BioXSD-1.1

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

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"/>
    
    <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 reference

http://edamontology.org/data_2043
http://edamontology.org/format_2352

GeneralNucleotideSequenceRecord complexType

diagram

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 reference

http://edamontology.org/data_2046
http://edamontology.org/format_2352

GeneralAminoacidSequenceRecord complexType

diagram

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 reference

http://edamontology.org/data_2047
http://edamontology.org/format_2352

NucleotideSequenceRecord complexType

diagram

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 reference

http://edamontology.org/data_2046
http://edamontology.org/format_2352

AminoacidSequenceRecord complexType

diagram

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 reference

http://edamontology.org/data_2047
http://edamontology.org/format_2352

BiosequenceAlignment complexType

diagram

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 reference

http://edamontology.org/data_0863
http://edamontology.org/format_2352

GeneralNucleotideSequenceAlignment complexType

diagram

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 reference

http://edamontology.org/data_1383

GeneralAminoacidSequenceAlignment complexType

diagram

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 reference

http://edamontology.org/data_1384

NucleotideSequenceAlignment complexType

diagram

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

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>

AlignedBiosequence/gap AlignedGeneralNucleotideSequence/gap AlignedGeneralAminoacidSequence/gap AlignedNucleotideSequence/gap AlignedAminoacidSequence/gap FeatureOccurrenceData/alignment/alignmentOfReference/gap

attributes

Name	Type	Use	Default	Fixed	annotation
pos	InsertionInteger	required
len	PositiveInteger	required

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

type

restriction of SequenceSegment

properties

base	SequenceSegment

used by

elements

AlignedBiosequence/insert AlignedGeneralNucleotideSequence/insert AlignedGeneralAminoacidSequence/insert AlignedNucleotideSequence/insert AlignedAminoacidSequence/insert FeatureOccurrenceData/alignment/alignmentOfReference/insert

NB. Keep 'min' < 'max', use 'strand' if necessary

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

used by

elements

AlignedBiosequence/frameshift AlignedGeneralAminoacidSequence/frameshift AlignedAminoacidSequence/frameshift FeatureOccurrenceData/alignment/alignmentOfReference/frameshift

attributes

Name	Type	Use	Default	Fixed	annotation
pos	InsertionInteger	required
bases	derived by: NonzeroInteger	required

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

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

AlignedGeneralNucleotideSequence complexType

diagram

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

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

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

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

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>
          
        </xs:element>
        <xs:element name="equalConcept" type="SemanticConcept" minOccurs="0" maxOccurs="unbounded" sawsdl:modelReference="http://edamontology.org/data_1015"/>
        
      </xs:sequence>
      <xs:element name="equalConcept" type="SemanticConcept" maxOccurs="unbounded" sawsdl:modelReference="http://edamontology.org/data_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>
      
    </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>


</xs:complexType>

model reference

http://edamontology.org/data_1015
http://edamontology.org/format_2352

FeatureTypeDetails complexType

diagram

children

specificFeatureName specificFeatureConcept specificFeatureAlias databaseEntry note association

used by

elements

FeatureOccurrenceData/featureTypeDetails FeatureType/properties

documentation

Specific properties of a feature

source

model reference

http://edamontology.org/data_1021
http://edamontology.org/format_2352

FeatureOccurrenceData complexType

diagram

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

model reference

http://edamontology.org/data_1021
http://edamontology.org/format_2352

FeatureRecord complexType

diagram
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 reference	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

Evidence complexType

diagram

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 reference

http://edamontology.org/data_2042
http://edamontology.org/format_2352

MethodResult complexType

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>

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

children

method methodIdRef score verdict

<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

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

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
name	ScoreName
index	Name
unit	Name
note	Text

documentation

Type of score of an experiment or computation

source

model reference

http://edamontology.org/data_1772
http://edamontology.org/format_2352

Score complexType

diagram

type

extension of ScoreType

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
name	ScoreName
index	Name
unit	Name
note	Text
value	ScoreValue	required
scoreTypeIdRef	LocalId

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 reference

http://edamontology.org/data_1772
http://edamontology.org/format_2352

GeneralSequencePoint complexType

diagram

used by

element	GeneralSequencePosition/point
complexType	SequencePoint

NB. Omit 'pos' attribute only if 'certainty'="Unknown"

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 reference

http://edamontology.org/data_1016
http://edamontology.org/format_2352

SequencePoint complexType

diagram

type

restriction of GeneralSequencePoint

properties

base	GeneralSequencePoint

used by

element

SequencePosition/point

attributes

Name	Type	Use	Default	Fixed	annotation
pos	PositiveInteger	required
strand	Strand
certainty	Certainty	prohibited

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

used by

element	GeneralSequencePosition/insertion
complexType	SequenceInsertionPoint

NB. Omit 'pos' attribute only if 'certainty'="Unknown"

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 reference

http://edamontology.org/data_1016

SequenceInsertionPoint complexType

diagram

type

restriction of GeneralSequenceInsertionPoint

properties

base	GeneralSequenceInsertionPoint

used by

element

SequencePosition/insertion

attributes

Name	Type	Use	Default	Fixed	annotation
pos	InsertionInteger	required
strand	Strand
certainty	Certainty	prohibited

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

used by

elements	GeneralOutsideSequencePosition/insertion GeneralOutsideSequencePosition/point
complexType	OutsideSequencePoint

NB. Omit 'pos' attribute only if 'certainty'="Unknown"

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 reference

http://edamontology.org/data_1016

OutsideSequencePoint complexType

diagram

type

restriction of GeneralOutsideSequencePoint

properties

base	GeneralOutsideSequencePoint

used by

elements

OutsideSequencePosition/insertion OutsideSequencePosition/point

attributes

Name	Type	Use	Default	Fixed	annotation
pos	NonzeroInteger	required
strand	Strand
certainty	Certainty	prohibited

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

used by

element	GeneralSequencePosition/segment
complexType	SequenceSegment

NB. Keep 'min' < 'max', use 'strand' if necessary. Omit 'min' attribute only if 'minCertainty'="Unknown"

max

PositiveInteger

documentation

NB. Keep 'max' > 'min', use 'strand' if necessary. Omit 'max' attribute only if 'maxCertainty'="Unknown"

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' < '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"/>

</xs:complexType>

model reference

http://edamontology.org/data_1017

SequenceSegment complexType

diagram

type

restriction of GeneralSequenceSegment

properties

base	GeneralSequenceSegment

used by

element	SequencePosition/segment
complexType	Insert

NB. Keep 'min' < 'max', use 'strand' if necessary

NB. Keep 'max' > 'min', use 'strand' if necessary

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' < '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

used by

element	GeneralOutsideSequencePosition/segment
complexType	OutsideSequenceSegment

NB. Keep 'min' < 'max', use 'strand' if necessary. Omit 'min' attribute only if 'minCertainty'="Unknown"

max

NonzeroInteger

documentation

NB. Keep 'max' > 'min', use 'strand' if necessary. Omit 'max' attribute only if 'maxCertainty'="Unknown"

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' < '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 reference

http://edamontology.org/data_1017

OutsideSequenceSegment complexType

diagram

type

restriction of GeneralOutsideSequenceSegment

properties

base	GeneralOutsideSequenceSegment

used by

element

OutsideSequencePosition/segment

NB. Keep 'min' < 'max', use 'strand' if necessary

NB. Keep 'max' > 'min', use 'strand' if necessary

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' < '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

used by

element	GeneralSequencePosition/nextPartition
complexType	SequencePartition

NB. Omit 'max' attribute only if 'certainty'="Unknown"

<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

type

restriction of GeneralSequencePartition

properties

base	GeneralSequencePartition

used by

element

SequencePosition/nextPartition

attributes

Name	Type	Use	Default	Fixed	annotation
max	PositiveInteger	required
certainty	Certainty	prohibited

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

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

model reference

http://edamontology.org/data_1014

SequencePosition complexType

diagram

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

GeneralOutsideSequencePosition complexType

diagram

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 reference

http://edamontology.org/data_1014

OutsideSequencePosition complexType

diagram

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

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 reference

http://edamontology.org/data_1598
http://edamontology.org/format_2352

TranslationData complexType

diagram

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 reference

http://edamontology.org/data_1317
http://edamontology.org/format_2352

AminoacidTranslationData complexType

diagram

type

restriction of TranslationData

properties

base	TranslationData

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

used by

elements	FeatureTypeDetails/association/associatedDatabase FeatureRecord/annotation/condensedReferences/database FeatureRecord/blockWithOccurrenceReferences/database FeatureRecord/blockWithOccurrenceReferences/annotation/condensedReferences/database
complexType	EntryReference

General URI of the database

URL of a WSDL file describing the referenced Web service (can be WSDL version 1.0, 1.1, 2.0)

wsdlService

xs:NMTOKEN

documentation

A 'wsdl:service' 'name' in the WSDL file referenced in 'wsdl'

wsdlPort

xs: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'

webserviceEndpointAddress

Uri

documentation

URI of the referenced Web service endpoint

webserviceOperation

xs: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

webserviceInputParameters

derived 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

webserviceInputValues

derived 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

webserviceVersion

Name

documentation

Version of the Web service referenced in 'wsdl' or 'webserviceEnpointAddress'

webserviceDate

xs: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>
    
    
</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"/>




</xs:complexType>

model reference

http://edamontology.org/format_2352

EntryReference complexType

diagram

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

General URI of the database

URL of a WSDL file describing the referenced Web service (can be WSDL version 1.0, 1.1, 2.0)

wsdlService

xs:NMTOKEN

documentation

A 'wsdl:service' 'name' in the WSDL file referenced in 'wsdl'

wsdlPort

xs: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'

webserviceEndpointAddress

Uri

documentation

URI of the referenced Web service endpoint

webserviceOperation

xs: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

webserviceInputParameters

derived by: Name

documentation

webserviceInputValues

Version of the Web service referenced in 'wsdl' or 'webserviceEnpointAddress'

webserviceDate

xs:date

documentation

The date when this Web-service reference was valid (created or last time updated)

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>
    
    
    
</xs:complexContent>

</xs:complexType>

OntologyReference complexType

diagram

used by

elements	FeatureRecord/annotation/condensedReferences/ontology FeatureRecord/blockWithOccurrenceReferences/ontology FeatureRecord/blockWithOccurrenceReferences/annotation/condensedReferences/ontology
complexType	SemanticConcept

General URI of the controlled vocabulary (ontology)

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"/>

</xs:complexType>

model reference

http://edamontology.org/data_2338
http://edamontology.org/data_2352

SemanticConcept complexType

diagram

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

General URI of the controlled vocabulary (ontology)

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)

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 reference

http://edamontology.org/data_0966
http://edamontology.org/data_1087
http://edamontology.org/data_2352

Species complexType

diagram

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

General URI of the database

URL of a WSDL file describing the referenced Web service (can be WSDL version 1.0, 1.1, 2.0)

wsdlService

xs:NMTOKEN

documentation

A 'wsdl:service' 'name' in the WSDL file referenced in 'wsdl'

wsdlPort

xs: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'

webserviceEndpointAddress

Uri

documentation

URI of the referenced Web service endpoint

webserviceOperation

xs: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

webserviceInputParameters

derived by: Name

documentation

webserviceInputValues

Version of the Web service referenced in 'wsdl' or 'webserviceEnpointAddress'

webserviceDate

xs:date

documentation

The date when this Web-service reference was valid (created or last time updated)

Date when this reference was fully valid: created or last time updated

speciesName

Name

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

speciesNote

Text

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>
        
      </xs:attribute>
      <xs:attribute name="speciesNote" type="Text" sawsdl:modelReference="http://www.w3.org/2000/01/rdf-schema#comment"/>
    </xs:extension>
</xs:complexContent>

</xs:complexType>

SequenceReference complexType

diagram

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

General URI of the database

URL of a WSDL file describing the referenced Web service (can be WSDL version 1.0, 1.1, 2.0)

wsdlService

xs:NMTOKEN

documentation

A 'wsdl:service' 'name' in the WSDL file referenced in 'wsdl'

wsdlPort

xs: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'

webserviceEndpointAddress

Uri

documentation

URI of the referenced Web service endpoint

webserviceOperation

xs: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

webserviceInputParameters

derived by: Name

documentation

webserviceInputValues

Version of the Web service referenced in 'wsdl' or 'webserviceEnpointAddress'

webserviceDate

xs:date

documentation

The date when this Web-service reference was valid (created or last time updated)

Date when this reference was fully valid: created or last time updated

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>
    
    
</xs:complexContent>

</xs:complexType>

Method complexType

diagram

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

URL of a WSDL file describing the referenced Web service (can be WSDL version 1.0, 1.1, 2.0)

wsdlService

xs:NMTOKEN

documentation

A 'wsdl:service' 'name' in the WSDL file referenced in 'wsdl'

wsdlPort

xs: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'

webserviceEndpointAddress

Uri

documentation

URI of the referenced Web service endpoint

webserviceOperation

xs: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

webserviceInputParameters

derived by: Name

documentation

webserviceInputValues

Version of the Web service referenced in 'wsdl' or 'webserviceEnpointAddress'

webserviceDate

xs:date

documentation

The date when this Web-service reference was valid (created or last time updated)

source

model reference

http://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>

</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>


</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

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

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

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

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

RecommendedVerdict simpleType

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

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

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>

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

GeneralOutsideSequencePosition/correspondance OutsideSequencePosition/correspondance

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>
        <xs: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</xs:documentation>
      </xs:annotation>
    </xs:enumeration>
</xs:restriction>
</xs:simpleType>

RecommendedDatabaseName simpleType

Kind	Value	annotation
maxLength	1000
pattern	\S(\S\|\s\S)*
enumeration	EMBL
enumeration	EMBLCON
enumeration	EMBLANN
enumeration	EMBLCDS
enumeration	EMBLSVA
enumeration	Ensembl Gene
enumeration	Ensembl Transcript
enumeration	UniProt
enumeration	UniProt/Swiss-Prot
enumeration	UniProt/TrEMBL
enumeration	UniSave
enumeration	UniRef100
enumeration	UniRef90
enumeration	UniRef50
enumeration	UniParc
enumeration	IPI
enumeration	RefSeq
enumeration	InterPro
enumeration	PDB
enumeration	HGVbase
enumeration	GenomeReviews
enumeration	EPO Proteins
enumeration	JPO Proteins
enumeration	KIPO Proteins
enumeration	USPO Proteins
enumeration	PubMed
enumeration	Medline
enumeration	DDBJ/GenBank/EMBL
enumeration	PDB
enumeration	DAD
enumeration	PRF
enumeration	Patent
enumeration	NCBI Taxonomy
enumeration	NCBI Genetic Code

documentation

Predefined, recommended database name of a public database

source

RecommendedOntologyName simpleType

Kind	Value	annotation
maxLength	1000
pattern	\S(\S\|\s\S)*
enumeration	Gene Ontology
enumeration	Sequence Ontology
enumeration	ChEBI
enumeration	EDAM

documentation

Predefined, recommended name of a public ontology or controlled vocabulary

source

<xs:simpleType name="RecommendedOntologyName">
<xs:annotation>
    <xs:documentation>Predefined, recommended name of a public ontology or controlled vocabulary</xs:documentation>
</xs:annotation>
<xs:restriction base="Name">
    <xs:enumeration value="Gene Ontology"/>
    <xs:enumeration value="Sequence Ontology"/>
    <xs:enumeration value="ChEBI"/>
    <xs:enumeration value="EDAM"/>
</xs:restriction>
</xs:simpleType>

FeatureOccurrenceData/appliesToWholeSequence FeatureOccurrenceData/variation/missing GeneralSequencePosition/nextPoint SequencePosition/nextPoint AlignedBiosequence/reversedDirection AlignedGeneralNucleotideSequence/reversedDirection AlignedGeneralAminoacidSequence/reversedDirection AlignedNucleotideSequence/reversedDirection AlignedAminoacidSequence/reversedDirection TranslationData/reversedTranslationDirection GeneralSequencePosition/samePartition SequencePosition/samePartition GeneralSequencePosition/samePoint SequencePosition/samePoint

source

<xs:complexType name="Flag"/>

AnyInteger simpleType

type

xs:long

used by

element	FeatureOccurrenceData/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

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

simpleTypes	InsertionInteger PositiveInteger
attributes	Frameshift/@bases GeneralOutsideSequenceSegment/@max OutsideSequenceSegment/@max GeneralOutsideSequenceSegment/@min OutsideSequenceSegment/@min GeneralOutsideSequencePoint/@pos OutsideSequencePoint/@pos

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

attributes

Gap/@pos Frameshift/@pos GeneralSequenceInsertionPoint/@pos SequenceInsertionPoint/@pos

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

attributes

Gap/@len GeneralSequenceSegment/@max SequenceSegment/@max GeneralSequencePartition/@max SequencePartition/@max GeneralSequenceSegment/@min SequenceSegment/@min GeneralSequencePoint/@pos SequencePoint/@pos

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

Probability ScoreValue

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

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 GeneralSequencePartition/@certainty SequencePartition/@certainty GeneralSequenceSegment/@maxCertainty SequenceSegment/@maxCertainty GeneralOutsideSequenceSegment/@maxCertainty OutsideSequenceSegment/@maxCertainty GeneralSequenceSegment/@minCertainty SequenceSegment/@minCertainty GeneralOutsideSequenceSegment/@minCertainty OutsideSequenceSegment/@minCertainty

documentation

Quantitative or qualitative certainty

source

<xs:simpleType name="Certainty">
<xs:annotation>
<xs:documentation>Quantitative or qualitative certainty</xs:documentation>
</xs:annotation>
<xs:union memberTypes="Probability QualitativeCertainty"/>
</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>

ScoreValue simpleType

type

union of (AnyDecimal, Name, RecommendedVerdict, RecommendedReliability)

<xs:simpleType name="ScoreValue">
<xs:union memberTypes="AnyDecimal Name RecommendedVerdict RecommendedReliability"/>
</xs:simpleType>

Uri simpleType

type

restriction of xs:string

used by

attributes

SemanticConcept/@conceptUri DatabaseReference/@dbUri EntryReference/@entryUri OntologyReference/@ontologyUri Method/@uri

facets

Kind	Value	annotation
maxLength	1000
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

Text simpleType

type

restriction of xs:string

used by

elements	BiosequenceRecord/note GeneralNucleotideSequenceRecord/note GeneralAminoacidSequenceRecord/note NucleotideSequenceRecord/note AminoacidSequenceRecord/note BiosequenceAlignment/note GeneralNucleotideSequenceAlignment/note GeneralAminoacidSequenceAlignment/note NucleotideSequenceAlignment/note AminoacidSequenceAlignment/note FeatureTypeDetails/note FeatureOccurrenceData/occurrenceNote
attributes	ScoreType/@note GeneticCode/codon/@note Species/@speciesNote

facets

Kind	Value	annotation
minLength	1
maxLength	1000000
whiteSpace	preserve

documentation

Any plain text, possibly formatted. Can include new lines, tabs, or any number of consecutive spaces

source

<xs:simpleType name="Text" sawsdl:modelReference="http://edamontology.org/data_0969 http://edamontology.org/format_2330">
<xs:annotation>
    <xs:documentation>Any plain text, possibly formatted. Can include new lines, tabs, or any number of consecutive spaces</xs:documentation>
</xs:annotation>
<xs:restriction base="xs:string">
    <xs:minLength value="1"/>
    <xs:whiteSpace value="preserve"/>
    <xs:maxLength value="1000000"/>
</xs:restriction>


</xs:simpleType>

Name simpleType

type

restriction of xs:string

used by

elements	FeatureType/className FeatureType/equalAlias FeatureType/name AminoacidSequenceRecord/name NucleotideSequenceRecord/name GeneralAminoacidSequenceRecord/name GeneralNucleotideSequenceRecord/name BiosequenceRecord/name FeatureOccurrenceData/occurrenceName FeatureTypeDetails/association/relationName FeatureRecord/blockWithOccurrenceReferences/annotation/occurrence/association/relationName AlignedBiosequence/sequenceName FeatureRecord/referenceSequence/sequenceName FeatureTypeDetails/specificFeatureAlias FeatureTypeDetails/specificFeatureName SequenceReference/supersequenceName AlignedBiosequence/variantNote FeatureRecord/referenceSequence/variantNote
simpleTypes	ChromosomeName DatabaseName OntologyName OutsidePositionCorrespondance QualitativeCertainty RecommendedDatabaseName RecommendedOntologyName RecommendedReliability RecommendedScoreName RecommendedVerdict Reliability ScoreName ScoreValue Strand Verdict
attributes	DatabaseReference/@dbVersion EntryReference/@entryVersion ScoreType/@index Method/@name OntologyReference/@ontologyVersion SequenceReference/@sequenceVersion Species/@speciesName SemanticConcept/@term ScoreType/@unit SequenceReference/@variantNote Method/@version