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BIOMIST : BIO Medical research Imaging SemanTic data management 

ANR CONTINT 2013 - n° ANR-13-CORD-0007 


Poster Image

One year from the beginning of the project we have the following results:

  • The internal communication tools (backlog management, document sharing, teleconference, source code management, continuous integration platform…) and external communication (web site) have been deployed.
  • The consortium agreement is being signed.
  • A first set of requirements on the general process have been collected, refined and analyzed concerning image acquisition, study & subject definition, processing, scientific papers…
  • The technical architecture of the project: computers, licenses, OS,.. have been acquired and deployed.
  • The data model has been designed by comparison with existing models: GIN data model, XNAT, OntoNeuroLOG …
  • Technical workflows has been defined: acquisition, storage, links with computing grids.
  • Processing workflows are being tested.
  • Data migration and alignment to the new model from the existing GIN database is done.
  • Relations have been established with the projects Codde (ANR-13-CORD-0017), NeuroLOG (ANR-06-TLOG-024), i-Share (
  • Several software development frameworks for graph representation have been tried (Gephi, Cytoscape, Tulip), however the graph data model used is not comprehensive enough for our needs. We have then developed our own graph representation that may be adapted in order to be compatible with the Gexf format (understood by existing frameworks), this representation allows us to define multi-dimensional and multivariate configurable graphs. The tools for manipulation and presentation of this representation are being developed.
  • User interface for acquisition and request definition integrated with the PLM software are being developed.
  • Four scientific papers have been accepted (see publications section)


This first year has been dedicated to the deployment of the fundamental needs for the project : deployment of the technical infrastructure, integration of the image processing workflows, definition and deployment of the PLM tool, its data model and classifications, requirement acquisition and analysis, and definition of the basic user interfaces. Currently, the main obstacle to general usage is that the user interface is too “technical”.

The definition of a user interface unifying in a same paradigm the presentation and manipulation of the complex set of data representation that is used throughout the main process of a neurofunctional study is the main objective of the second year of the project.

The objective for the end of the project is to validate all the concepts and tools developed by taking part in an actual study where the acquired data will used in parallel between the Biomist architecture and process and the existing process and comparing the usability and performance of both systems.