession ExtendedGenbankAccession ExtendedUniprotAccession NcbiGeneticCodeId NcbiTaxonomyId OboTermId PubmedId
facets
Kind Value annotation 
pattern [A-Za-z0-9\-._~]+ 
Documentation Generalisation of bioinformatic accession numbers (stable primary keys/identifiers)
source <xs:simpleType name="Accession" sawsdl:modelReference="http://purl.org/edam/data/0000976">
  <xs:annotation>
    <xs:documentation>Generalisation of bioinformatic accession numbers (stable primary keys/identifiers)</xs:documentation>
  </xs:annotation>
  <xs:restriction base="xs:string">
    <xs:pattern value="[A-Za-z0-9\-._~]+"/>
  </xs:restriction>
</xs:simpleType>

EmblAccession  simpleType
type Accession
facets
Kind Value annotation 
pattern [A-Za-z0-9\-._~]+ 
source <xs:simpleType name="EmblAccession" sawsdl:modelReference="http://purl.org/edam/data/0001107">
  <xs:restriction base="Accession"/>
</xs:simpleType>

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

UniprotAccession  simpleType
type restriction of ExtendedUniprotAccession
facets
Kind Value annotation 
pattern [A-NR-Z][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] 
Documentation UniProt accession number, without the sequence version and splice-variant suffix
source <xs:simpleType name="UniprotAccession" sawsdl:modelReference="http://purl.org/edam/data/0001099">
  <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="[A-NR-Z][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]"/>
  </xs:restriction>
</xs:simpleType>

ExtendedGenbankAccession  simpleType
type restriction of Accession
used by
simpleType GenbankAccession
facets
Kind Value annotation 
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 
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 
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://purl.org/edam/data/0001108">
  <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 
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 
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 
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 
pattern [0-9]{1,9} 
source <xs:simpleType name="PubmedId">
  <xs:restriction base="Accession">
    <xs:pattern value="[0-9]{1,9}"/>
  </xs:restriction>
</xs:simpleType>

NcbiTaxonomyId  simpleType
type restriction of Accession
facets
Kind Value annotation 
pattern [0-9]{1,9} 
Documentation NCBI Taxonomy ID (0 ... 999999999; i.e. a subset of 32-bit (4B) signed int)
source <xs:simpleType name="NcbiTaxonomyId" sawsdl:modelReference="http://purl.org/edam/data/0001179">
  <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="[0-9]{1,9}"/>
  </xs:restriction>
</xs:simpleType>

NcbiGeneticCodeId  simpleType
type restriction of Accession
facets
Kind Value annotation 
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>

OboTermId  simpleType
type restriction of Accession
facets
Kind Value annotation 
pattern [0-9]{6,7} 
Documentation Term ID in an OBO-Foundry ontology
source <xs:simpleType name="OboTermId" sawsdl:modelReference="http://purl.org/edam/data/0001087">
  <xs:annotation>
    <xs:documentation>Term ID in an OBO-Foundry ontology</xs:documentation>
  </xs:annotation>
  <xs:restriction base="Accession">
    <xs:pattern value="[0-9]{6,7}"/>
  </xs:restriction>
</xs:simpleType>

Feature  complexType
diagram BioXSD-1.0_p101.png
children name equalTerm equalAlias className classTerm properties
used by
elements FeatureData/association/associatedFeature AnnotatedSequence/annotation/feature AnnotatedSequence/blockWithOccurenceReferences/annotation/feature
source <xs:complexType name="Feature">
  <xs:sequence>
    <xs:element name="name" type="Name">
      <xs:annotation>
        <xs:documentation>Human-readable display name of the feature</xs:documentation>
      </xs:annotation>
    </xs:element>
    <xs:element name="equalTerm" type="OntologyTerm" minOccurs="0" maxOccurs="unbounded"/>
    <xs:element name="equalAlias" type="Name" minOccurs="0" maxOccurs="unbounded">
      <xs:annotation>
        <xs:documentation>Alternative human-readable display name of the feature</xs:documentation>
      </xs:annotation>
    </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="classTerm" type="OntologyTerm" minOccurs="0" maxOccurs="unbounded"/>
    <xs:element name="properties" type="FeatureData" minOccurs="0"/>
  </xs:sequence>
</xs:complexType>

FeatureData  complexType
diagram BioXSD-1.0_p108.png
children databaseEntry specificFeatureName specificFeatureTerm specificFeatureAlias customNote association
used by
elements Feature/properties FeatureOccurence/properties
Documentation Specific properties of a feature
source <xs:complexType name="FeatureData">
  <xs:annotation>
    <xs:documentation>Specific properties of a feature</xs:documentation>
  </xs:annotation>
  <xs:sequence>
    <xs:element name="databaseEntry" type="EntryReference" minOccurs="0" maxOccurs="unbounded"/>
    <xs:element name="specificFeatureName" type="Name" minOccurs="0"/>
    <xs:element name="specificFeatureTerm" type="OntologyTerm" minOccurs="0" maxOccurs="unbounded"/>
    <xs:element name="specificFeatureAlias" type="Name" minOccurs="0" maxOccurs="unbounded"/>
    <xs:element name="customNote" type="FreeText" minOccurs="0"/>
    <xs:element name="association" minOccurs="0" maxOccurs="unbounded">
      <xs:complexType>
        <xs:sequence>
          <xs:element name="relationName" type="Name" minOccurs="0"/>
          <xs:element name="relationTerm" type="OntologyTerm" minOccurs="0" maxOccurs="unbounded"/>
          <xs:choice>
            <xs:element name="associatedFeature" type="Feature" maxOccurs="unbounded"/>
            <xs:element name="associatedTerm" type="OntologyTerm" maxOccurs="unbounded"/>
            <xs:element name="associatedDatabaseEntry" type="EntryReference" maxOccurs="unbounded"/>
          </xs:choice>
        </xs:sequence>
      </xs:complexType>
    </xs:element>
  </xs:sequence>
</xs:complexType>

FeatureOccurence  complexType
diagram BioXSD-1.0_p120.png
children appliesToWholeSequence position evidence properties frame translationData variation alignment
used by
elements AnnotatedSequence/annotation/occurence AnnotatedSequence/blockWithOccurenceReferences/annotation/occurence
Documentation Occurence of a feature in a reference sequence. Positioned or non-positioned (applied to the whole sequence)
source <xs:complexType name="FeatureOccurence">
  <xs:annotation>
    <xs:documentation>Occurence of a feature in a reference sequence. Positioned or non-positioned (applied to the whole sequence)</xs:documentation>
  </xs:annotation>
  <xs:sequence>
    <xs:choice>
      <xs:element name="appliesToWholeSequence" type="Empty"/>
      <xs:element name="position" type="GeneralSequencePosition"/>
    </xs:choice>
    <xs:element name="evidence" type="Evidence" minOccurs="0" maxOccurs="unbounded"/>
    <xs:element name="properties" type="FeatureData" minOccurs="0"/>
    <xs:element name="frame" minOccurs="0">
      <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="translationData" type="TranslationData" minOccurs="0"/>
    <xs:element name="variation" minOccurs="0" maxOccurs="unbounded">
      <xs:complexType>
        <xs:sequence>
          <xs:element name="original" type="Biosequence" minOccurs="0" maxOccurs="unbounded"/>
          <xs:choice maxOccurs="unbounded">
            <xs:element name="variant" type="Biosequence"/>
            <xs:element name="missing" type="Empty"/>
          </xs:choice>
          <xs:element name="position" type="SequencePosition" minOccurs="0">
            <xs:annotation>
              <xs:documentation>NB. Corresponds to a position in the reference sequence (not to a position within the feature occurence)</xs:documentation>
            </xs:annotation>
          </xs:element>
        </xs:sequence>
      </xs:complexType>
    </xs:element>
    <xs:element name="alignment" minOccurs="0" sawsdl:modelReference="http://purl.org/edam/data/0001381">
      <xs:complexType>
        <xs:sequence>
          <xs:element name="alignmentOfReference" minOccurs="0">
            <xs:complexType>
              <xs:sequence>
                <xs:element name="gap" type="Gap" minOccurs="0" maxOccurs="unbounded"/>
                <xs:element name="frameshift" type="Frameshift" minOccurs="0" maxOccurs="unbounded"/>
                <xs:element name="sequenceScore" type="Result" minOccurs="0" maxOccurs="unbounded"/>
              </xs:sequence>
            </xs:complexType>
            <xs:unique name="uniqueGapStart_ar">
              <xs:selector xpath="gap"/>
              <xs:field xpath="@start"/>
            </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="uniqueGapStart_as">
              <xs:selector xpath="gap"/>
              <xs:field xpath="@start"/>
            </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>

AnnotatedSequence  complexType
diagram BioXSD-1.0_p52.png
children sequenceRecord sequenceReference customSequenceName chromosome species genomeBuild method annotation blockWithOccurenceReferences
Documentation Sequence annotated with sequence features
source <xs:complexType name="AnnotatedSequence" sawsdl:modelReference="http://purl.org/edam/data/0001255">
  <xs:annotation>
    <xs:documentation>Sequence annotated with sequence features</xs:documentation>
  </xs:annotation>
  <xs:sequence>
    <!--= Reference sequence =-->
    <xs:choice>
      <xs:element name="sequenceRecord" type="BiosequenceRecord"/>
      <xs:element name="sequenceReference" type="SequenceReference"/>
      <xs:element name="customSequenceName" type="Name"/>
      <xs:sequence>
        <xs:element name="chromosome" type="ChromosomeName" minOccurs="0"/>
        <xs:element name="species" type="Species"/>
        <xs:element name="genomeBuild" type="EntryReference" minOccurs="0"/>
      </xs:sequence>
    </xs:choice>
    <xs:element name="method" type="Method" minOccurs="0" maxOccurs="unbounded" sawsdl:modelReference="http://purl.org/edam/data/0000856"/>
    <xs:choice maxOccurs="unbounded">
      <!--= Annotation by a feature =-->
      <xs:element name="annotation">
        <xs:complexType>
          <xs:sequence>
            <!--= Feature type =-->
            <xs:element name="feature" type="Feature"/>
            <!--= Feature occurence(s) (instance(s)) =-->
            <xs:element name="occurence" type="FeatureOccurence" minOccurs="0" maxOccurs="unbounded"/>
          </xs:sequence>
        </xs:complexType>
      </xs:element>
      <!--= Annotation by a block of inter-related features =-->
      <xs:element name="blockWithOccurenceReferences">
        <xs:complexType>
          <xs:sequence>
            <!--= Annotation by a feature (in a block) =-->
            <xs:element name="annotation" maxOccurs="unbounded">
              <xs:complexType>
                <xs:sequence>
                  <!--= Feature type (in a block) =-->
                  <xs:element name="feature" type="Feature"/>
                  <!--= Feature occurence(s) (instance(s)) (in a block) =-->
                  <xs:element name="occurence" minOccurs="0" maxOccurs="unbounded">
                    <xs:complexType>
                      <xs:complexContent>
                        <xs:extension base="FeatureOccurence">
                          <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="relationTerm" type="OntologyTerm" minOccurs="0" maxOccurs="unbounded"/>
                                  <xs:element name="associatedFeatureOccurence" type="LocalReference" minOccurs="0" maxOccurs="unbounded"/>
                                </xs:sequence>
                              </xs:complexType>
                            </xs:element>
                          </xs:sequence>
                          <xs:attribute name="localId" type="LocalReference"/>
                        </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/occurence"/>
          <xs:field xpath="@localId"/>
        </xs:unique>
      </xs:element>
    </xs:choice>
  </xs:sequence>
</xs:complexType>
Model Referencehttp://purl.org/edam/data/0001255

Evidence  complexType
diagram BioXSD-1.0_p93.png
children predicted experimental
used by
element FeatureOccurence/evidence
source <xs:complexType name="Evidence">
  <xs:choice>
    <xs:element name="predicted" type="PredictionResult"/>
    <xs:element name="experimental" type="ExperimentalEvidence"/>
  </xs:choice>
</xs:complexType>

MethodResult  complexType
diagram BioXSD-1.0_p194.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" type="Method"/>
    <xs:element name="score" type="Score" minOccurs="0" maxOccurs="unbounded"/>
  </xs:sequence>
</xs:complexType>

Result  complexType
diagram BioXSD-1.0_p231.png
children methodId score
used by
elements FeatureOccurence/alignment/alignmentOfReference/sequenceScore AlignedBiosequence/sequenceScore AlignedGeneralNucleotideSequence/sequenceScore AlignedGeneralAminoacidSequence/sequenceScore AlignedNucleotideSequence/sequenceScore AlignedAminoacidSequence/sequenceScore
source <xs:complexType name="Result">
  <xs:sequence>
    <xs:element name="methodId" type="LocalReference"/>
    <xs:element name="score" type="Score" minOccurs="0" maxOccurs="unbounded"/>
  </xs:sequence>
</xs:complexType>

PredictionResult  complexType
diagram BioXSD-1.0_p226.png
children method methodId 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://purl.org/edam/data/0000856"/>
      <xs:element name="methodId" type="LocalReference" sawsdl:modelReference="http://purl.org/edam/data/0000856"/>
    </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-1.0_p96.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://purl.org/edam/data/0000856"/>
    <xs:element name="citation" type="EntryReference" minOccurs="0" maxOccurs="unbounded" sawsdl:modelReference="http://purl.org/edam/data/0000970"/>
    <xs:element name="verdict" type="Verdict" minOccurs="0"/>
    <xs:element name="reliability" type="Reliability" minOccurs="0"/>
  </xs:sequence>
</xs:complexType>

Score  complexType
diagram BioXSD-1.0_p234.png
children type typeTerm index value unit position
used by
elements MethodResult/score Result/score PredictionResult/score
Documentation Score of a prediction
source <xs:complexType name="Score" sawsdl:modelReference="http://purl.org/edam/data/0001772">
  <xs:annotation>
    <xs:documentation>Score of a prediction</xs:documentation>
  </xs:annotation>
  <xs:sequence>
    <xs:element name="type" type="ScoreName"/>
    <xs:element name="typeTerm" type="OntologyTerm" minOccurs="0"/>
    <xs:element name="index" type="Name" minOccurs="0"/>
    <xs:element name="value" type="AnyDecimal"/>
    <xs:element name="unit" type="Name" minOccurs="0"/>
    <xs:element name="position" type="SequencePosition" minOccurs="0">
      <xs:annotation>
        <xs:documentation>NB. Corresponds to a position in the reference sequence (not to a position within the feature occurence)</xs:documentation>
      </xs:annotation>
    </xs:element>
  </xs:sequence>
</xs:complexType>
Model Referencehttp://purl.org/edam/data/0001772

GeneralSequencePoint  complexType
diagram BioXSD-1.0_p173.png
type extension of PositiveInteger
properties
base PositiveInteger
used by