Marco Brandizi's Site

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

Bioinformatics

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...

Awkward identifiers

[Figures about TO gene]
Today I discovered that a gene named "to" exists. It's not difficult to imagine how much hope you have to find it in Google. That's interesting: it was mentioned on a discussion about the use of natural language identifiers in computer science modelling. But actually maybe it is a case that shows how the Semantic Web could be useful. And complement Google. Well, Google is still able to find meaning info by means of the extended name, "takeout". So, if you already know what "to" means you'll probaly look up it on a by-keyword search engine via "takeout" + something else (drosophila, gene). I wonder if marking something like "to" with something like "is the label for..." could actually improve searches. Uhm... probably relating "to or whatever" to other resources, such as publication or chromosome or who is studying this gene, to which disease or biological process is related to, etc. Uhm... Uhm... anyway I am impressed by this "to" thing...

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.

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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