We have been working on the identification and extraction of DNA sequences and automated database population. Data reported in the biomedical literature are an aid for primer and probe design for microorganism identification, genotyping and gene expression studies. Unfortunately, there are only a few online databases established as repositories for empirically validated primer and probe sequences. 

Thus, we created an original method for automatically detecting and extracting infectious disease-related primer and probe sequences from scientific papers, applied to all the PubMed Central repository. The data obtained from the manuscripts were then fed into the PubDNA finder database, the first public online resource linking scientific papers to sequences of nucleic acids.

The need for an updated list of resources is increasing critically. In Biomedical Informatics Group, we have created an innovative system that allows to automatically discover, retrieve and index bioinformatics resources. BioInformatics Resource Inventory (BIRI) has been developed and is maintained in an automated manner, based on existing articles in “ISI Web of Knowledge” and “Pubmed“, using techniques of natural language processing and “Text Mining“.

Philosophy of Science

Based on the classical works of Kuhn, Lakatos and Popper on the Philosophy of Science has analyzed the basic foundations of disciplines such as Medical Informatics and Bioinformatics. Over the recent years there have been ample discussions and have been published numerous articles on the scientific basis of these two disciplines to find areas to establish new plans of I+D and identify the main challenges to achieve. In this sence, the Philosophy of Science provides an effective method for this type of analysis.
Below is the outline of the interaction between medical informatics and bioinformatics proposed by Kulikowski and Maojo in 2003:

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