The goal of the LabKey Server Experiment framework is to facilitate the recording, comparison, and transfer of annotated experimental data. With the xar.xml and its structure of basic objects, it attempts to answer the how and where of experimental annotations. In the near term, the LabKey Server system will evolve to better address the who and why of experimental annotations. For example, xar.xml authoring tools will make it easier for researchers to describe their experiments, and for bioinformatics experts to specify experimental attributes that they deem useful to their analyses. Tools for collecting annotation values based on the protocol specification may help lab technicians ensure the results of a run are fully described. LabKey Server already provides some answers to why annotations are worth the effort with the graphical Experiment Navigator view and the ability to tie sample data to MS2 results. The value of annotations will become much clearer as LabKey Server adds the ability to filter, sort and compare results based on annotation values.

The framework, however, does not attempt to settle the what of experimental annotations. A xar.xml can record and transfer any type of annotation, including

• Custom properties defined by an individual researcher
• Properties described in a shared vocabulary (also known as an ontology)
• Complete, structured, standardized descriptions of experiments

The Functional Genomics Experiment (FuGE) project addresses this third and most thorough description of an experiment. The FuGE object model is designed to be the foundation for developing standard experiment descriptions in specific functional areas such as flow cytometry or gel fractionation. FuGE-based experiment descriptions will be contained in Xml documents that are based on schemas generated from the object model. (More details on FuGE can be found at http://fuge.sourceforge.net).

The xar.xml format is not an implementation of FuGE, but is designed to be compatible with the FuGE model as it emerges. This compatibility cuts across multiple features:

• Many of the basic terms and concepts in the LabKey SErver framework are borrowed from the FuGE model. In particular, the base Material, Data, Protocol and ProtocolApplication objects have essentially the same roles and relationships in xar.xml and in FuGE.
• Like FuGE, objects in a xar.xml are identified by Life Sciences Identifiers (LSIDs).
• The ontology-defined annotations (properties) are compatible and could be attached to objects in either framework

As LabKey Server users begin to adopt FuGE-based standard experiment descriptions, FuGE instance documents could be incorporated into a xar file and referenced by the xar.xml manifest in the same way other standard xml documents such as mzXML files are incorporated. The LabKey Server data loader would then ensure that the FuGE description documents are saved with the experimental data. Moreover, the user should be able to select specific attributes described in the FuGE document and make them visible and selectable in LabKey Server queries in the same way that attributes described directly in the xar.xml format are available.