Category Archives: project

SIFR project Ontology and web semantic

The SIFR project investigate the scientific and technical challenges in building ontology-based services to leverage biomedical ontologies.

My work is on the the annotators web service which purpose it to:

  1. Provide a unique access point to several server running the ontology annotators developed by the NCBO, such as their bioportal.bioontology.org/annotator.
  2. Wrap new functionalities around these annotators. In particular I work on adding RDF output format and the annotation scoring methods which have been published in

XData project Data integration on hadoop cluster

The XData project is a french collaborative project between industrials, startups as well as big companies, and academics. Its main objective is to develop innovative  commercial product constructed from the integration of private data with open data.

I mostly work on the xdata “movement analytics” application. More specifically on:

  1. The data integration of the movement data type: any type of data that represent people movement such as housing or companies moving, as well as tourist displacement. The integration is done in two main parts: first a generalized data structure cas defined with a generic data descriptor to allow importing any data set containing movement data ; second an automated data query algorithm has been defined to select suitable movement entry with respect to geographical and temporal area and granularity.
  2. The transfer of the stand alone prototype of the web application, which use mysql and spring technologies, on the hadoop cluster of the xdata project, in particular using spark and hive.

RSML The language of root architecture

With several of the main actors in root system measurement and analysis, we have develop the RSML file format. It allows to store 2D or 3D image metadata, plant and root properties and geometries, continuous functions along individual root paths and a suite of annotations at the image, plant or root scales, at one or several time points. The plant ontologies are used to describe botanical entities that are relevant at the scale of root system architecture.

Go to the RSML web site

Rhizoscan High-throughput Root System Architecture extraciton from images

The RhizoScan is a project, founded by Rhizopolis and Numev, to develop image and graph analysis technologies to automatically process image of root systems and extract their architecture.

See the RhizoScan python package.

Poster at the 7th internation conference on Functional-Structural Plant Model
Poster at the CSHL meeting: Automated Imaging and High Throughput Phenotyping