Marco Brandizi's Site

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


The EBI RDF Platform: Linked Open Data for the Life Sciences.

Jupp, S., J. Malone, J. Bolleman, M. Brandizi, M. Davies, L. Garcia, A. Gaulton, S. Gehant, C. Laibe, N. Redaschi, et al., "The EBI RDF Platform: Linked Open Data for the Life Sciences.", Bioinformatics, 2014 Jan 11.

MOTIVATION: RDF is an emerging technology for describing, publishing and linking life science data. As a major provider of bioinformatics data and services, the European Bioinformatics Institute (EBI) is committed to making data readily accessible to the community in ways that meet existing demand. The EBI RDF platform has been developed to meet an increasing demand to coordinate RDF activities across the institute and provides a new entry point to querying and exploring integrated resources available at the EBI.


Adventures with Biological Samples and Linked Data

A few notes on the work behind the conversion of the EBI Biosamples Database data into Linked Data.

Call for Papers: Software, Open Standards, and Computational Approaches for Collaboration in Life Sciences

[Idea light with world drawn upon, courtesy of]DEADLINE IS NOW EXTENDED TO March, 14th.

Internet and the World Wide Web have made possible unimaginable levels of information sharing and collaboration in science, as well as in other human activities. In life science, software-based collaboration occurs at different scale levels, from small collocated scientific groups to large international communities. It also happens in various ways, from tight-interaction in ontology design to crowd-sourced data annotation and analysis. The idea of the web of data has been particularly successful in the biomedical field, given its potential to ease integration and exploration of large, complex, and heterogeneous data sets. Advanced knowledge representation and data exchange standards have been widely used for such purpose. These same approaches are applied in developing collaboration models and software to support such models.

ArrayExpress update--trends in database growth and links to data analysis tools.

Rustici, G., N. Kolesnikov, M. Brandizi, T. Burdett, M. Dylag, I. Emam, A. Farne, E. Hastings, J. Ison, M. Keays, et al., "ArrayExpress update--trends in database growth and links to data analysis tools.", Nucleic Acids Res, 2012 Nov 27.

The ArrayExpress Archive of Functional Genomics Data ( is one of three international functional genomics public data repositories, alongside the Gene Expression Omnibus at NCBI and the DDBJ Omics Archive, supporting peer-reviewed publications. It accepts data generated by sequencing or array-based technologies and currently contains data from almost a million assays, from over 30 000 experiments. The proportion of sequencing-based submissions has grown significantly over the last 2 years and has reached, in 2012, 15% of all new data. All data are available from ArrayExpress in MAGE-TAB format, which allows robust linking to data analysis and visualization tools, including Bioconductor and GenomeSpace. Additionally, R objects, for microarray data, and binary alignment format files, for sequencing data, have been generated for a significant proportion of ArrayExpress data.

graph2tab, a library to convert experimental workflow graphs into tabular formats.

Brandizi, M., N. Kurbatova, U. Sarkans, and P. Rocca-Serra, "graph2tab, a library to convert experimental workflow graphs into tabular formats.", Bioinformatics, 2012 May 3.


Motivations: Spreadsheet-like tabular formats are ever more popular in the biomedical field as a mean for experimental reporting. The problem of converting the graph of an experimental workflow into a table-based representation occurs in many such formats and is not easy to solve.

Results: We describe graph2tab, a library that implements methods to realise such a conversion in a size-optimised way. Our solution is generic and can be adapted to specific cases of data exporters or data converters that need to be implemented.

Availability and Implementation: The library source code and documentation are available at


Supplementary Information: A supplementary document describes the theoretical and technical details about the library implementation.

The BioSample Database (BioSD) at the European Bioinformatics Institute.

Gostev, M., A. Faulconbridge, M. Brandizi, J. Fernandez-Banet, U. Sarkans, A. Brazma, and H. Parkinson, "The BioSample Database (BioSD) at the European Bioinformatics Institute.", Nucleic Acids Res, vol. 40, issue Database issue, pp. D64-70, 2012 Jan.

The BioSample Database is a new database at EBI that stores information about biological samples used in molecular experiments, such as sequencing, gene expression or proteomics. The goals of the BioSample Database include: (i) recording and linking of sample information consistently within EBI databases such as ENA, ArrayExpress and PRIDE; (ii) minimizing data entry efforts for EBI database submitters by enabling submitting sample descriptions once and referencing them later in data submissions to assay databases and (iii) supporting cross database queries by sample characteristics. Each sample in the database is assigned an accession number.

Knowledge sharing and collaboration in translational research, and the DC-THERA Directory.

Splendiani, A., M. Gündel, J. M. Austyn, D. Cavalieri, C. Scognamiglio, and M. Brandizi, "Knowledge sharing and collaboration in translational research, and the DC-THERA Directory.", Brief Bioinform, vol. 12, issue 6, pp. 562-75, 2011 Nov.

...In this article we introduce the DC-THERA Directory, which is an information system designed to support knowledge management for this research community and beyond. We present how the use of metadata and Semantic Web technologies can effectively help to organize the knowledge generated by modern collaborative research, how these technologies can enable effective data management solutions during and beyond the project lifecycle, and how resources such as the DC-THERA Directory fit into the larger context of e-science...

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.

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.

(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.

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.

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:


Subscribe to RSS - Bioinformatics
Fervens was created by Design Disease for WordPress, brought to you by Smashing Magazine.
Ported to Drupal by Leow Kah Thong - Freelance Drupal Developer.