MetaXP/Specification

MetaXP Specification

Introduction

MetaXP is a search facility for expression data. It enables the user to quickly access experiments and their results by formulating queries such as "Give me all temperature-related stress experiments containing gene XY" or "Give me a list of all up-regulated genes in experiments on Xanthomonas campestris". MetaXP combines data from EMMA, GenDB and ProDB. The data is imported from each of these databases and processed for searchability.

Search Interface

Possible search results are lists of genes and experiments. Possible search parameters are (c.f. fig. 1):

• the organism
• experiment design and description
• status of the regulation of genes (e.g. up or down regulated, same regulation level)
• if there is a specific value for the expression level stated, the user should be able to search for a range of these values.

All these search parameter can set to a wildcard (i.e. have no influence on the search; default) and can be combined with the operations “and” and “but not”. Also the search system should be extendable to accommodate additional combinations of search parameters.

Implementation Details

The object-model will be created with the O2DBI system. The search facility will be created as an additional layer on top of these classes. In order to simplify the implementation of the graphical user interface (GUI) the search layer will have an introspection mechanism that provides the GUI with information on what can be searched for, what search parameter can entered and how these search parameters can be combined.

Schedule

• The main aim is to have a running prototype early next year (Jan 2005).
• A coarse list of milestones for such a prototype would be:
  • Project setup (i.e. requesting GPMS project, setting up database).
  • Implementation of an import prototype for EMMA (which will require refinements in the object-model). This includes an evaluation and definition of required information for an import.
  • Implementation of a search layer and search user interface. The search layer will need several controlled vocabularies. These will be implemented in simple text files (CSV or RDF).
• This prototype is then shown to Biologists to evaluate the usability of the user interface and to find missing features
• The milestones of the main tool are then:
  • Implementation of requests of the Biology experts
  • Refinements of the EMMA import facility and implementation of a GenDB and ProDB import facility.
  • Optimisation of the search layer and implementation of a database for the controlled vocabularies.