Marco Brandizi's Site

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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.

Formal aspects of Ontologies for Knowledge Representation and Applications

A work done for the PhD course on Artificial Intelligence.

Bioinformatics, data management and integration, Semantic Web and perspectives

Presented at BTBS Bioinformatics Master, 2005 editition. Here the docs.

Web Services and Bioinformatics, Taverna, BioMOBY

A work done for the PhD course on Web Services.

Modeling the TLR signalling with Pi-Calculus

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

PhD, Use cases and base modeling

Modeling Knowledge about Microarray Analysis

The document below is a description of my PhD project.

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