Current projects

Biomedical event extraction

Projects in the past

BioModels Database

I was the main developer of BioModels Database when I was working in Dr. Nicolas Le Novere's team from 2005 to 2009.

BioModels Database is a scientific resource for storing, simulating and analysing biological quantitative models of biochemical interests. All the models in BioModels Database have been described in the peer-reviewed scientific literature.

The models stored in the curated branch of BioModels Database are compliant with MIRIAM, the standard of model curation and annotation. The models have been simulated by curators to check that when run in simulations, they provide the same results as described in the publication. Model components are annotated, so the users can conveniently identify each model element and retrieve further information from other resources.

Modellers can submit the models in SBML and CellML. Models can subsequently be downloaded in SBML, CellML, VCML, XPP, SciLab, BioPAX. The reaction networks of models are presented in some graphic formats, such as PNG, SVG and graphic Java applet, in which some networks were presented by following Systems Biology Graphical Notation. And a summary of model is available in PDF.

Deposition of models upon publication is currently supported by Nature Publishing Group, PLoS and BioMed Central.

External references:


CALBC is a series of challenges (2009~2011) to create a diversely annotated corpus. The result of the integration process will be a silver standard corpus (SSC).


Semantic Enrichment of Scientific Literature (SESL) is a feasibility study for the extraction of disease related facts from the full text scientific literature. Extraction of information related to Diabetes II.