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Scientific Papers

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.


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...

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:

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