My Work

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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.

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.



Error #AEF039483CD: I was programmed by a damned jerk

I've been told of all the good Software Engineering principles, and good programming and all that jazz since my childhood. Be simple. Be clear. Be modular. Reuse. Document.

Here We Are

ArrayExpress update–from an archive of functional genomics experiments to the atlas of gene expression

ArrayExpress http://www.ebi.ac.uk/arrayexpress consists of three components: the ArrayExpress Repository-a public archive of functional genomics experiments and supporting data, the ArrayExpress Warehouse-a database of gene expression profiles and other bio-measurements and the ArrayExpress Atlas-a new summary database and meta-analytical tool of ranked gene expression across multiple experiments and different biological conditions. The Repository contains data from over 6000 experiments comprising approximately 200 000 assays, and the database doubles in size every 15 months. The majority of the data are array based, but other data types are included, most recently-ultra high-throughput sequencing transcriptomics and epigenetic data. The Warehouse and Atlas allow users to query for differentially expressed genes by gene names and properties, experimental conditions and sample properties, or a combination of both. In this update, we describe the ArrayExpress developments over the last two years.

http://view.ncbi.nlm.nih.gov/pubmed/19015125

CiteXplore

The First RSBI (ISA-TAB) Workshop: "Can a Simple Format Work for Complex Studies?"

This article summarizes the motivation for, and the proceedings of, the first ISA-TAB workshop held December 6-8, 2007, at the EBI, Cambridge, UK. This exploratory workshop, organized by members of the Microarray Gene Expression Data (MGED) Society's Reporting Structure for Biological Investigations (RSBI) working group, brought together a group of developers of a range of collaborative systems to discuss the use of a common format to address the pressing need of reporting and communicating data and metadata from biological, biomedical, and environmental studies employing combinations of genomics, transcriptomics, proteomics, and metabolomics technologies along with more conventional methodologies. The expertise of the participants comprised database development, data management, and hands-on experience in the development of data communication standards. The workshop's outcomes are set to help formalize the proposed Investigation, Study, Assay (ISA)-TAB tab-delimited format for representing and communicating experimental metadata. This article is part of the special issue of OMICS on the activities of the Genomics Standards Consortium (GSC).

http://dx.doi.org/10.1089/omi.2008.0019
CiteXplore

Networking with Dendritic Cells

I've recently gone to the hearth of Mediterranean, Athens, for the annual meeting of the DC-THERA network, an FP6 project. A number of people and organisations collaborate in the context of this project, under the hat of  dendritic cells research (DC). Even me, the amateurish biologist, can guess the importance of this kind of cells for the Immune system, and their consequent importance for the development of a number of vaccines and therapies.

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.