This project is read-only.

Welcome to the XEML project page.

This project aims to document biological experiments with a maximum power in terms of data processing, not only to obtain reliable molecular and physiological data, but also to make metadata amenable for integrative studies.
Main user interface of the XEML Interactive Designer. The main window visualises the time course of a physiological experiment with the relevant experimental interventions and changes in environmental conditions through to sampling for subsequent (metabolite profile) analyses. The left pane displays the available ontologies and their terms along with the possible values, eg. Quantitiy = abolute values​​, Response Range = relative values​​, or Free Text = free text (lower window).

The language:
The eXtensible Experiment Markup Language (XEML) is a XML dialect. The language provides a flexible way to formulate experimental setups, encompassing information about environmental parameters in a continuous timeline, individual germplasm information, sampling structure and handling from specified plant material, sample data mapping to heterogeneous databases and general annotations. This requires the integration of different ontologies/vocabulary. For environmental parameters we developed a new controlled vocabulary to best capture the environmental conditions. The different plant organs are already well covered by the plant ontology which can thus be easily used with XEML. For germplasm the decision is still open, but a currently a simple solution with custom annotations works as a stop-gap.

The XEML framework:
XEML is not just a documentation language;
the XEML-framework provides the support for creation, editing and validation of XEML files, as well as the integration of different ontologies/vocabulary and heterogeneous databases in a modular way. Therefore, the framework forms the base for further tool development which benefits from the structured metadata.

Related tools:
XiD – The Xeml Interactive Designer provides a rich user interface for timeline visualization and intuitive data creation/editing of well formatted files.
SampleCompiler - The framework implements a data provider infrastructure. The sample compiler takes advantages of this to bring together metadata and analyte data from different data sources (e.g. enzymes, metabolites, transcripts) in useabe table format for other analysis software (e.g. R, MatLab, Excel).
A friendly ClickOnce installation of the Xeml Interactive Designer can be found here:
Your feedback is welcome!

Last edited Apr 29, 2014 at 11:55 AM by drjahu, version 17