Marco Brandizi's Site

Welcome to a 5-min-lazyness site...

My Work

Managing Microarray Knowledge with the Semantic Web

[MannOnto, relatedAssertions] Geeez! Eventually I have submitted the thesis and given the defense presentation! My PhD project is about representing the results coming from microarray data analysis. I represent concepts like: sets of differentially expressed genes, results from clustering algorithms, claims about the role of genes in a biological pathway. I use Semantic Web technologies and an OWL model (ontology) to provide a formal representation of such knowledge. All is focused on assertions (e.g.: "IL2 is expressed under LPS infection condition"), which may be supported by experimental evidence (e.g.: a data set) or other kinds of evaluations, including ranking and comments from the users. Moreover, users and their roles (e.g.: is an expert on Immunology) may be considedered, especially for ranking the assertions. I have also developed a demo, based on the Makna Semantic Wiki.


PhD project, yet another ontology

I have reviewed the OWL file once more. I have done it after analysis of study cases and considerations on making useful inference with OWL. Details are reported in the doc.

A Database for Genomic Expression Data Management

This is the project that made me discover the charm of Bioinformatics, Microarrays and Biology. Here you can find:

Gene Lists, Microarray Knowledge, Semantic Web

I've started this discussion on the semweb-lifesci mailing list.

I was interested in how to handle gene lists in OWL (and other lists of gene expression related entities). The discussion has expanded toward: MAGE-OM in RDF format, microarrays and Semantic Web, Semantic web technologies...

PhD, Progress report of Mar 2006

Now I am working on my project from the EBI. This is a progress report where I show the application of the Semantic Web to my stuff.

Decorations @EBI

Modeling the TLR signalling with Pi-Calculus

A work made for the PhD course on Theoretical Computer Science. Here the docs.

Modeling Knowledge about Microarray Analysis

The document below is a description of my PhD project.

Leaf what?

I have been involved in the start-up company Leaf Bioscience, which closed in 2010.


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