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GenomeThreader.rng.txt
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GenomeThreader.rng.txt
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<?xml version="1.0" encoding="ISO-8859-1"?>
<grammar xmlns="http://relaxng.org/ns/structure/1.0"
datatypeLibrary="http://www.w3.org/2001/XMLSchema-datatypes">
<!-- This grammar corresponds to gthXML v1.2, which is reverse
compatible with gthXML v1.1 and v1.0 documents.
Michael E Sparks ([email protected])
16 August 2007
Change log:
gthXML v1.2 added the optional "MetWAMer_annot" element
to the "orf_entry" element of "probable_ORFs".
The "header" element is now optional.
gthXML v1.1 added the optional "gDNA_id" attribute
to the "none" element of "probable_ORFs".
-->
<!--
Copyright (c) 2003,2004,2005,2006,2007 Michael E Sparks
All rights reserved.
Permission to use, copy, modify, and distribute this software for any
purpose with or without fee is hereby granted, provided that the above
copyright notice and this permission notice appear in all copies.
THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
-->
<start>
<element name="GTH_output"
ns="http://www.genomethreader.org/GTH_output/">
<attribute name="GTH_XML_version"/>
<optional>
<element name="header"
ns="http://www.genomethreader.org/GTH_output/header/">
<ref name="header-CONTENT"/>
</element>
</optional>
<oneOrMore>
<element name="alignment_module">
<zeroOrMore>
<element name="spliced_alignment"
ns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
<ref name="spliced_alignment-CONTENT"/>
</element>
</zeroOrMore>
<choice>
<element name="total_number_ESTs_reported">
<data type="integer"/>
</element>
<element name="total_number_proteins_reported">
<data type="integer"/>
</element>
</choice>
</element>
<optional>
<element name="PGL_module"
ns="http://www.genomethreader.org/GTH_output/PGL_module/">
<ref name="PGL_module-CONTENT"/>
</element>
</optional>
</oneOrMore>
</element>
</start>
<!-- ____________________________________________________________________________ -->
<define name="header-CONTENT"
ns="http://www.genomethreader.org/GTH_output/header/">
<element name="source">
<attribute name="program"/>
<attribute name="version"/>
<attribute name="build_date"/>
<attribute name="run_date"/>
</element>
<zeroOrMore>
<element name="gDNA_template_files">
<oneOrMore>
<element name="temp_name">
<text/>
</element>
</oneOrMore>
</element>
</zeroOrMore>
<element name="reference_files">
<oneOrMore>
<element name="file">
<attribute name="ref_name"/>
<attribute name="type">
<choice>
<value>ESTcDNA</value>
<value>Protein</value>
</choice>
</attribute>
</element>
</oneOrMore>
</element>
<element name="splice_site_parameters">
<attribute name="parameter_type"/>
<attribute name="species"/>
</element>
<element name="parameters">
<oneOrMore>
<element name="parameter">
<attribute name="name"/>
<attribute name="value"/>
</element>
</oneOrMore>
</element>
<element name="overall_reference_type">
<choice>
<value>ESTcDNA</value>
<value>Protein</value>
<value>Mixed</value>
</choice>
</element>
</define>
<!-- ____________________________________________________________________________ -->
<define name="spliced_alignment-CONTENT"
ns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
<element name="reference">
<attribute name="ref_file"/>
<attribute name="ref_id"/>
<optional>
<attribute name="ref_strand">
<choice>
<value>+</value>
<value>-</value>
</choice>
</attribute>
</optional>
<attribute name="ref_description"/>
<element name="seq">
<text/>
</element>
</element>
<element name="gDNA_segment">
<oneOrMore>
<element name="template">
<attribute name="temp_file"/>
<attribute name="temp_id"/>
<attribute name="temp_strand">
<choice>
<value>+</value>
<value>-</value>
</choice>
</attribute>
<attribute name="temp_description"/>
<element name="position">
<attribute name="start">
<data type="integer"/>
</attribute>
<attribute name="stop">
<data type="integer"/>
</attribute>
</element>
</element>
</oneOrMore>
</element>
<element name="predicted_gene_structure">
<element name="exon-intron_info">
<interleave>
<oneOrMore>
<element name="exon">
<attribute name="e_serial">
<data type="integer"/>
</attribute>
<element name="gDNA_exon_boundary">
<attribute name="g_start">
<data type="integer"/>
</attribute>
<attribute name="g_stop">
<data type="integer"/>
</attribute>
<attribute name="g_length">
<data type="integer"/>
</attribute>
</element>
<element name="reference_exon_boundary">
<attribute name="r_type">
<choice>
<value>cDNA</value>
<value>Protein</value>
</choice>
</attribute>
<attribute name="r_start">
<data type="integer"/>
</attribute>
<attribute name="r_stop">
<data type="integer"/>
</attribute>
<attribute name="r_length">
<data type="integer"/>
</attribute>
<attribute name="r_score">
<data type="decimal"/>
</attribute>
</element>
</element>
</oneOrMore>
<zeroOrMore>
<element name="intron">
<attribute name="i_serial">
<data type="integer"/>
</attribute>
<element name="gDNA_intron_boundary">
<attribute name="i_start">
<data type="integer"/>
</attribute>
<attribute name="i_stop">
<data type="integer"/>
</attribute>
<attribute name="i_length">
<data type="integer"/>
</attribute>
<element name="donor">
<attribute name="d_prob">
<data type="decimal"/>
</attribute>
<optional>
<attribute name="d_score">
<data type="decimal"/>
</attribute>
</optional>
</element>
<element name="acceptor">
<attribute name="a_prob">
<data type="decimal"/>
</attribute>
<optional>
<attribute name="a_score">
<data type="decimal"/>
</attribute>
</optional>
</element>
</element>
<optional>
<element name="shorter_than_min_intron_len">
<empty/>
</element>
</optional>
</element>
</zeroOrMore>
</interleave>
</element>
<optional>
<element name="PPA_line">
<attribute name="polyA_start">
<data type="integer"/>
</attribute>
<attribute name="polyA_stop">
<data type="integer"/>
</attribute>
</element>
</optional>
<element name="MATCH_line">
<attribute name="gen_id"/>
<attribute name="gen_strand">
<choice>
<value>+</value>
<value>-</value>
</choice>
</attribute>
<attribute name="ref_id"/>
<optional>
<attribute name="ref_strand">
<choice>
<value>+</value>
<value>-</value>
</choice>
</attribute>
</optional>
<element name="total_alignment_score">
<data type="decimal"/>
</element>
<element name="cumulative_length_of_scored_exons">
<data type="integer"/>
</element>
<element name="coverage">
<attribute name="percentage">
<data type="decimal"/>
</attribute>
<attribute name="high_type">
<choice>
<value>C</value>
<value>P</value>
<value>G</value>
</choice>
</attribute>
</element>
</element>
<element name="PGS_line">
<element name="gDNA">
<attribute name="gen_id"/>
<attribute name="gen_strand">
<choice>
<value>+</value>
<value>-</value>
</choice>
</attribute>
</element>
<choice>
<element name="rDNA">
<attribute name="rDNA_strand">
<choice>
<value>+</value>
<value>-</value>
</choice>
</attribute>
<attribute name="rDNA_id"/>
</element>
<element name="rProt">
<attribute name="rProt_id"/>
</element>
</choice>
<element name="gDNA_exon_coordinates">
<oneOrMore>
<element name="exon">
<attribute name="e_start">
<data type="integer"/>
</attribute>
<attribute name="e_stop">
<data type="integer"/>
</attribute>
</element>
</oneOrMore>
</element>
</element>
<element name="alignment">
<element name="genome_strand">
<text/>
</element>
<choice>
<element name="mrna_strand">
<text/>
</element>
<group>
<element name="genomeProt">
<text/>
</element>
<element name="queryProt">
<text/>
</element>
</group>
</choice>
</element>
<optional>
<element name="hqPGS_line">
<element name="hqgDNA">
<attribute name="gen_id"/>
<attribute name="gen_strand">
<choice>
<value>+</value>
<value>-</value>
</choice>
</attribute>
</element>
<choice>
<element name="hqrDNA">
<attribute name="rDNA_strand">
<choice>
<value>+</value>
<value>-</value>
</choice>
</attribute>
<attribute name="rDNA_id"/>
</element>
<element name="hqrProt">
<attribute name="rProt_id"/>
</element>
</choice>
<element name="hqgDNA_exon_coordinates">
<oneOrMore>
<element name="hqexon">
<attribute name="e_start">
<data type="integer"/>
</attribute>
<attribute name="e_stop">
<data type="integer"/>
</attribute>
</element>
</oneOrMore>
</element>
</element>
</optional>
</element>
</define>
<!-- ____________________________________________________________________________ -->
<define name="PGL_module-CONTENT"
ns="http://www.genomethreader.org/GTH_output/PGL_module/">
<oneOrMore>
<element name="predicted_gene_location">
<element name="PGL_line">
<attribute name="PGL_serial">
<data type="integer"/>
</attribute>
<attribute name="PGL_strand">
<choice>
<value>+</value>
<value>-</value>
</choice>
</attribute>
<attribute name="PGL_start">
<data type="integer"/>
</attribute>
<attribute name="PGL_stop">
<data type="integer"/>
</attribute>
</element>
<oneOrMore>
<element name="AGS_information">
<element name="AGS_line">
<attribute name="AGS_serial">
<data type="integer"/>
</attribute>
<element name="exon_coordinates">
<oneOrMore>
<element name="exon">
<attribute name="e_start">
<data type="integer"/>
</attribute>
<attribute name="e_stop">
<data type="integer"/>
</attribute>
</element>
</oneOrMore>
</element>
</element>
<element name="SCR_line">
<interleave>
<zeroOrMore>
<element name="exon-intron">
<attribute name="don_prob">
<data type="decimal"/>
</attribute>
<attribute name="acc_prob">
<data type="decimal"/>
</attribute>
<attribute name="e_score">
<data type="decimal"/>
</attribute>
</element>
</zeroOrMore>
<element name="exon-only">
<attribute name="e_score">
<data type="decimal"/>
</attribute>
</element>
</interleave>
</element>
<element name="exon-intron_info"
ns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/exon-intron_info/">
<interleave>
<oneOrMore>
<element name="exon">
<attribute name="e_serial">
<data type="integer"/>
</attribute>
<attribute name="e_score">
<data type="decimal"/>
</attribute>
<element name="gDNA_exon_boundary">
<attribute name="e_start">
<data type="integer"/>
</attribute>
<attribute name="e_stop">
<data type="integer"/>
</attribute>
<attribute name="e_length">
<data type="integer"/>
</attribute>
</element>
</element>
</oneOrMore>
<zeroOrMore>
<element name="intron">
<attribute name="i_serial">
<data type="integer"/>
</attribute>
<attribute name="don_prob">
<data type="decimal"/>
</attribute>
<attribute name="acc_prob">
<data type="decimal"/>
</attribute>
<element name="gDNA_intron_boundary">
<attribute name="i_start">
<data type="integer"/>
</attribute>
<attribute name="i_stop">
<data type="integer"/>
</attribute>
<attribute name="i_length">
<data type="integer"/>
</attribute>
</element>
</element>
</zeroOrMore>
</interleave>
</element>
<element name="supporting_evidence"
ns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/supporting_evidence/">
<oneOrMore>
<element name="PGS_line">
<element name="gDNA_exon_coordinates">
<oneOrMore>
<element name="exon">
<attribute name="start">
<data type="integer"/>
</attribute>
<attribute name="stop">
<data type="integer"/>
</attribute>
</element>
</oneOrMore>
</element>
<choice>
<element name="referenceDNA">
<attribute name="id"/>
<attribute name="strand">
<choice>
<value>+</value>
<value>-</value>
</choice>
</attribute>
</element>
<element name="referenceProtein">
<attribute name="id"/>
</element>
</choice>
</element>
</oneOrMore>
</element>
<oneOrMore>
<element name="three_phase_translation"
ns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/">
<element name="description">
<attribute name="PGL_serial">
<data type="integer"/>
</attribute>
<attribute name="AGS_serial">
<data type="integer"/>
</attribute>
<attribute name="gDNA_strand">
<choice>
<value>+</value>
<value>-</value>
</choice>
</attribute>
</element>
<element name="translation">
<element name="gDNA_template">
<text/>
</element>
<element name="first_frame">
<text/>
</element>
<element name="second_frame">
<text/>
</element>
<element name="third_frame">
<text/>
</element>
</element>
<element name="probable_ORFs"
ns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/probable_ORFs/">
<choice>
<oneOrMore>
<element name="orf_entry">
<element name="id_line">
<element name="gDNA">
<attribute name="id"/>
<attribute name="strand">
<choice>
<value>+</value>
<value>-</value>
</choice>
</attribute>
</element>
<element name="serials">
<attribute name="PGL_serial">
<data type="integer"/>
</attribute>
<attribute name="AGS_serial">
<data type="integer"/>
</attribute>
<attribute name="PPS_serial">
<data type="integer"/>
</attribute>
</element>
<element name="orf_info">
<element name="exon_boundaries">
<oneOrMore>
<element name="exon">
<attribute name="start">
<data type="integer"/>
</attribute>
<attribute name="stop">
<data type="integer"/>
</attribute>
</element>
</oneOrMore>
</element>
<element name="frame">
<choice>
<value>0</value>
<value>1</value>
<value>2</value>
</choice>
</element>
<element name="number_coding_nucleotides">
<data type="integer"/>
</element>
<element name="number_encoded_amino_acids">
<data type="integer"/>
</element>
</element>
</element>
<element name="predicted_protein_sequence">
<text/>
</element>
<zeroOrMore>
<!-- MetWAMer is a post-processing system that refines
translation start and stop sites of predicted
protein sequences. It is possible to append
multiple MetWAMer_annot elements, derived using
different prediction methods.
-->
<element name="MetWAMer_annot">
<attribute name="method"/>
<attribute name="orf_amino_bound">
<data type="integer"/>
</attribute>
<attribute name="start_codon">
<data type="integer"/>
</attribute>
<attribute name="stop_codon">
<data type="integer"/>
</attribute>
</element>
</zeroOrMore>
</element>
</oneOrMore>
<element name="none">
<optional>
<attribute name="gDNA_id"/>
</optional>
</element>
</choice>
</element>
</element>
</oneOrMore>
</element>
</oneOrMore>
</element>
</oneOrMore>
</define>
<!-- ____________________________________________________________________________ -->
</grammar>