<?xml version="1.0" encoding="UTF-8"?>
<transactions>
    <root>
    	<chado />
    </root>
    <preamble>
        <cv op="lookup" id="SOFA">
	    <name>sequence</name>
	</cv>
        <cv op="lookup" id="SO">
	    <name>sequence</name>
	</cv>
	<cv op="lookup" id="pub type">
	    <name>pub type</name>
	</cv>
	<cv op="lookup" id="property type">
	    <name>feature_property</name>
	</cv>
	<cv op="lookup" id="null">
	    <name>null</name>
	</cv>
	<cv op="lookup" id="relationship">
	    <name>relationship</name>
	</cv>
	<cvterm id="chromosome" op="lookup">
    	    <name>chromosome</name>
	    <cv_id>SOFA</cv_id>
        </cvterm>
	<cvterm op="lookup" id="gene">
	    <cv_id>SOFA</cv_id>
	    <name>gene</name>
	</cvterm>
	<cvterm op="lookup" id="transcript">
	    <cv_id>SOFA</cv_id>
	    <name>transcript</name>
	</cvterm>
	<cvterm op="lookup" id="exon">
	    <cv_id>SOFA</cv_id>
	    <name>exon</name>
	</cvterm>
	<cvterm op="lookup" id="mRNA">
	    <cv_id>SOFA</cv_id>
	    <name>mRNA</name>
	</cvterm>
	<cvterm op="lookup" id="transposable_element">
	    <cv_id>SOFA</cv_id>
	    <name>transposable_element</name>
	</cvterm>	
	<cvterm op="lookup" id="tRNA">
	    <cv_id>SOFA</cv_id>
	    <name>tRNA</name>
	</cvterm>	
	<cvterm op="lookup" id="snRNA">
	    <cv_id>SOFA</cv_id>
	    <name>snRNA</name>
	</cvterm>
	<cvterm op="lookup" id="snoRNA">
	    <cv_id>SOFA</cv_id>
	    <name>snoRNA</name>
	</cvterm>
	<cvterm op="lookup" id="ncRNA">
	    <cv_id>SOFA</cv_id>
	    <name>ncRNA</name>
	</cvterm>
	<cvterm op="lookup" id="rRNA">
	    <cv_id>SOFA</cv_id>
	    <name>rRNA</name>
	</cvterm>	
	<cvterm op="lookup" id="miRNA">
	    <cv_id>SOFA</cv_id>
	    <name>miRNA</name>
	</cvterm>
	<cvterm op="lookup" id="pseudogene">
	    <cv_id>SOFA</cv_id>
	    <name>pseudogene</name>
	</cvterm>	
	<cvterm op="lookup" id="remark">
	    <cv_id>SOFA</cv_id>
	    <name>remark</name>
	</cvterm>	
	<cvterm op="lookup" id="promoter">
	    <cv_id>SOFA</cv_id>
	    <name>promoter</name>
	</cvterm>	
	<cvterm op="lookup" id="insertion_site">
	    <cv_id>SOFA</cv_id>
	    <name>insertion_site</name>
	</cvterm>											
	<cvterm op="lookup" id="repeat_region">
	    <cv_id>SOFA</cv_id>
	    <name>repeat_region</name>
	</cvterm>												
	<cvterm op="lookup" id="protein">
	    <cv_id>SO</cv_id>
	    <name>protein</name>
	</cvterm>
	<cvterm op="lookup" id="curator">
	    <cv_id>pub type</cv_id>
	    <name>curator</name>
	</cvterm>
	<cvterm op="lookup" id="synonym">
	    <cv_id>null</cv_id>
	    <name>synonym</name>
	</cvterm>
	<cvterm op="lookup" id="partof">
	    <cv_id>relationship</cv_id>
	    <name>part_of</name>
	</cvterm>
	<cvterm op="force" id="producedby">
	    <cv_id>relationship</cv_id>
	    <name>derives_from</name>
	</cvterm>
	<cvterm op="lookup" id="problem">
	    <cv_id>property type</cv_id>
	    <name>problem</name>
	</cvterm>
	<cvterm op="lookup" id="dicistronic">
	    <cv_id>property type</cv_id>
	    <name>dicistronic</name>
	</cvterm>
	<cvterm op="lookup" id="owner">
	    <cv_id>property type</cv_id>
	    <name>owner</name>
	</cvterm>
        <cvterm op="lookup" id="comment">
	    <cv_id>property type</cv_id>
	    <name>comment</name>
	</cvterm>
	<cvterm op="lookup" id="date">
	    <cv_id>property type</cv_id>
	    <name>date</name>
	</cvterm>
	<cvterm op="lookup" id="status">
	    <cv_id>property type</cv_id>
	    <name>status</name>
	</cvterm>	
	<!-- The following property names are not in the flybase. It has to either
	     add or don't output from Apollo. Or force them into the database.
	 -->
	<cvterm op="lookup" id="non_canonical_splice_site">
	    <cv_id>SO</cv_id>
	    <name>non_canonical_splice_site</name>
	</cvterm>
	<cvterm op="lookup" id="non_canonical_start_codon">
	    <cv_id>SO</cv_id>
	    <name>non_canonical_start_codon</name>
	</cvterm>		
	<cvterm op="force" id="finished">
	    <cv_id>property type</cv_id>
	    <name>finished</name>
	</cvterm>
	<cvterm op="force" id="missing_start_codon">
	    <cv_id>property type</cv_id>
	    <name>missing_start_codon</name>
	</cvterm>
	<cvterm op="force" id="missing_stop_codon">
	    <cv_id>property type</cv_id>
	    <name>missing_stop_codon</name>
	</cvterm>		
<!--	<organism op="lookup" id="organism">
	    <genus>Oryza</genus>
	    <species>sativa</species>
	</organism>-->
	<organism op="lookup" id="organism">
            <genus>Dictyostelium</genus>
            <species>discoideum</species>
        </organism>
	<db op="lookup" id="DB:null">
	    <name>null</name>
	</db>
	<db op="lookup" id="DB:GR">
	    <name>DB:GR</name>
	</db>
    </preamble>
    <!-- A list of defaul values -->
    <default>
    	<parameter name="$organism" value="organism" />
    </default>
    <!-- This list of definitions are actually the table definitions in the chado database. 
         Right now it is hard coded in apollo.dataadapter.chado.ChadoTransaction and its subclasses. 
	 There should be a way to automatic generate these xml elements based on these templates. 
	 However, it is a little difficult for update. -->
    <definition>
        <featureloc>
	    <feature_id>$feature_id</feature_id>
	    <srcfeature_id>$parentID</srcfeature_id>
	    <fmin>$start</fmin>
	    <fmax>$end</fmax>
	    <strand>$phase</strand>
	</featureloc>
	<feature_relationship>
	    <subject_id>$subject_id</subject_id>
	    <object_id>$object_id</object_id>
	    <type_id>$type_id</type_id>
	    <value>$value</value>
	</feature_relationship>
	<feature>
	    <name>$name</name>
	    <uniquename>$id</uniquename>
	    <organism_id>$organism</organism_id>
	    <type_id>$type</type_id>
	    <seqlen>$seqlen</seqlen>
	    <!-- This is optional. It used only for peptides -->
	    <residues>$residues</residues>
	</feature>
	<dbxref>
	    <accession>$accession</accession>
	    <db_id>$db</db_id>
	</dbxref>	
	<featureprop>
	    <feature_id>$feature_id</feature_id>
	    <type_id>$typename</type_id>
	    <value>$value</value>
	    <rank>$rank</rank>
	</featureprop>
	<synonym>
	    <name>$synonym</name>
            <!-- What is this for? -->
            <synonym_sgml>$synonym_sgml</synonym_sgml>
            <!-- Can it be other types? -->
	    <!-- In the current flybase@brebior, there is no other type -->
            <type_id>synonym</type_id>
        </synonym>	
	<feature_synonym>
	    <feature_id>$feature_id</feature_id>
	    <is_internal>0</is_internal>
            <synonym_id>$synonym_id</synonym_id>
	    <!-- name for assign synonym -->
	    <!-- Have to specify a pub_id SOFAmewher? -->
            <pub_id>$pub_id</pub_id>
            <is_current>1</is_current>	    
	</feature_synonym>	
	<pub>
	    <uniquename>$uniquename</uniquename>
	    <type_id>$type_id</type_id>
	</pub>	
     </definition>
</transactions>