Marco Brandizi's Site

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My new job @EBI

So, I came back at the EBI in March. I am now working at the BioInvestigation Index project (formerly BioMAP), for which I brushed up the good old Java.
 

What is it about?

[isa-tab]In short: we aim at integrating the submission and access of transcriptomics data, proteomics data and metabolomics data. We will leverage on the EBI existing repositories, ArrayExpress and PRIDE. We are also developing a submission tabular format, ISA-TAB, which is inspired by MAGE-TAB and FUGE.

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...

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...

Dei taxi liberalizzati [Italian]

Penso di essere di Sinistra fin da prima che nascessi. Ma certe volte mi viene il dubbio di essermi sempre sbagliato, che uso questa parola in modo molto diverso da quello in cui la usano molti altri.

Cosa dovrebbe volere chi è di Sinistra? Un mondo dove lo Stato decide come deve funzionare l'economia, cosa e quanto produrre, quanto poco possono consumare gratuitamente tutti tutto e solo quello che passa lo Stato?

Antitheft device

By the way: I hate the burglar alarms which wake me up on Sunday at 6.00 am. And I wonder why you should expect someone cares about your f. car! :-\

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.

Stupid me

Uhm... I am afraid today we both haven't toothbrushed yet...

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