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ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level

Summary: The first open source software suite that; (i) assists in the annotation and local management of experimental metadata from high-throughput studies employing one or a combination of omics and other technologies, (ii) empowers experimentalists and curators to use community-defined checklists and ontologies, and (iii) facilitates submission to international public repositories.

Philippe Rocca-Serra, Marco Brandizi, Eamonn Maguire, Nataliya Sklyar, Chris Taylor, Kimberly Begley, Dawn Field, Stephen Harris, Winston Hide, Oliver Hofmann, Steffen Neumann, Peter Sterk , Weida Tong  and Susanna-Assunta Sansone

Availability and Implementation: Software, documentation, case studies and implementations at: http://isatab.sourceforge.net/

Contact: isatools@googlegroups.com

Associate Editor: Dr. Jonathan Wren

Full content available here.

Internet closed, due to World Cup (and not only)

[Net Consumerism Icons]





Here we go again: World Cup begins and, as any other big sports event, on line TV from your country is blocked if you're abroad. And it's not the only restrictions that limit your freedom, including your chance to be a European citizen. There are technical solutions that allows one to overcome the sharks and you'll discover them in this post. Although there is quite more than that.






 

 

DC-THERA Directory, a Knowledge Management System for the support of the European Dendritic Cell Immunology Community

[dc-research.eu logo]Abstract. DC-THERA Directory is a web portal to support collaboration, communication and knowledge sharing within DC-THERA, a community focused on immunology. We show how we have faced the problem of repres- enting and managing highly heterogeneous and interconnected knowledge. One aspect of the application interface is the search and navigation through web ontologies. Another aspect is the dynamic representation of information entities having variable sets of properties. These results have been achieved by adopting a modelling approach that combines traditional object-oriented modelling with a triple-based knowledge representation. We discuss advantages of such an approach, especially for what concerns the possible future integration of other information sources.

Il dissenno di prima [Italian]

[Vauro, da www.vauro.net] Finché ci sono ancora, godiamoci gli scampoli di informazione degna del nome. Che fa riflettere sul come la vicenda del terremoto in Abruzzo sia la metafora del sisma infinito che devasta un paese intero. Che fa riflettere su come si potrebbe risorgere dalle macerie, se solo ci si svegliasse.







 

Obiettori pelosi [Italian]

[Covatutto, macchina incubatrice]

...Perché invece, domanda retorica, il legislatore non si occupa di mettere mano a questa ridicola contraddizione dei ginecoloci anti-abortisiti? Perché non si dibatte circa i pericoli per la salute, derivanti dal fatto che questa è in mano a certi personaggi? A persone, cioè, che aderiscono a sette clericali e pretendono, per altro per ipocrite ragioni di carriera, di mischiare la scienza medica con le mistificazioni superstiziose?

Per esempio, qualcuno si è mai chiesto che cosa succede ad una ragazza e alla sua vita...


 

The BioInvestigation Index and ISA Tools are out!

[The BII Architecture]

After a long time me and other brilliant guys from the NET Project team have been working, finally we have released a public version of the BioiInvestigation index and binaries for local installation! (Sources coming soon, just give us time to clean up/document etc.).

What is it?

The BII project provides an infrastructure for storage 'n retrieval of multi-omics experiments (we call them studies), i.e.: studies which of typical design is: prepare a sample and take out different measurements on it, such as microarray data, proteomics, 2D-gels, sequencing etc. We aim at keeping together the meta-data about these experiments (experiment design, sample characteristics and preparation), as well as leveraging on existing omic-specific repositories and format (e.g.: ArrayExpress + MAGETAB, PRIDE + PRIDEML).

How does it work?

We cover the whole pipeline consisting of prepare-submission/submit/search-stored-information. Submissions can be crafted by means of the ISATAB format, a tabular, spreadsheet-based format, which is a compromise between the need for an (end)user-friendly format and the need for something decently structured and formal (a similar approach was followed for the definition of MAGETAB). Things are further eased by the ISAcreator, a graphical Java tool that works similarly to Excel (or OpenOffice Calc, I don't like to mention MS only...), with the difference that ISAcreator has many more nice ISATAB-specific features. For instance, one of the most interesting things is that it connects to ontology servers (OLS or Bioportal) and allows you to select the right annotation terms for your submission.



Ippocrate, mandagli un segno [Italian]

[Immigrati, per favore non ci lasciate soli con gli Italiani]Secondo me questi pseudo-medici sporchi collaborazionisti non potranno lamentarsi se verranno svergognati sulla pubblica piazza. Se qualcuno avrà l'idea di identificarli, di pubblicare i loro nomi, le foto delle loro facce di merda, gli indirizzi dei reparti in cui lavorano, magari anche il modello, colore e targa delle loro auto.

Non si fa, viola la privacy, ma dubito che proprio tutti sapranno resistere alla tentazione di reagire con rabbia a queste bestiali, feroci violazioni della dignità umana, al modo criminale in cui si mette in pericolo la salute pubblica, quella degli stranieri e quella degli Italiani, alla infinita ipocrisia con cui degli avanzi di galera al potere invocano legge e ordine, e a quella con cui una massa di stronzi, raccomandati, evasori fiscali, corrotti e degenerati fino alla punta dei peli nello stomaco, vota, plaude e bela.

Non si fa, ma, per cercare di evitare il peggio, vale la pena menzionare che pulire il rossetto indelebile dalla carrozzeria è decisamente molto fastitioso, ma dovrebbe essere meno grave del reato di danneggiamento. Non saprei circa l'inquadramento giuridico del lancio di uova marce e pomodori, se qualcuno vuol dare lumi, qui sotto c'è il link per i commenti.





 

 

 

 

Redoing the microarray analyses

[Galileo Galilei on a money note]Nature Genetics has recently published this interesting work on repeatability of gene expression analysis. That microarray is a powerful tool used for study a number of biological phenomena is nowadays obvious. As it is that a microarray study should be repeatable, being it an instance of the experimental approach the science is based on. So, those who try to verify the repeatability of such kind of experiments are certainly welcome (sorry for repetitions... ;-) ). Even when one considers only a part of it, as they do, by focusing on the possibility to redo the analysis, starting from the raw data or the processed ones (i.e.: normalised).

What we learn from the paper is, IMHO, that the situation is better than what one would have expected, but there is still quite room to improve.

They started from an initial list of 20 papers, they choose a single conclusion from each of them (i.e.: a single figure or table) and tried to come at the same one, by redoing the analysis reported. An important part of the test is that they purposely didn't contacted the original authors, rather they tried to get all what they needed from the paper and from the data published in ArrayExpress or GEO, hence exploiting the available data annotations.

8 Marzo col califfo [Italian]

[Iranian women demonstration, from atlasshrugs2000.typepad.com]Per chi avesse ancora bisogno di capire in che stato di selvaggio sottosviluppo si è ridotto questo paese, pregasi leggere questa notizia.

Dopo averlo fatto, non ci si dovrebbe più meravigliare se la rabbia esplode solo quando la stuprata è Italiana e lo stupratore è lo sporco zingaro o il bastardo clandestino. Mentre cala, altrettanto feroce, il silenzio sul restante 80% delle violenze sessuali che le donne subiscono tra le mura domestiche, da Italianissimi maschi perbene, giusto un po' stupratori, ma senza necessità di permesso di soggiorno.





 

(Late) notes from ISWC 2008

I've eventually found time to review the notes from the last International Semantic Web Conference conference and put them in a clean document. Yes, it's a bit late, but I like to put this here and maybe someone will still find it interesting.

If you like the longer reading, please see the slides below. If you're looking for just short impressions, I can summarize them as follows.