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<?xml version="1.0" encoding="UTF-8"?>
<?oxygen RNGSchema="file:../cafe_variome.rnc" type="compact"?>
<!--
http://www.cafevariome.org/docs/cafevariome_tab_delimited.txt
-->
<cafe_variome xmlns="http://varioml.org/xml/1.0" >
<source id="Laboratory ID" >
<name>leicester_lab</name>
<url>http://www.le.ac.uk/genetics</url>
<contact>
<name>Author Name</name>
<email>ol8@leicester.ac.uk</email>
<db_xref source="orcid" accession="122323"/>
</contact>
</source>
<!-- Variant
id = local unique ID for variant observation
type = reference template used for naming the variant (DNA, RNA and AA)
copy_count = number of observed copies. 1 = one autosomal sister chromosome (or one male nonautosomal X/Y), 2 = both autosomal sister chromosomes.
-->
<variant type="DNA" id="Variant ID" copy_count="1">
<gene source="HGNC" accession="COL1A1"/>
<ref_seq accession="NG_007400.1"/>
<name scheme="HGVS">c.579delT</name>
<!-- observation target (has optional type attribute with values: family, population and individual
This is an abstraction which can be something between individual, group of individuals or a population sample.
-->
<panel>
<!-- optional list of actual subjects/individuals who are part of the panel-->
<individual>
<gender code="1"/>
<!-- anonymized local subject id -->
<original_id accession="abcde123567"/>
<role term="Index case"/> <!-- role of subject -->
</individual>
<!-- Population and phenotype characteristics which are common to all panel members.
We give the information here and not as properties of individual to avoid unnecessary nesting and repetition.
Individual level information can be given also, but it is not yet agreed on: -->
<phenotype term="Osteogenesis imperfecta"/><!-- note that the phenotype(s) given here is not necessary consequence of the variant-->
<population type="ethnic" term="japanise"/><!-- there can be also more than one populations terms with types like race, region...-->
</panel>
<!-- Explicit causal relationship between variant and phenotype can be given here (optional).
In this example we are using terms defined in LOVD (thus the source of them is LOVD)
There can be more than one pathogenicity entries.
-->
<pathogenicity source="LOVD" term="pathogenic">
<phenotype term="Osteogenesis imperfecta"/>
<!-- optional evidence code. Term is from ECO evidence ontology -->
<evidence_code term="curator inference" accession=”ECO:0000205” source="obo.eco"/>
</pathogenicity>
<!-- optional detection method(s) are listed here: -->
<variant_detection technique="sequencing" template="DNA"/>
<genetic_origin term="paternal"> <!--somatic, maternal, de novo, de novo on paternal allele, parent #1 or #2 (phase) -->
<evidence_code term="inferred"/><!-- values like inferred, confirmed (or some ECO terms)-->
</genetic_origin>
<!-- optional location on chrmosome sequence. E.g.
http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/data/index.shtml -->
<location>
<!-- ref_seq is DBXref.. all attributes of DbXRefs are given here as an example -->
<ref_seq accession="NC_000017.10" source="GRC" name="GRCh37:17">
<!-- <db_xref accession="CM000679.1" source="genbank"/> DBXRefs can have also aliases, but these can be omitted in CV-->
</ref_seq>
<chr>17</chr>
<start>11111</start>
<end>11111</end>
</location>
<sharing_policy type="openAccess">
<embargo_end_date>2002-12-12</embargo_end_date>
<use_permission accession="CC0" uri="http://creativecommons.org/publicdomain/zero/1.0/"
term="Creative commons"/>
</sharing_policy>
<!--publications as list of dbxrefs -->
<db_xref source="pubmed" accession="12345"/>
<db_xref source="doi" accession="ISSTA.2002.1048560" uri="http://dx.doi.org/10.1109/ISSTA.2002.1048560"/>
<comment>
<text>Variant inherited from affected father</text>
</comment>
</variant>
</cafe_variome>