2.2.4 Data format

The data format which is used in VAMP is XML (eXtensive Markup Language). Two types of XML file are necessary to run VAMP:

• Array files which contain the information related to a molecular profile: for each experiment there is a file which stores both array-level information (e.g. patient ID, number of clone, date of experiment, ...) and clone-level information (e.g. clone name, ratio value, chromosome number, location, ...). The Array files are organized according to the following hierarchy: team $\rightarrow$ projects $\rightarrow$ Array files. Each team may contain several projects and each project may contain several array files.
• the Import file which contains the list of projects and arrays that can be loaded within the VAMP, as described in section 3.2.1

VAMP distribution provides two scripts that generate these XML files automatically, as described in section 2.2.4:

vampTxt2xml

generates Array XML files from CSV (comma separated values) files.

Files are available from the Download :

vampTxt2xml:

http://bioinfo-out.curie.fr/vamp/doc/script/vamp_txt2xml

Array XML files:

http://bioinfo-out.curie.fr/vamp/doc/data/xml/douglas/Cancer3.xml

CSV files:

http://bioinfo-out.curie.fr/vamp/doc/data/txt/douglas/Cancer3.csv

The xml data file need to be copied into the root directory defined in the tag:

$<$Parameter key="importData:baseURL" value="file:///yourRootDirectory/"$>$ as described in configuration file syscfg.xml, section 2.2.3.

vampProject2import

creates an Import XML file from the Array files belonging to a given directory.

Files are available from the Download :

vampProject2import:

http://bioinfo-out.curie.fr/vamp/doc/script/vampProject2import

Import XML file:

http://bioinfo-out.curie.fr/vamp/doc/data/import_data_public_xml/public.xml

In case you need to generate your Array files without using these scripts, subsection 2.2.4 provides a detailed description of corresponding XML tags.