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<?xml version="1.0" encoding="UTF-8"?>
<?oxygen RNGSchema="file:../cafe_variome.rnc" type="compact"?>
<?xml-model href="../cafe_variome_validator.sch" type="application/xml" schematypens="http://purl.oclc.org/dsdl/schematron"?>
<cafe_variome xmlns="http://varioml.org/xml/1.0">
<source id="sourceid0001" uri="http://alamut.com">
<name>Alamut Database</name>
<contact>
<name>Contact person..</name>
</contact>
</source>
<!-- EXAMPLE 1 -->
<variant id="{5a4a5af9-693c-4771-a6ad-2cd2d851e7fe}" type="DNA"> <!-- version number should be given as a suffix?-->
<gene source="hgnc.symbol" accession="COL1A1"/> <!-- symbols used. HGNC-ID for id numbers (not agreed yet) -->
<ref_seq source="refseq" accession="NC_000017.10"/> <!-- standard accession number for chromosome sequences ?-->
<name scheme="HGVS">g.48270186_48270188del</name>
<!-- panels and panel members having the variant: -->
<panel type="family" id="1">
<individual id="1">
</individual>
<!-- properties which are common to all panel members (individuals) are given here-->
<organism term="homo sapiens"/>
</panel>
<variant_type source="obo.so" accession="SO:0000159" term="deletion"/>
<!-- we can have more than one pathogenicity statements. Statement can have reference to a panel it is based on
-->
<pathogenicity term="Non-pathogenic" panel_ref="1"> <!-- terms are not yet standardized -->
<phenotype source="omim" accession="166210" term="osteogenesis imperfecta, type-1"/>
<comment><text content_type="text/html"><![CDATA[HTML TEXT HERE]]></text></comment>
</pathogenicity>
<seq_changes><!-- sequence consequences -->
<variant type="AA">
<ref_seq accession="NM_000088.3"/>
<name scheme="HGVS">p.Glu615_Ala616delinsAsp</name>
</variant>
</seq_changes>
<aliases> <!-- We give name on coding DNA reference here: -->
<variant type="DNA">
<ref_seq accession="NM_000088.3"/>
<name scheme="HGVS">c.1845_1847del</name>
</variant>
</aliases>
<!-- explicit location (optional)-->
<location>
<ref_seq source="refseq" accession="NC_000017.10"/>
<start>48270186</start>
<end>48270188</end>
</location>
<sharing_policy type="openAccess" />
<protocol_id accession="CMGS_VGKL_5"/> <!-- check this. what is classification index ? -->
</variant>
<!-- EXAMPLE 2 -->
<variant id="{09b3d78f-39c7-42e0-b5a1-9894e28d69f0}" type="DNA">
<gene source="hgnc.symbl" accession="COL1A1"/>
<ref_seq source="refseq" accession="NC_000017.10"/>
<name scheme="HGVS">g.48270179_48270180del</name>
<panel><organism term="homo sapiens"/></panel>
<!-- http://www.sequenceontology.org/miso/current_release/term/SO:0001059 -->
<variant_type source="obo.so" accession="SO:0000159" term="deletion"/>
<pathogenicity term="Non-pathogenic">
<phenotype source="OMIM" accession="166210" term="osteogenesis imperfecta, type-1"/>
</pathogenicity>
<seq_changes>
<variant type="AA">
<ref_seq accession="NM_000088.3"/>
<name scheme="HGVS">p.Gln619GlyfsX14</name>
</variant>
</seq_changes>
<aliases>
<variant type="DNA">
<ref_seq accession="NM_000088.3"/>
<name scheme="HGVS">c.1853_1854del</name>
</variant>
</aliases>
<sharing_policy type="openAccess" />
<protocol_id accession="CMGS_VGKL_5"/>
</variant>
</cafe_variome>