Research Activities
I have different experiences and interests for research in Informatics (cf. note on the left for the Informatics vs. Computer Science discussion) from artificial intelligence to biomedical informatics. I made my PhD thesis at the crossing of 3 mains approaches of distributed systems and since September 2007, as a postdoc in Stanford, I am getting involved in a more applied research context: annotation using biomedical ontologies.
This page describes the different activities I am (or I was) involved in.
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Topics of interest
- Semantic annotation
- Ontologies
- Semantic Web
- Data integration
- Biomedical Informatics
- Sematic distance & similarity
- Service-oriented computing
- Distributed systems
- Multi-Agents Systems (MAS)
- Web
- Grid
- Functional and applicative programming languages
- E-learning
- Distant collaboration
- Collaborative construction of ontologies
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The Open Biomedical Annotator Web service
The Open Biomedical Annotator (OBA) is an ontology-based Web service that annotates public datasets with biomedical ontology concepts based on their textual metadata. The biomedical community can use the annotator service to tag datasets automatically with ontology concepts. These concepts come from the Unified Medical Language System (UMLS) Metathesaurus and the National Center for Biomedical Ontology (NCBO) BioPortal ontologies.
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The Open Biomedical Resource (OBR) index 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 biomedical 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 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 and develop the Open Biomedical Resource (OBR) index (previously called Ontrez), an index of biomedical resources indexed/annotated with biomedical ontology concepts.
Users can use ontologies to find relevant experimental data and information related to a specific concept. The OBR index is constructed by using the OBA web service workflow to automatically annotate resource elements coming from different public online biomedical resources.
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 OBR index is accessible in BioPortal, where a user searching or browsing an ontology in BioPortal will get for a given ontology concept all the resources elements that have been annotated with this concept and which represent a potential relevant information for him/her (cf. image).
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More information and details on http://obs.bioontology.org/
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The Open Biomedical Services (OBS)
In the context of the OBR/OBA project we develop and use a bunch of biomedical ontology based services. These services are used in the OBR and OBA workflow, especially in the semantic expansion step. For example, IS_A hierarchy services and mapping services are used to expand the annotations created by the concept recognition tool.
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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.
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Previous Research Teams
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They are talking about us...
Genomeweb BioInform, the Integrated Informatics News Source, March 2009.
Le Journal Permanent de L'Humanisme Méthodologique, May 2006.
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