Welcome to the XEML project page.

This project aims to realize a standard for the control and documentation of experimental design and growth, with a maximum of power in terms of data processing, not only to obtain reliable molecular and physiological data, but also to make plant growth metadata of amenable for studies in integrative biology. The project consists of two parts and related projects:

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 simple solution with custom annotations works as a stop-gap.

The framework:
XEML is not just a documentation language; the XEML-framework
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. The designer will be also hosted at CodePlex in the near future.
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).