Ontrez and BioPortal

Within the National Center for Biomedical Ontology project we are developing a Web application called BioPortal to access biomedical ontologies. This library contains a large collection of ontologies in biomedicine in different format (OBO, OWL etc.) such as NCI Thesaurus, ICD, FMA. Users can browse and search this repository of ontologies both online and via a Web services API.

One of the goals of the NCBO (the Open Biomedical Ontologies (OBO) core) is to provide the bio medical researchers community with a set of ontology based services and allow these users to develop their activities directly using these services (ontologies view, search, versioning, mapping, etc.).

Another important goal of NCBO (the Open Biomedical Data (OBD) core) is to leverage the use of these biomedical ontologies by providing users with a set of data and information related to these ontologies: to use the high level and structured knowledge representation that ontologies represent to construct a database of relevant biomedical experimental data resources content that have been annotated with biomedical ontology concepts ( ontology based annotation).

Within this activity, we (with Dr. Nigam Shah, MD, PhD) conceptualize, develop and experiment a tool named “Ontrez” which consists in using ontologies to find relevant experimental data and information related to a specific concept. The Ontrez pipeline, automatically annotates (using a concept recognition tool) elements coming from different public online biomedical resources and use ontologies semantics to expanse the annotations. Resources are for example Gene Expression Omnibus, Array Express, ClinicalTrials.gov or PubMed. We currently use a dictionary that contains both ontologies and terminologies from BioPortal and UMLS. The classic use case for Ontrez is: a user searching or browsing an ontology in BioPortal will get for a given ontology term all the resources elements that have been annotated with this term and which represent a potential relevant information for him/her (cf. image).

Soon a web page on NCBO web site will describe Ontrez. Here you can find a first NCBO internal research report that present the Ontrez project.

Dynamic Service Generation - PhD thesis research work

I worked at the crossing of 3 domains: Service-Oriented Computing (Web service, components, business process, etc.), Multi-Agents Systems (modelling, interaction, architecture) and GRID (resources sharing, Grid service, Grid computing). I propose in my thesis an alternative vision of the concept of service based on agent (human or artificial) conversations through Grid infrastructure. This is called Dynamic Service Generation (DSG).

I have proposed an agent communication and representation model, called STROBE, which addresses several aspects of DSG.

In particular, I was interested in the agent-Grid integration. I have proposed a GRID-MAS integrated model formalized with a description language called the Agent-Grid Integration Language (AGIL).

I have defended (November 16, 2006) my PhD at University Montpellier 2 within the doctoral school Information, Structures, Systèmes. I had a MENRT fellowship since 3 years and my supervisor was Pr. Stefano A. Cerri.

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Grid services based collaborative environment

Within the context of the ELeGI project I worked on a collaborative environment construct over a Grid infrastructure called the Grid Shared Desktop (GSD). The GSD is Web-accessible environment that provides members of a virtual community with a set of desktops supporting collaboration in both synchronous and asynchronous mode. The GSD is a powerful interface relying on Grid service architecture to communicate user representations and build collaborative knowledge. We experimented the GSD with a community of chemists tackling the problem of collaborative construction of an ontology (using the ontology editor Protégé within the GSD). This work was mainly lead by Dr. Pascal Dugenie.

Previous Research Teams

• The Kayou team at LIRMM

Previous Collaborations (before 2007)

• Monica Crubezy, and the Stanford Medical Informatics team, Stanford University, CA, USA.
  Objective : collaborative ontology construction (with the Protégé ontology editor).


• John Domingue & Enrico Motta and the Knowledge Media Institute team, at Open University, Milton Keynes, UK. Objective : work on Semantic Web Services and Grid.