/usr/share/freecontact/BioXSD-1.1.xsd is in freecontact 1.0.21-6build2.
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<!--============== LICENCE ================
Available under the Creative Commons BY-ND 3.0 licence with additionally allowed:
a) inclusion, xs:extensions, and xs:restrictions in user's XML namespace (that is URI domain associated with the user; or a generic "public" domain for URIs, with user-specific path);
b) public redistribution of versions with custom xs:appinfo-s or sawsdl:..SchemaMapping-s in the original 'bioxsd.org' XML namespace under the assumption that the XSD is synchronised with the minor releases of BioXSD at bioxsd.org. (The content of the additional xs:appinfo and sawsdl:..SchemaMapping must be in user's or third-party's namespaces.)
Note: Redistribution of BioXSD is allowed only in the original 'bioxsd.org' XML namespace and under the assumption that the XSD is synchronised with the minor releases of BioXSD at bioxsd.org.
Contributions to new canonical versions, in the 'bioxsd.org' XML namespace, are welcome under supervision of the BioXSD consortium (in order to keep BioXSD a common, canonical data model).
============== PUBLICATION ==============
Kalaš M., Puntervoll P., Joseph A., Bartaševičiūtė E., Töpfer A., Venkataraman P., Pettifer S., Bryne J.C., Ison J., Blanchet C., Rapacki K., Jonassen I. (2010)
BioXSD: the common data-exchange format for everyday bioinformatics web services. Bioinformatics, 26, i540-i546.
=== ABOUT, DOCUMENTATION, INFORMATION ===
http://bioxsd.org
=============== CONTACT ================
support@bioxsd.org
================ CREDITS ================
XML Schema and documentation: Matúš Kalaš
Contributions to design, requirements, implementations, and testing: László Kaján & Rostlab folks, Edita Karosiene, Sveinung Gundersen & HyperBrowser/GTrack team, OpenBio* and EMBOSS developers, participants in the EMBRACE project, and all software developers and data providers that use or explore BioXSD
Semantic annotation: Matúš Kalaš, Jon Ison (EDAM), acknowledgement to Andrea Splendiani and Jerven Bolleman (RDF gurus)
Senior scientists: Inge Jonassen, Kristoffer Rapacki, Pål Puntervoll, Christophe Blanchet
Acknowledgement for conceptual support: Gert Vriend, Steffen Möller, Steve Pettifer, Rodrigo Lopez, Renzo Kottmann (GCDML), Jan Christian Bryne, Toshiaki Katayama (BioHackathon), the EMBRACE project
And for technical support: Torbjørn Lium, Alexandr Oltu, Armin Töpfer, Lóránd-János Szentannai
BioXSD has been and is further being developed as a part of multiple collaborative projects. There has never been any funding dedicated exclusively to BioXSD.
Projects that contributed to BioXSD are mainly: eSysbio and ELIXIR.NO (both from the Research Council of Norway), EMBRACE (European Commission FP6)
And: Center for Disease Systems Biology (Villum Foundation), HIPCAL (l'Agence Nationale de la Recherche), FUGE Bioinformatics platform (Research Council of Norway)
And also: BioHackathon (Japan Science and Technology Agency)
========== RELEASE INFORMATION ==========
For version information, changelog, and release dates, please refer to the bottom of this file.
======================================-->
<xs:schema
version="1.1.2"
targetNamespace="http://bioxsd.org/BioXSD-1.1"
xmlns="http://bioxsd.org/BioXSD-1.1"
xmlns:xs="http://www.w3.org/2001/XMLSchema"
xmlns:sawsdl="http://www.w3.org/ns/sawsdl"
elementFormDefault="qualified"
attributeFormDefault="unqualified"
>
<xs:annotation>
<xs:documentation>BioXSD: The common XML Schema (canonical data model) for bioinformatics Web services and everyday bioinformatics.
Defines XML exchange formats for: sequences, sequence annotations, sequence similarity/alignments, references and supporting types of data</xs:documentation>
</xs:annotation>
<!--= Validated:
XML Schema validated successfully by
Altova XMLSpy 2009 32-bit and 2013 64-bit (text, schema)
XSV (at http://www.w3.org/2001/03/webdata/xsv and in oXygen XMl Editor 64-bit 14.2)
MSXML.NET (in oXygen XMl Editor 64-bit 14.2)
Eclipse (Eclipse Java EE IDE for Web Developers. Helios Service Release 1)
Validome (with http://bioxsd.org/BioXSD-1.1.xsd)
=-->
<!--============================ SIMPLE SEQUENCES ============================-->
<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>
<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:pattern value="[ACDEFGHIKLMNPQRSTVWYBJZXUO]+"/>
<xs:maxLength value="1000000000"/>
</xs:restriction>
</xs:simpleType>
<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>
<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>
<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>
<xs:simpleType name="BaseQualityString">
<xs:restriction base="xs:string">
<xs:pattern value="[!-~]+"/>
</xs:restriction>
</xs:simpleType>
<!--=========================== SEQUENCE RECORDS ===========================-->
<xs:complexType name="BiosequenceRecord" sawsdl:modelReference="http://edamontology.org/data_2043 http://edamontology.org/format_2352">
<xs:annotation>
<xs:documentation>Nucleotide or amino-acid sequence record including the generic sequence and optional metadata</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="sequence" type="Biosequence"/>
<xs:element name="species" type="Species" minOccurs="0">
<xs:annotation>
<xs:documentation>Biological source of the sequence/biopolymer</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="reference" type="SequenceReference" minOccurs="0">
<xs:annotation>
<xs:documentation>Identification of the sequence record. May refer to data the sequence originates from: a database entry or an explicit super-sequence.
NB. ID/accession is part of the 'reference'</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="name" type="Name" minOccurs="0" sawsdl:modelReference="http://www.w3.org/2000/01/rdf-schema#label http://edamontology.org/data_2154"/><!--"Sequence name"(2154)-->
<xs:element name="note" type="Text" minOccurs="0" sawsdl:modelReference="http://www.w3.org/2000/01/rdf-schema#comment"/>
<xs:element name="translationData" type="TranslationData" minOccurs="0"/>
<xs:element name="inlineBaseQuality" type="BaseQualityString" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
<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>
<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>
<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>
<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>
<!--=========================== ALIGNMENTS ===========================-->
<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>
<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>
<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>
<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>
<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>
<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>
<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>
<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>
<xs:complexType name="AlignedBiosequence">
<xs:sequence>
<xs:element name="localAlignmentPosition" type="SequencePosition" minOccurs="0">
<xs:annotation>
<xs:documentation>Coordinates of the locally aligned sub-sequence. (Not present means global alignment)</xs:documentation>
</xs:annotation>
</xs:element>
<xs:choice>
<xs:element name="sequenceRecord" type="BiosequenceRecord"/>
<xs:element name="sequenceReference" type="SequenceReference"/>
<xs:element name="sequenceName" type="Name" sawsdl:modelReference="http://edamontology.org/data_2154"/>
<xs:sequence>
<xs:element name="species" type="Species"/>
<xs:element name="genomeBuild" type="EntryReference" sawsdl:modelReference="http://purl.org/dc/elements/1.1/version http://edamontology.org/data_2041 http://edamontology.org/data_2340"/><!--"Genome build identifier"(2340)--><!--"Genome version information"(2041)-->
<xs:element name="chromosome" type="ChromosomeName"/>
<xs:element name="subsequencePosition" type="SequencePosition" minOccurs="0">
<xs:annotation>
<xs:documentation>Coordinates of a sub-sequence within the chromosome</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="variantAccession" type="Accession" minOccurs="0" sawsdl:modelReference="http://edamontology.org/data_1063 http://edamontology.org/data_2091"/>
<xs:element name="variantNote" type="Name" minOccurs="0" sawsdl:modelReference="http://edamontology.org/data_1063"/>
</xs:sequence>
</xs:choice>
<xs:element name="gap" type="Gap" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="insert" type="Insert" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="frameshift" type="Frameshift" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="reversedDirection" type="Flag" minOccurs="0"/>
<xs:element name="sequenceScore" type="Result" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
<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>
<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>
<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>
<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>
<!--=========================== FEATURE ===========================-->
<xs:complexType name="FeatureType" sawsdl:modelReference="http://edamontology.org/data_1015 http://edamontology.org/format_2352"><!--"Sequence feature identifier"(1015)--><!--"BioXSD"(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"><!--"Sequence feature identifier"(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"/><!--"Sequence feature identifier"(1015)-->
</xs:sequence>
<xs:element name="equalConcept" type="SemanticConcept" maxOccurs="unbounded" sawsdl:modelReference="http://edamontology.org/data_1015"/><!--"Sequence feature identifier"(1015)-->
</xs:choice>
<xs:element name="equalAlias" type="Name" minOccurs="0" maxOccurs="unbounded" sawsdl:modelReference="http://edamontology.org/data_1015"><!--"Sequence feature identifier"(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>
<xs:complexType name="FeatureTypeDetails" sawsdl:modelReference="http://edamontology.org/data_1021 http://edamontology.org/format_2352"><!--"Sequence feature qualifier"(1021)--><!--"BioXSD"(2352)-->
<xs:annotation>
<xs:documentation>Specific properties of a feature</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="specificFeatureName" type="Name" minOccurs="0" sawsdl:modelReference="http://edamontology.org/data_1020"/><!--"Sequence feature qualifier"(1021)-->
<xs:element name="specificFeatureConcept" type="SemanticConcept" minOccurs="0" maxOccurs="unbounded"/><!--"Sequence feature qualifier"(1021)-->
<xs:element name="specificFeatureAlias" type="Name" minOccurs="0" maxOccurs="unbounded" sawsdl:modelReference="http://edamontology.org/data_1020"/><!--"Sequence feature qualifier"(1021)-->
<xs:element name="databaseEntry" type="EntryReference" minOccurs="0" maxOccurs="unbounded">
<xs:annotation>
<xs:documentation>Pointer to a database entry specifying the feature-type details</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="note" type="Text" minOccurs="0" sawsdl:modelReference="http://www.w3.org/2000/01/rdf-schema#comment"/>
<xs:element name="association" minOccurs="0" maxOccurs="unbounded" sawsdl:modelReference="http://edamontology.org/data_2093 http://edamontology.org/format_2352">
<xs:complexType>
<xs:sequence>
<xs:element name="relationName" type="Name" minOccurs="0"/>
<xs:element name="relationConcept" type="SemanticConcept" minOccurs="0" maxOccurs="unbounded"/>
<xs:choice>
<xs:element name="associatedConcept" type="SemanticConcept" maxOccurs="unbounded"/>
<xs:element name="associatedDatabaseEntry" type="EntryReference" maxOccurs="unbounded"/>
<xs:element name="associatedDatabase" type="DatabaseReference" maxOccurs="unbounded"/>
<xs:element name="associatedFeature" type="FeatureType" maxOccurs="unbounded"/>
</xs:choice>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
<xs:complexType name="FeatureOccurrenceData" sawsdl:modelReference="http://edamontology.org/data_1021 http://edamontology.org/format_2352">
<xs:annotation>
<xs:documentation>Occurrence of a feature in a reference sequence. Positioned or non-positioned (non-positioned means applied to the whole sequence)</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:choice>
<xs:element name="appliesToWholeSequence" type="Flag"/>
<xs:element name="position" type="GeneralSequencePosition"/>
</xs:choice>
<xs:element name="occurrenceEntryReference" type="EntryReference" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="occurrenceName" type="Name" minOccurs="0"/>
<xs:element name="occurrenceNote" type="Text" minOccurs="0"/>
<xs:element name="featureTypeDetails" type="FeatureTypeDetails" minOccurs="0"/>
<xs:element name="score" type="Score" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="evidence" type="Evidence" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="frame" minOccurs="0" sawsdl:modelReference="http://edamontology.org/data_2126">
<xs:annotation>
<xs:documentation>NB. Should be 0 for non-translated but transcribed features. Should be 'strand'*(('min'-1) mod 3 + 1) for translated features within a whole-chromosome annotation</xs:documentation>
</xs:annotation>
<xs:simpleType>
<xs:restriction base="AnyInteger">
<xs:minInclusive value="-3"/>
<xs:maxInclusive value="3"/>
</xs:restriction>
</xs:simpleType>
</xs:element>
<xs:element name="phase" type="Phase" minOccurs="0"/>
<xs:element name="variation" minOccurs="0" maxOccurs="unbounded" sawsdl:modelReference="http://edamontology.org/data_0918 http://edamontology.org/format_2352">
<xs:complexType>
<xs:sequence>
<xs:element name="canonicalVariant" type="Biosequence" minOccurs="0"/>
<xs:choice>
<xs:element name="variant" type="Biosequence" maxOccurs="unbounded"/>
<xs:element name="missing" type="Flag"/>
</xs:choice>
<xs:element name="score" type="Score" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="position" type="SequencePosition" minOccurs="0">
<xs:annotation>
<xs:documentation>NB. Corresponds to a position within the feature occurrence</xs:documentation>
</xs:annotation>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="alignment" minOccurs="0" sawsdl:modelReference="http://edamontology.org/data_1381 http://edamontology.org/format_2352">
<xs:complexType>
<xs:sequence>
<xs:element name="alignmentOfReference" minOccurs="0">
<xs:complexType>
<xs:sequence>
<xs:element name="gap" type="Gap" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="insert" type="Insert" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="frameshift" type="Frameshift" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="sequenceScore" type="Result" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
<xs:unique name="uniqueGapPos_ar">
<xs:selector xpath="gap"/>
<xs:field xpath="@pos"/>
</xs:unique>
<xs:unique name="uniqueInsertPos_ar">
<xs:selector xpath="insert"/>
<xs:field xpath="@min"/>
<xs:field xpath="@max"/>
</xs:unique>
<xs:unique name="uniqueFrameshiftPos_ar">
<xs:selector xpath="frameshift"/>
<xs:field xpath="@pos"/>
</xs:unique>
</xs:element>
<xs:element name="alignedSequence" type="AlignedBiosequence">
<xs:unique name="uniqueGapPos_as">
<xs:selector xpath="gap"/>
<xs:field xpath="@pos"/>
</xs:unique>
<xs:unique name="uniqueInsertPos_as">
<xs:selector xpath="insert"/>
<xs:field xpath="@min"/>
<xs:field xpath="@max"/>
</xs:unique>
<xs:unique name="uniqueFrameshiftPos_as">
<xs:selector xpath="frameshift"/>
<xs:field xpath="@pos"/>
</xs:unique>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
<!--=========================== FEATURE BUNDLES ===========================-->
<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"><!--"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: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"><!--"Sequence annotation track"(3002)--><!--"BioXSD format"(2352)-->
<xs:annotation>
<xs:documentation>Annotation by a particular feature or property. Corresponds to one sequence annotation track</xs:documentation>
</xs:annotation>
<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"><!--"Sequence annotation track"(3002)--><!--"BioXSD format"(2352)-->
<xs:annotation>
<xs:documentation>Annotation by a particular feature or property. Corresponds to one sequence annotation track</xs:documentation>
</xs:annotation>
<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>
</xs:complexType>
<!--=========================== RESULTS, SCORE, EVIDENCE ===========================-->
<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>
<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>
<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>
<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>
<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>
<xs:complexType name="ScoreType" sawsdl:modelReference="http://edamontology.org/data_1772 http://edamontology.org/format_2352">
<xs:annotation>
<xs:documentation>Type of score of an experiment or computation</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="concept" type="SemanticConcept" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="method" type="Method" minOccurs="0" maxOccurs="unbounded" sawsdl:modelReference="http://edamontology.org/data_0856"/>
<xs:element name="methodIdRef" type="LocalId" minOccurs="0" maxOccurs="unbounded" sawsdl:modelReference="http://edamontology.org/data_0007 http://edamontology.org/data_2337 http://edamontology.org/data_0977 http://edamontology.org/format_2352 http://edamontology.org/data_0856"/>
</xs:sequence>
<xs:attribute name="name" type="ScoreName"/>
<xs:attribute name="index" type="Name"/>
<xs:attribute name="unit" type="Name"/>
<xs:attribute name="note" type="Text" sawsdl:modelReference="http://www.w3.org/2000/01/rdf-schema#comment"/>
</xs:complexType>
<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>
<!--=========================== SEQUENCE POSITIONS ===========================-->
<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>
<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>
<xs:complexType name="GeneralSequenceInsertionPoint" sawsdl:modelReference="http://edamontology.org/data_1016">
<xs:annotation>
<xs:documentation>Position of an insertion into the sequence, possibly with a certain level of uncertainty.
NB. Insertion *behind* (to the right of) the given point in the direction of the sequence; *-1* for preceeding the sequence</xs:documentation>
</xs:annotation>
<xs:attribute name="pos" type="InsertionInteger">
<xs:annotation>
<xs:documentation>NB. Omit 'pos' attribute only if 'certainty'="Unknown"</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="strand" type="Strand"/>
<xs:attribute name="certainty" type="Certainty" default="Certain"/>
</xs:complexType>
<xs:complexType name="SequenceInsertionPoint">
<xs:annotation>
<xs:documentation>Certain position of an insertion into the sequence.
NB. Insertion *behind* (to the right of) the given point in the direction of the sequence; *-1* for preceeding the sequence</xs:documentation>
</xs:annotation>
<xs:complexContent>
<xs:restriction base="GeneralSequenceInsertionPoint">
<xs:attribute name="pos" type="InsertionInteger" use="required"/>
<xs:attribute name="certainty" type="Certainty" use="prohibited"/>
</xs:restriction>
</xs:complexContent>
</xs:complexType>
<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>
<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>
<xs:complexType name="GeneralSequenceSegment" sawsdl:modelReference="http://edamontology.org/data_1017"><!--"Sequence range"(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>
<xs:complexType name="SequenceSegment">
<xs:annotation>
<xs:documentation>Certain position in the sequence referring to a scontinuous 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>
<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>
<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>
<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>
<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>
<xs:complexType name="GeneralSequencePosition" sawsdl:modelReference="http://edamontology.org/data_1014"><!--"Sequence position specification"(1014)-->
<xs:annotation>
<xs:documentation>Position in the sequence, referring either to a subsequence, a single point, an insertion, or outside of the sequence, possibly uncertain</xs:documentation>
</xs:annotation>
<xs:choice>
<xs:element name="point" type="GeneralSequencePoint" maxOccurs="unbounded"/>
<xs:element name="insertion" type="GeneralSequenceInsertionPoint"/>
<xs:element name="segment" type="GeneralSequenceSegment" maxOccurs="unbounded"/>
<xs:element name="nextPoint" type="Flag"/>
<xs:element name="nextPartition" type="GeneralSequencePartition"/>
<xs:element name="samePoint" type="Flag"/>
<xs:element name="samePartition" type="Flag"/>
<xs:element name="outside" type="GeneralOutsideSequencePosition"/>
</xs:choice>
</xs:complexType>
<xs:complexType name="SequencePosition">
<xs:annotation>
<xs:documentation>Certain position in the sequence, referring either to a subsequence, a single point, an insertion, or outside of the sequence</xs:documentation>
</xs:annotation>
<xs:complexContent>
<xs:restriction base="GeneralSequencePosition">
<xs:choice>
<xs:element name="point" type="SequencePoint" maxOccurs="unbounded"/>
<xs:element name="insertion" type="SequenceInsertionPoint"/>
<xs:element name="segment" type="SequenceSegment" maxOccurs="unbounded"/>
<xs:element name="nextPoint" type="Flag"/>
<xs:element name="nextPartition" type="SequencePartition"/>
<xs:element name="samePoint" type="Flag"/>
<xs:element name="samePartition" type="Flag"/>
<xs:element name="outside" type="OutsideSequencePosition"/>
</xs:choice>
</xs:restriction>
</xs:complexContent>
</xs:complexType>
<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>
<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>
<!--=========================== GENETIC CODE, TRANSLATION DATA ===========================-->
<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>
<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>
<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>
<!--=========================== REFERENCES ===========================-->
<xs:attributeGroup name="WebserviceReference">
<xs:annotation>
<xs:documentation>A reference to a SOAP Web service</xs:documentation>
</xs:annotation>
<xs:attribute name="wsdl" type="Uri"/>
<xs:attribute name="wsdlService" type="xs:NMTOKEN"/>
<xs:attribute name="wsdlPort" type="xs:NMTOKEN"/>
<xs:attribute name="webserviceOperation" type="xs:NMTOKEN"/>
<xs:attribute name="webserviceVersion" type="Name"/>
<xs:attribute name="webserviceDate" type="xs:date">
<xs:annotation>
<xs:documentation>Date when this Web-service reference was fully valid: created or last time updated</xs:documentation>
</xs:annotation>
</xs:attribute>
</xs:attributeGroup>
<xs:complexType name="DatabaseReference" sawsdl:modelReference="http://edamontology.org/format_2352"><!--"Database identifier"(1048)--><!--"Identifier"(0842)--><!--"BioXSD"(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"><!--"Database identifier"(1048)--><!--"Identifier"(0842)-->
<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"/><!--"Database version information"(1670)-->
<xs:attribute name="localCopyOfDb" type="xs:boolean" default="false"/>
<xs:attributeGroup ref="WebserviceReference"/>
</xs:complexType>
<xs:complexType name="EntryReference"><!--"Identifier"(0842)-->
<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"/><!--"Accession"(2091)--><!--"Identifier"(0842)-->
<xs:attribute name="entryVersion" type="Name" sawsdl:modelReference="http://edamontology.org/data_2090 http://purl.org/dc/elements/1.1/version"/><!--"Database entry version information"(2090)-->
<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>
<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"/><!--"Version information"(0953)-->
<xs:attribute name="localCopyOfOntology" type="xs:boolean" default="false"/>
</xs:complexType>
<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>
<xs:complexType name="Species"><!--"Organism identifier"(1869)-->
<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"><!--"Species name"(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>
<xs:complexType name="SequenceReference"><!--"Sequence identifier"(1063)-->
<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"/><!--"Sequence version information"(1771)-->
<xs:attribute name="variantAccession" type="Accession" sawsdl:modelReference="http://purl.org/dc/elements/1.1/identifier http://edamontology.org/data_1063"/><!--"Sequence identifier"(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>
<xs:complexType name="Method" sawsdl:modelReference="http://edamontology.org/data_0007 http://edamontology.org/data_2337 http://edamontology.org/data_0977 http://edamontology.org/format_2352">
<xs:sequence>
<xs:element name="categoryConcept" type="SemanticConcept" minOccurs="0" maxOccurs="unbounded" sawsdl:modelReference="http://edamontology.org/data_0958 http://edamontology.org/operation_0004"/>
<xs:element name="citation" type="EntryReference" minOccurs="0" maxOccurs="unbounded" sawsdl:modelReference="http://edamontology.org/data_0958 http://edamontology.org/data_0970 "/>
</xs:sequence>
<xs:attribute name="name" type="Name" use="required" sawsdl:modelReference="http://edamontology.org/data_1190"/>
<xs:attribute name="uri" type="Uri" sawsdl:modelReference="http://edamontology.org/data_0977"/>
<xs:attribute name="version" type="Name" sawsdl:modelReference="http://purl.org/dc/elements/1.1/version http://edamontology.org/data_1671"><!--"Tool version information"(1671)-->
</xs:attribute>
<xs:attribute name="date" type="xs:date" sawsdl:modelReference="http://edamontology.org/data_2156 http://edamontology.org/data_2337"/>
<xs:attributeGroup ref="WebserviceReference"/>
</xs:complexType>
<xs:simpleType name="LocalId" sawsdl:modelReference="http://purl.org/dc/elements/1.1/identifier http://edamontology.org/data_0842"><!--"Identifier"(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>
<!--=========================== ACCESSIONS ===========================-->
<xs:simpleType name="Accession" sawsdl:modelReference="http://purl.org/dc/elements/1.1/identifier http://edamontology.org/data_0842 http://edamontology.org/data_2091"><!--"Identifier"(0842)--><!--"Accession"(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:pattern value="[A-Za-z0-9\-._~]+"/>
<xs:maxLength value="1000"/>
</xs:restriction>
</xs:simpleType>
<xs:simpleType name="EmblAccession" sawsdl:modelReference="http://edamontology.org/data_1107">
<xs:restriction base="Accession">
</xs:restriction>
</xs:simpleType>
<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="[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]"/>
<xs:pattern value="[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]"/>
<xs:pattern value="[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9][.-][0-9]+"/>
<xs:pattern value="[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9][.-][0-9]+"/>
</xs:restriction>
</xs:simpleType>
<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="[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]"/>
<xs:pattern value="[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]"/>
</xs:restriction>
</xs:simpleType>
<xs:simpleType name="ExtendedGenbankAccession">
<xs:restriction base="Accession">
<xs:pattern value="[A-Z][0-9]{5}(.[0-9]+)?"/>
<xs:pattern value="[A-Z]{2}[0-9]{6}(.[0-9]+)?"/>
<xs:pattern value="[A-Z]{3}[0-9]{5}(.[0-9]+)?"/>
<xs:pattern value="[A-Z]{4}[0-9]{8,10}(.[0-9]+)?"/>
<xs:pattern value="[A-Z]{5}[0-9]{7}(.[0-9]+)?"/>
<xs:pattern value="[A-Z]{2}_[0-9]{6}(.[0-9]+)?"/>
<xs:pattern value="[A-Z]{2}_[0-9]{9}(.[0-9]+)?"/>
<xs:pattern value="[A-Z]{2}_[A-Z]{4}[0-9]{8,10}(.[0-9]+)?"/>
</xs:restriction>
</xs:simpleType>
<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>
<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>
<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>
<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>
<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>
<xs:simpleType name="PubmedId">
<xs:restriction base="Accession">
<xs:pattern value="[1-9][0-9]{0,8}"/>
</xs:restriction>
</xs:simpleType>
<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>
<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>
<!--=========================== ENUMERATIONS ===========================-->
<xs:simpleType name="RecommendedScoreName">
<xs:restriction base="Name">
<xs:enumeration value="p-value" sawsdl:modelReference="http://edamontology.org/data_1669"/>
<xs:enumeration value="E-value" sawsdl:modelReference="http://edamontology.org/data_1667"/>
<xs:enumeration value="Standard deviation"/>
<xs:enumeration value="Bit" sawsdl:modelReference="http://edamontology.org/data_2335"/>
<xs:enumeration value="Z-score"/>
<xs:enumeration value="Probability"/>
<xs:enumeration value="Q3" sawsdl:modelReference="http://edamontology.org/NumberOfBlahblah"/>
<xs:enumeration value="SOV" sawsdl:modelReference="http://edamontology.org/SegmentOverlap"/>
</xs:restriction>
</xs:simpleType>
<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>
<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>
<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 reffered 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>
<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>
<xs:simpleType name="OutsidePositionCorrespondance" sawsdl:modelReference="http://edamontology.org/format_2352">
<xs:annotation>
<xs:documentation>Correspondance 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 correspondance 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>
<xs:simpleType name="RecommendedDatabaseName">
<xs:annotation>
<xs:documentation>Predefined, recommended database name of a public database</xs:documentation>
</xs:annotation>
<xs:restriction base="Name">
<xs:enumeration value="EMBL"/>
<xs:enumeration value="EMBLCON"/>
<xs:enumeration value="EMBLANN"/>
<xs:enumeration value="EMBLCDS"/>
<xs:enumeration value="EMBLSVA"/>
<xs:enumeration value="Ensembl Gene"/>
<xs:enumeration value="Ensembl Transcript"/>
<xs:enumeration value="UniProt"/>
<xs:enumeration value="UniProt/Swiss-Prot"/>
<xs:enumeration value="UniProt/TrEMBL"/>
<xs:enumeration value="UniSave"/>
<xs:enumeration value="UniRef100"/>
<xs:enumeration value="UniRef90"/>
<xs:enumeration value="UniRef50"/>
<xs:enumeration value="UniParc"/>
<xs:enumeration value="IPI"/>
<xs:enumeration value="RefSeq"/>
<xs:enumeration value="InterPro"/>
<xs:enumeration value="PDB"/>
<xs:enumeration value="HGVbase"/>
<xs:enumeration value="GenomeReviews"/>
<xs:enumeration value="EPO Proteins"/>
<xs:enumeration value="JPO Proteins"/>
<xs:enumeration value="KIPO Proteins"/>
<xs:enumeration value="USPO Proteins"/>
<xs:enumeration value="PubMed"/>
<xs:enumeration value="Medline"/>
<xs:enumeration value="DDBJ/GenBank/EMBL"/>
<xs:enumeration value="PDB"/>
<xs:enumeration value="DAD"/>
<xs:enumeration value="PRF"/>
<xs:enumeration value="Patent"/>
<xs:enumeration value="NCBI Taxonomy"/>
<xs:enumeration value="NCBI Genetic Code"/>
</xs:restriction>
</xs:simpleType>
<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>
<!--=========================== BASIC GENERAL TYPES (chosen subset of xs built-ins) ===========================-->
<xs:complexType name="Flag"/>
<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>
<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>
<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>
<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>
<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>
<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>
<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>
<xs:simpleType name="Certainty">
<xs:annotation>
<xs:documentation>Quantitave or qualitative certainty</xs:documentation>
</xs:annotation>
<xs:union memberTypes="Probability QualitativeCertainty"/>
</xs:simpleType>
<xs:simpleType name="Verdict">
<xs:union memberTypes="Name RecommendedVerdict"/>
</xs:simpleType>
<xs:simpleType name="Reliability">
<xs:union memberTypes="Name RecommendedReliability"/>
</xs:simpleType>
<xs:simpleType name="ScoreValue">
<xs:union memberTypes="AnyDecimal Name RecommendedVerdict RecommendedReliability"/>
</xs:simpleType>
<xs:simpleType name="Uri" sawsdl:modelReference="http://purl.org/dc/elements/1.1/identifier http://edamontology.org/data_0842 http://edamontology.org/data_1047 http://edamontology.org/format_2334"><!--"Identifier"(0842)-->
<xs:annotation>
<xs:documentation>An absolute Unified Resource Identifier (URI), possibly a Web link.
NB. Supports a subset of RFC 3986 generic syntax (selected schemes, DNS only, no user info, constrained port and characters)</xs:documentation>
</xs:annotation>
<xs:restriction base="xs:string">
<xs:pattern value="http://[a-z0-9]([a-z0-9]|\-[a-z0-9])*(\.[a-z0-9]([a-z0-9]|\-[a-z0-9])*)*(:[2-9][0-9]{3,})?(/([A-Za-z0-9\-._~!$'()*+,;=]|%[0-9A-F]{2})+)*(\?([A-Za-z0-9\-._~!$'()*+,;=/\?]|%[0-9A-F]{2})*)?(#([A-Za-z0-9\-._~!$'()*+,;=/\?]|%[0-9A-F]{2})*)?"/>
<xs:pattern value="https://[a-z0-9]([a-z0-9]|\-[a-z0-9])*(\.[a-z0-9]([a-z0-9]|\-[a-z0-9])*)*(:[2-9][0-9]{3,})?(/([A-Za-z0-9\-._~!$'()*+,;=]|%[0-9A-F]{2})+)*(\?([A-Za-z0-9\-._~!$'()*+,;=/\?]|%[0-9A-F]{2})*)?(#([A-Za-z0-9\-._~!$'()*+,;=/\?]|%[0-9A-F]{2})*)?"/>
<xs:pattern value="ftp://[a-z0-9]([a-z0-9]|\-[a-z0-9])*(\.[a-z0-9]([a-z0-9]|\-[a-z0-9])*)*(:[2-9][0-9]{3,})?(/([A-Za-z0-9\-._~!$'()*+,;=]|%[0-9A-F]{2})+)*(\?([A-Za-z0-9\-._~!$'()*+,;=/\?]|%[0-9A-F]{2})*)?(#([A-Za-z0-9\-._~!$'()*+,;=/\?]|%[0-9A-F]{2})*)?"/>
<xs:pattern value="urn:lsid:[a-z0-9]([a-z0-9]|\-[a-z0-9])*(\.[a-z0-9]([a-z0-9]|\-[a-z0-9])*)*:[A-Za-z0-9\-._~]+:[A-Za-z0-9\-._~]+(:[A-Za-z0-9\-._~]+)?"/>
<!--=As the whole BioXSD, these patterns are copyrighted and available under the Creative Commons attribution no-modification licence (CC-BY-ND 3.0; Derivation waived by xs:extension and xs:restriction in user's namespace; Address change requests to bioxsd.org)=-->
<xs:maxLength value="1000"/>
</xs:restriction>
</xs:simpleType>
<xs:simpleType name="Text" sawsdl:modelReference="http://edamontology.org/data_0969 http://edamontology.org/format_2330">
<!--"Free text"(0969)--><!--"Text format"(2330)-->
<xs:annotation>
<xs:documentation>Any plain text (possibly formatted)</xs:documentation>
</xs:annotation>
<xs:restriction base="xs:string">
<xs:minLength value="1"/>
<xs:whiteSpace value="preserve"/>
<xs:maxLength value="1000000"/>
</xs:restriction>
</xs:simpleType>
<xs:simpleType name="Name" sawsdl:modelReference="http://www.w3.org/2000/01/rdf-schema#label http://edamontology.org/data_2099 http://edamontology.org/format_2330">
<!--= NB. Different from xs:Name which is a valid name of an XML tag. =-->
<xs:restriction base="xs:string">
<xs:pattern value="\S(\S|\s\S)*"/>
<xs:maxLength value="1000"/>
</xs:restriction>
</xs:simpleType>
<xs:simpleType name="ChromosomeName" sawsdl:modelReference="http://edamontology.org/data_0987">
<xs:restriction base="Name">
<xs:pattern value="[A-Z][A-Za-z]*"/>
<xs:pattern value="[0-9]+[A-Za-z]*"/>
<xs:pattern value="[a-z]+[0-9]+[A-Za-z]*"/>
</xs:restriction>
</xs:simpleType>
<xs:simpleType name="DatabaseName" sawsdl:modelReference="http://www.w3.org/2000/01/rdf-schema#label http://edamontology.org/data_1056"><!--"Database name"(1056)-->
<xs:annotation>
<xs:documentation>Name of a public or private database (predefined or arbitrary name)</xs:documentation>
</xs:annotation>
<xs:union memberTypes="Name RecommendedDatabaseName"/>
</xs:simpleType>
<xs:simpleType name="OntologyName" sawsdl:modelReference="http://edamontology.org/data_1051">
<xs:annotation>
<xs:documentation>Name of a public or private ontology or controlled vocabulary (predefined or arbitrary name)</xs:documentation>
</xs:annotation>
<xs:union memberTypes="Name RecommendedOntologyName"/>
</xs:simpleType>
<xs:simpleType name="ScoreName">
<xs:union memberTypes="Name RecommendedScoreName"/>
</xs:simpleType>
<xs:simpleType name="Phase" sawsdl:modelReference="http://edamontology.org/data_2336">
<xs:annotation>
<xs:documentation>Phase of an incomplete peptide-coding nucleotide sequence, in the direction of translation</xs:documentation>
</xs:annotation>
<xs:restriction base="NonnegativeInteger">
<xs:maxInclusive value="2"/>
</xs:restriction>
</xs:simpleType>
</xs:schema>
<!--============== CHANGELOG ==================
version status published changes
==============================================
1.1.2 Current 1.1 2013-05-13 uniqueness constraints removed in restricted complex subtypes;
fixed="Certain" removed where use="prohibited";
maxLength constraint for nucleotide sequence removed (due to incompatibility with Xerces);
insert-s added to aligned sequences (in addition to gaps, for optimisation and convenience);
Flag extendable (and theoretically restrictable).
1.1.1 2012-01-13 samePoint/samePartition added (as choices of positions);
updated URIs of EDAM concepts;
a few xs:documentation-s updated.
1.1 2011-09-27 renamed: AnnotatedSequence to FeatureRecord, OntologyConcept to SemanticConcept, original to canonicalVariant, 'Unknown' to 'Value unknown';
added SAWSDL annotation by RDFS and Dublin Core, updated some of the annotation by EDAM;
LocalId value: max 4 characters from 63 allowed characters (16M possibilities).
1.1 beta1 (Current 2011-05-11 maxOccur=1 simple elements of many supplementary complexTypes now represented by attributes (applies to positions, references, and score);
1.1beta1, a few renamings (e.g. terms to concepts, isoform to variant, removal of 'custom', Empty to Flag);
!deprecated!) AnnotatedSequence only for 1 sequence/chromosome/scaffold/contig, no chromosome in positions [Annotation type for multiple sequences should appear in beta2];
all nested positions local with respect to encapsulating sequence/(multi)segment/partition/(tuple(='multi-point'));
dense positions added ('nextPoint', 'nextPartition') referring to preceeding position element in the data or to the start of the reference sequence/(multi)segment/partition;
score: any Name allowed as value (in addition to AnyDecimal), methods & methodIdRefs added;
condensedReferences added for feature occurrences;
one of 'name' or 'equalConcept' mandatory in Feature;
LocalId value: max 2 characters from 63 allowed characters;
(evolved from 1.0.3; order of definitions changed).
==============================================
1.0.3 unpublished inline read quality string added (FASTQ/Phred); BiosequenceAlignment can contain full AnnotatedSequence-s.
1.0.2 Current 1.0 2010-10-27 references/associations between feature occurrences modified; OboTermId removed; slight refactoring of positions (e.g. multiple points allowed).
1.0.1 2010-10-22 PubmedId added; annotation with EDAM improved.
1.0.0 2010-04-08 (based on 0.4 prototype).
================ CHANGELOG =================-->
|