<?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>