Welcome to the MetReS Project Web Page

The automated reconstruction of biological networks from the automated analysis of available biological information is one of the important goals of bioinformatics and computational biology. MetReS is a project that integrates different tools and methods to analyze various types of data and contribute to such a reconstruction. There are different aspects to this effort.

On the one hand we recognize the importance of automated text mining to assist in associating different biological and chemical entities to specific biological circuits and processes. To this effect we actively develop tools to achieve such associations.

One such tool, Biblio-MetReS extracts gene and/or protein interactions from the literature, which is one of the most important targets of text mining in biomedical research. In addition, v2.0 (upcoming shortly) will also automatically mine associations between those genes and specific processes and circuits, as well as between the processes themselves. Biblio-MetReS Player is also available to visualize the graphical results of Biblio-MetReS without having to re-do the analysis.

Please go to the Biblio-MetReS guide in order to download and learn how to use Biblio-MetReS.

Another tool that we developed in this effort is CheNER (also upcoming shortly), which automatically annotates chemical entities in scientific documents. This tool was developed in collaboration with the Structural Computational Biology Group at CNIO and you can also download it from their webpage (http://ubio.bioinfo.cnio.es/biotools/CheNER/).

Please go to the CheNER guide in order to download and learn how to use CheNER.

On the other hand, we are in the process of developing tools that use homology and comparative proteomics to also assist in network reconstruction. To this effect Homol-MetReS is in alpha testing and will be available soon. Other tools that use structural, evolutionary and omic information to assist in network reconstruction are also under development at the group.

Feedback, suggestions, and bug reports are more than welcome. To do so, please send us an e-mail at This email address is being protected from spambots. You need JavaScript enabled to view it. .

Related Research Groups:

Institut de Reçerca Biomèdica de Lleida (IRB)

Grup de Computació Distribuida (GCD)

Publications related to the project:

Biblio-MetReS: a bibliomic network reconstruction application and server

CheNER: Chemical named entity recognizer

Biblio-MetReS for user-friendly mining of genes and biological processes in scientific documents