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SRA.analysis.xsd
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<?xml version="1.0" encoding="UTF-8"?>
<!--
~ Copyright 2018 EMBL - European Bioinformatics Institute
~ Licensed under the Apache License, Version 2.0 (the "License"); you may not use this
~ file except in compliance with the License. You may obtain a copy of the License at
~ http://www.apache.org/licenses/LICENSE-2.0
~ Unless required by applicable law or agreed to in writing, software distributed under the
~ License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
~ CONDITIONS OF ANY KIND, either express or implied. See the License for the
~ specific language governing permissions and limitations under the License.
-->
<xs:schema xmlns:com="SRA.common" xmlns:xs="http://www.w3.org/2001/XMLSchema">
<xs:import namespace="SRA.common" schemaLocation="SRA.common.xsd"/>
<xs:complexType name="AnalysisFileType">
<xs:attribute name="filename" type="xs:string" use="required">
<xs:annotation>
<xs:documentation>The file name. </xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="filetype" use="required">
<xs:annotation>
<xs:documentation>The type of the file.</xs:documentation>
</xs:annotation>
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:enumeration value="tab"/>
<xs:enumeration value="bam"/>
<xs:enumeration value="bai"/>
<xs:enumeration value="cram"/>
<xs:enumeration value="crai"/>
<xs:enumeration value="vcf"/>
<xs:enumeration value="vcf_aggregate"/>
<xs:enumeration value="bcf"/>
<xs:enumeration value="tabix"/>
<xs:enumeration value="wig"/>
<xs:enumeration value="bed"/>
<xs:enumeration value="gff"/>
<xs:enumeration value="gfa"/>
<xs:enumeration value="fasta"/>
<xs:enumeration value="fastq"/>
<xs:enumeration value="flatfile"/>
<xs:enumeration value="chromosome_list"/>
<xs:enumeration value="sample_list"/>
<xs:enumeration value="readme_file"/>
<xs:enumeration value="phenotype_file"/>
<xs:enumeration value="BioNano_native"/>
<xs:enumeration value="Kallisto_native"/>
<xs:enumeration value="agp"/>
<xs:enumeration value="unlocalised_list"/>
<xs:enumeration value="info"/>
<xs:enumeration value="manifest"/>
<xs:enumeration value="csi"/>
<xs:enumeration value="bcf_aggregate"/>
<xs:enumeration value="other"/>
</xs:restriction>
</xs:simpleType>
</xs:attribute>
<xs:attribute name="checksum_method" use="required">
<xs:annotation>
<xs:documentation>The checksum method. </xs:documentation>
</xs:annotation>
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:enumeration value="MD5">
<xs:annotation>
<xs:documentation> Checksum generated by the MD5 method (md5sum in
unix). </xs:documentation>
</xs:annotation>
</xs:enumeration>
</xs:restriction>
</xs:simpleType>
</xs:attribute>
<xs:attribute name="checksum" type="xs:string" use="required">
<xs:annotation>
<xs:documentation>The file checksum.</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="unencrypted_checksum" type="xs:string" use="optional">
<xs:annotation>
<xs:documentation>The checksum of the unencrypted file (used in conjunction with the checksum of an encrypted file).
</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="checklist" type="xs:string">
<xs:annotation>
<xs:documentation>The name of the checklist.</xs:documentation>
</xs:annotation>
</xs:attribute>
</xs:complexType>
<xs:complexType name="AnalysisSetType">
<xs:sequence maxOccurs="unbounded" minOccurs="1">
<xs:element name="ANALYSIS" type="AnalysisType"/>
</xs:sequence>
</xs:complexType>
<xs:element name="ANALYSIS_SET" type="AnalysisSetType">
<xs:annotation>
<xs:documentation>A container of analysis objects. </xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="ANALYSIS" type="AnalysisType"/>
<xs:complexType name="AnalysisType">
<xs:annotation>
<xs:documentation>A SRA analysis object captures sequence analysis results including sequence alignments, sequence variations and sequence annotations.
</xs:documentation>
</xs:annotation>
<xs:complexContent>
<xs:extension base="com:ObjectType">
<xs:sequence>
<xs:element maxOccurs="1" minOccurs="0" name="TITLE" type="xs:string">
<xs:annotation>
<xs:documentation>Title of the analysis object which will be displayed in
search results. </xs:documentation>
</xs:annotation>
</xs:element>
<xs:element maxOccurs="1" minOccurs="0" name="DESCRIPTION" type="xs:string">
<xs:annotation>
<xs:documentation>Describes the analysis in detail.</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="STUDY_REF" minOccurs="0">
<xs:annotation>
<xs:documentation>Identifies the parent study.</xs:documentation>
</xs:annotation>
<xs:complexType>
<xs:complexContent>
<xs:extension base="com:RefObjectType"> </xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element>
<xs:element name="SAMPLE_REF" maxOccurs="unbounded" minOccurs="0">
<xs:annotation>
<xs:documentation>One of more samples associated with the
analysis.</xs:documentation>
</xs:annotation>
<xs:complexType>
<xs:complexContent>
<xs:extension base="com:RefObjectType">
<xs:attribute name="label" type="xs:string">
<xs:annotation>
<xs:documentation>A label associating the sample with sample references in data files.</xs:documentation>
</xs:annotation>
</xs:attribute>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element>
<xs:element name="EXPERIMENT_REF" maxOccurs="unbounded" minOccurs="0">
<xs:complexType>
<xs:complexContent>
<xs:extension base="com:RefObjectType"> </xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element>
<xs:element name="RUN_REF" maxOccurs="unbounded" minOccurs="0">
<xs:annotation>
<xs:documentation>One or more runs associated with the
analysis.</xs:documentation>
</xs:annotation>
<xs:complexType>
<xs:complexContent>
<xs:extension base="com:RefObjectType">
<xs:attribute name="label" type="xs:string">
<xs:annotation>
<xs:documentation>A label associating the run with run references in data files.</xs:documentation>
</xs:annotation>
</xs:attribute>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element>
<xs:element name="ANALYSIS_REF" maxOccurs="unbounded" minOccurs="0">
<xs:annotation>
<xs:documentation>One or more analyses associated with the
analysis.</xs:documentation>
</xs:annotation>
<xs:complexType>
<xs:complexContent>
<xs:extension base="com:RefObjectType">
<xs:attribute name="label" type="xs:string">
<xs:annotation>
<xs:documentation>A label associating the analysis with analysis references in data files.</xs:documentation>
</xs:annotation>
</xs:attribute>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element>
<xs:element maxOccurs="1" minOccurs="1" name="ANALYSIS_TYPE">
<xs:annotation>
<xs:documentation>The type of the analysis. </xs:documentation>
</xs:annotation>
<xs:complexType>
<xs:choice>
<xs:element name="REFERENCE_ALIGNMENT"
type="com:ReferenceSequenceType">
<xs:annotation>
<xs:documentation/>
</xs:annotation>
</xs:element>
<xs:element name="SEQUENCE_VARIATION">
<xs:complexType>
<xs:complexContent>
<xs:extension base="com:ReferenceSequenceType">
<xs:sequence>
<xs:element name="EXPERIMENT_TYPE" minOccurs="0"
maxOccurs="unbounded">
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:enumeration value="Whole genome sequencing"/>
<xs:enumeration
value="Whole transcriptome sequencing"/>
<xs:enumeration value="Exome sequencing"/>
<xs:enumeration value="Genotyping by array"/>
<xs:enumeration value="transcriptomics"/>
<xs:enumeration value="Curation"/>
<xs:enumeration value="Genotyping by sequencing"/>
<xs:enumeration value="Target sequencing"/>
</xs:restriction>
</xs:simpleType>
</xs:element>
<xs:element minOccurs="0" name="PROGRAM"
type="xs:string"/>
<xs:element name="PLATFORM" type="xs:string"
minOccurs="0"/>
<xs:element minOccurs="0" name="IMPUTATION"
type="xs:boolean"/>
</xs:sequence>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element>
<xs:element name="SEQUENCE_ASSEMBLY">
<xs:complexType>
<xs:sequence>
<xs:element name="NAME" type="xs:string"/>
<xs:element minOccurs="0" name="TYPE">
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:enumeration value="clone or isolate">
<xs:annotation>
<xs:documentation>An assembly of reads from an isolated cultured organism, tissues, cells or a cell line.
</xs:documentation>
</xs:annotation>
</xs:enumeration>
<xs:enumeration value="primary metagenome">
<xs:annotation>
<xs:documentation>An original metagenome assembly prior to binning from a sampled biome or collection of sampled biomes without attempt to separate taxa.
</xs:documentation>
</xs:annotation>
</xs:enumeration>
<xs:enumeration value="binned metagenome">
<xs:annotation>
<xs:documentation>A set of contigs drawn from primary or unbinned metagenomes grouped into a single-taxon set.
</xs:documentation>
</xs:annotation>
</xs:enumeration>
<xs:enumeration
value="Metagenome-Assembled Genome (MAG)">
<xs:annotation>
<xs:documentation>A single-taxon assembly based on a binned metagenome asserted to be a close representation to an actual individual genome (that could match an already existing isolate or represent a novel isolate).
</xs:documentation>
</xs:annotation>
</xs:enumeration>
<xs:enumeration
value="Environmental Single-Cell Amplified Genome (SAG)">
<xs:annotation>
<xs:documentation>A genome assembly from amplified environmental sampled single-cell DNA.
</xs:documentation>
</xs:annotation>
</xs:enumeration>
<xs:enumeration
value="COVID-19 outbreak">
<xs:annotation>
<xs:documentation>A genome assembly specific to COVID-19 outbreak.
</xs:documentation>
</xs:annotation>
</xs:enumeration>
<xs:enumeration
value="clinical isolate assembly">
<xs:annotation>
<xs:documentation>A bacterial pathogen genome assembly.
</xs:documentation>
</xs:annotation>
</xs:enumeration>
</xs:restriction>
</xs:simpleType>
</xs:element>
<xs:element name="PARTIAL" type="xs:boolean"> </xs:element>
<xs:element name="COVERAGE" type="xs:string"/>
<xs:element name="PROGRAM" type="xs:string"/>
<xs:element name="PLATFORM" type="xs:string"/>
<xs:element minOccurs="0" name="MIN_GAP_LENGTH"
type="xs:integer"/>
<xs:element minOccurs="0" name="MOL_TYPE">
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:enumeration value="genomic DNA"/>
<xs:enumeration value="genomic RNA"/>
<xs:enumeration value="viral cRNA"/>
</xs:restriction>
</xs:simpleType>
</xs:element>
<xs:element minOccurs="0" name="TPA" type="xs:boolean"/>
<xs:element minOccurs="0" name="AUTHORS"
type="xs:string"/>
<xs:element minOccurs="0" name="ADDRESS"
type="xs:string"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="SEQUENCE_FLATFILE">
<xs:complexType>
<xs:sequence>
<xs:element minOccurs="0" name="AUTHORS"
type="xs:string"/>
<xs:element minOccurs="0" name="ADDRESS"
type="xs:string"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="SEQUENCE_ANNOTATION" type="com:ReferenceSequenceType"></xs:element>
<xs:element name="REFERENCE_SEQUENCE">
<xs:complexType> </xs:complexType>
</xs:element>
<xs:element name="SAMPLE_PHENOTYPE">
<xs:annotation>
<xs:documentation/>
</xs:annotation>
<xs:complexType> </xs:complexType>
</xs:element>
<xs:element name="PROCESSED_READS" type="com:ReferenceSequenceType"></xs:element>
<xs:element name="GENOME_MAP">
<xs:complexType>
<xs:sequence>
<xs:element name="PROGRAM" type="xs:string"/>
<xs:element name="PLATFORM">
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:enumeration value="BioNano"/>
</xs:restriction>
</xs:simpleType>
</xs:element>
<xs:element minOccurs="0" name="DESCRIPTION"
type="xs:string"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="AMR_ANTIBIOGRAM"/>
<xs:element name="PATHOGEN_ANALYSIS"/>
<xs:element name="COVID19_CONSENSUS"/>
<xs:element name="COVID19_FILTERED_VCF"/>
<xs:element name="PHYLOGENY_ANALYSIS"/>
<xs:element name="ASSEMBLY_GRAPH">
<xs:complexType>
<xs:sequence>
<xs:element maxOccurs="unbounded" name="ASSEMBLY"
type="com:ReferenceAssemblyType"></xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="TRANSCRIPTOME_ASSEMBLY">
<xs:complexType>
<xs:sequence>
<xs:element name="NAME" type="xs:string"/>
<xs:element name="PROGRAM" type="xs:string"/>
<xs:element name="PLATFORM" type="xs:string"/>
<xs:element minOccurs="0" name="TPA" type="xs:boolean"/>
<xs:element minOccurs="0" name="AUTHORS"
type="xs:string"/>
<xs:element minOccurs="0" name="ADDRESS"
type="xs:string"/>
<xs:element minOccurs="0" name="TYPE">
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:enumeration value="isolate">
<xs:annotation>
<xs:documentation>An assembly of reads from an isolated cultured organism, tissues, cells or a cell line.
</xs:documentation>
</xs:annotation>
</xs:enumeration>
<xs:enumeration value="metatranscriptome">
<xs:annotation>
<xs:documentation>An original metatranscriptome assembly from a sampled biome or collection of sampled biomes without attempt to separate taxa.
</xs:documentation>
</xs:annotation>
</xs:enumeration>
</xs:restriction>
</xs:simpleType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="TAXONOMIC_REFERENCE_SET">
<xs:complexType>
<xs:sequence>
<xs:element name="NAME" type="xs:string"/>
<xs:element name="TAXONOMY_SYSTEM" type="xs:string"/>
<xs:element minOccurs="0" name="TAXONOMY_SYSTEM_VERSION"
type="xs:string"/>
<xs:element minOccurs="0" name="CUSTOM_FIELDS">
<xs:complexType>
<xs:sequence maxOccurs="unbounded" minOccurs="0">
<xs:element name="FIELD">
<xs:complexType>
<xs:sequence>
<xs:element name="NAME"/>
<xs:element name="DESCRIPTION"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="ASSEMBLY_ANNOTATION" type="com:ReferenceSequenceType"></xs:element>
<xs:element name="SEQUENCE_CONSENSUS"/>
<xs:element name="FILTERED_VARIATION"/>
</xs:choice>
</xs:complexType>
</xs:element>
<xs:sequence>
<xs:element name="FILES">
<xs:annotation>
<xs:documentation>Files associated with the
analysis.</xs:documentation>
</xs:annotation>
<xs:complexType>
<xs:sequence>
<xs:element maxOccurs="unbounded" minOccurs="1" name="FILE"
type="AnalysisFileType"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
<xs:element maxOccurs="1" minOccurs="0" name="ANALYSIS_LINKS">
<xs:annotation>
<xs:documentation> Links to resources related to this analysis.
</xs:documentation>
</xs:annotation>
<xs:complexType>
<xs:sequence minOccurs="1">
<xs:element name="ANALYSIS_LINK" type="com:LinkType"
maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element maxOccurs="1" minOccurs="0" name="ANALYSIS_ATTRIBUTES">
<xs:annotation>
<xs:documentation>Properties and attributes of an analysis. These can be
entered as free-form tag-value pairs.</xs:documentation>
</xs:annotation>
<xs:complexType>
<xs:sequence minOccurs="1">
<xs:element name="ANALYSIS_ATTRIBUTE" type="com:AttributeType"
maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
<xs:attribute name="analysis_center" type="xs:string" use="optional">
<xs:annotation>
<xs:documentation>If applicable, the center name of the institution responsible
for this analysis. </xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="analysis_date" type="xs:dateTime" use="optional">
<xs:annotation>
<xs:documentation>The date when this analysis was produced. </xs:documentation>
</xs:annotation>
</xs:attribute>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:schema>