ProgenetiXML is the custom XML format for storing and distributing oncogenomic data from (a)CGH experiments, and associated clinical information. It is limited to the "best case" data available from publications, and not equipped for clinical data management (no implementation of patient criteria, besides blinded clinical parameters).

<?xml version="1.0" encoding="ISO-8859-1" standalone='yes'?>
<!DOCTYPE PROGENETIXCASESET [

<!ELEMENT PROGENETIXCASESET (EXPORTDAY, PROGENETIXCASE\+)>
<!-- PROGENETIXCASESET is the root level element -->

	<!ELEMENT EXPORTDAY (#PCDATA)>
	<!-- EXPORTDAY is usually generated by the parser; purely informative -->

	<!ELEMENT PROGENETIXCASE (CASEID, MITELMANEXPERIMENT?, KARYO_CGH?, KARYO_ACGH?, KARYO_BANDING?, TECHNIQUE?, DIAGNOSIS, ICDO3?, LOCCODE?, PUBMED?, ICDO3TEXT?, LOCTEXT?, CLINICALGROUP?, GPANNOTATION, SORTNOTE?, INSUBSETS?, CLINICAL)>
	<!-- instances of PROGENETIXCASE contain all case specific data -->

		<!ELEMENT CASEID (#PCDATA)>
		<!-- unique case identifier -->

		<!ELEMENT MITELMANEXPERIMENT (#PCDATA)>
		<!--
		### deprecated ###
		was used internally for linking banding cases to the Mitelman database 
		-->

		<!ELEMENT KARYO_CGH (#PCDATA)>
		<!-- ish cgh ISCN annotation of chromosomal CGH data -->

		<!ELEMENT GP_CGH (#PCDATA)>
		<!--
		Golden Path specific status information; produced by Progenetix parser from the ISCN style
		annotation. Example:
		"chr6:0-30000000:1::chr8:0-45200000:-1::chr8:45200000-146274826:1::"
		-->

		<!ELEMENT KARYO_ACGH (#PCDATA)>
		<!-- ish cgh ISCN annotation of array CGH data -->

		<!ELEMENT GP_ACGH (#PCDATA)>
		<!--
		Golden Path specific status information; either directly from the GP based original data 
		(segments file, output of log2 data analysis) , or secondary as produced by Progenetix 
		parser from original ISCN annotation. This is determined by the value of the DATATYPE field.
		-->

		<!ELEMENT KARYO_BANDING (#PCDATA)>
		<!-- ISCN annotation of metaphase banding / MFISH / SKY / composite data -->

		<!ELEMENT GP_BANDING (#PCDATA)>
		<!--
		Golden Path specific status information; produced by Progenetix parser from the ISCN style
		annotation. Example:
		"chr6:0-30000000:1::chr8:0-45200000:-1::chr8:45200000-146274826:1::"
		-->

		<!ELEMENT TECHNIQUE (#PCDATA)>
		<!--
		comma separated; possible values are "CGH", "aCGH", "banding", "MFISH", "SKY"
		KARYO data is interpreted independent of these values, but wrong annotation may lead to
		exclusion from online analysis steps etc.
		-->

		<!ELEMENT DATATYPE (#PCDATA)>
		<!-- to distinguish original ISCN annotation from array derived Golden Path intervals;
		this determines which aCGH information is used for downstream functions -->

		<!ELEMENT DIAGNOSIS (#PCDATA)>
		<!-- free text, e.g. "neuroblastoma, infant" -->

		<!ELEMENT ICDO3 (#PCDATA)>
		<!-- ICD-O-3 code, e.g. "9500/3" -->

		<!ELEMENT LOCCODE (#PCDATA)>
		<!-- ICD locus code, e.g. "C47" -->

		<!ELEMENT PUBMED (#PCDATA)>
		<!-- PMID -->

		<!ELEMENT ICDO3TEXT (#PCDATA)>
		<!--
		reference ICD-O-3 text, e.g. "Neuroblastoma, NOS"
		for reference, you may use the Progenetix site
		-->

		<!ELEMENT LOCTEXT (#PCDATA)>
		<!--
		reference ICD locus text, e.g. "peripheral nervs incl. autonomous"
		for reference, you may use the Progenetix site
		-->

		<!ELEMENT CLINICALGROUP (#PCDATA)>
		<!--
		a synthetic diagnostic group, e.g. derived from ICD codes of related entities
		example: "Ca.: breast ca." will be derived from cases with epithelial NPL ICD code and the 
		locus "breast"
		this is not yet defined for all disease categories
		-->

		<!ELEMENT SORTNOTE (#PCDATA)>
		<!-- for a unique label -->

		<!ELEMENT INSUBSETS (#PCDATA)>
		<!-- for multiple, comma-separated tags -->

		<!ELEMENT CLINICAL (AGE?, GENDER?, TNM?, GRADE?, STAGE?, LNPOS?, METAST?, RECURR?, TRECURR?, DEATH?, FOLLOWUP?)>
		<!-- 
		wrapper element for clinical data
		please use "NA" for unknown content, or leave empty
		-->

			<!ELEMENT AGE (#PCDATA)>
			<!-- in years -->

			<!ELEMENT GENDER (#PCDATA)>
			<!-- male or female -->

			<!ELEMENT TNM (#PCDATA)>
			<!-- partial are recognized, e.g. "T2N1" or "N0" -->

			<!ELEMENT GRADE (#PCDATA)>
			<!-- "II" etc. or "2" etc. -->

			<!ELEMENT STAGE (#PCDATA)>
			<!-- "II" etc. or "2" etc. -->

			<!ELEMENT LNPOS (#PCDATA)>
			<!-- "0" or "1" -->

			<!ELEMENT METAST (#PCDATA)>
			<!-- "0" or "1" -->

			<!ELEMENT RECURR (#PCDATA)>
			<!-- "0" or "1" -->

			<!ELEMENT TRECURR (#PCDATA)>
			<!-- time in months -->

			<!ELEMENT DEATH (#PCDATA)>
			<!-- "0" = alive or "1" = dead -->

			<!ELEMENT FOLLOWUP (#PCDATA)>
			<!-- time in months -->

]>
<PROGENETIXCASESET>
	<EXPORTDAY>2009-09-29</EXPORTDAY>
	<PROGENETIXCASE>
		<CASEID>OlfNB-gul-05</CASEID>
		<KARYO_CGH/>
		<GP_CGH/>
		<KARYO_ACGH>ish cgh enh(1p35.2p35.3, 1p36.11, 3p22.3, 3q26.2, 4q27, 9p24.3, 11p15.5, 11q13.1, 12q24.31, 13q34, 19p13.2)  dim(1p36.11, 3p21.31, 3q26.2, 12q14.3, 18q12.2q12.3)</KARYO_ACGH>
		<GP_ACGH>::chr1:23800000-27799999:-1::chr1:23800000-32199999:1::chr11:0-2799999:1::chr11:63100000-67099999:1::chr12:63400000-65999999:-1::chr12:119100000-124499999:1::chr13:109100000-114142980:1::chr18:31000000-41799999:-1::chr19:6900000-12599999:1::chr3:32100000-36499999:1::chr3:44700000-51399999:-1::chr3:169200000-172499999:-1::chr3:169200000-172499999:1::chr4:120600000-123999999:1::chr9:0-2199999:1</GP_ACGH>
		<TECHNIQUE>aCGH</TECHNIQUE>
		<DATATYPE>ISCN</DATATYPE>
		<DIAGNOSIS>Olfactory neuroblastoma</DIAGNOSIS>
		<ICDO3>9522/3</ICDO3>
		<LOCCODE>C729</LOCCODE>
		<PMID>18408657</PMID>
		<ICDO3TEXT>Olfactory neuroblastoma</ICDO3TEXT>
		<LOCTEXT>Nervous system, NOS</LOCTEXT>
		<CLINICALGROUP>CNS: neuroblastic</CLINICALGROUP>
		<GPANNOTATION/>
		<INSUBSETS>Progenetix_collection</INSUBSETS>
		<CLINICAL>
			<AGE>40</AGE>
			<GENDER>female</GENDER>
			<STAGE>II</STAGE>
			<DEATH>0</DEATH>
			<FOLLOWUP>149</FOLLOWUP>
		</CLINICAL>
	</PROGENETIXCASE>
</PROGENETIXCASESET>