Marco Brandizi's Site

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

My Work

Linked Open Data @SOD 2014

Me during SOD PresentationI haven't had much time recently to update this personal web site, I realise it seems abandoned. Well, the good news is that what I've been busy with is cool! :-)
 

For instance, end of March, I enjoyed working with my Italian friends from the Spaghetti Open Data Group, to deliver a 1-day tutorial on Linked Data and their applications for the cause of Open Data to the People! I was very happy of the people I worked with, they was great in providing a comprehensive presentation of different aspects of Linked Data essentials and why they're important for making data available to people in their most useful form.

There is a Google Doc, containing all the links to the materials we used that day, including presentations, demo and exercise data-to-RDF projects.

I've partiallty reused such material to prepare a much shorter presentation, going to talk about this here.

 

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.

AVAILABILITY: http://www.ebi.ac.uk/rdf.

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 http://www.ideachampions.com/weblogs/Big-Idea.jpg]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.

Open Data during the G8 Week: the SEMIC 2013 Conference

[Dublin Rugby Stadium, SEMIC 2013 Venue]

A few notes from the SEMIC 2013 conference that I've recent attended, which happended the same days of the Open Data Charts release, by the G8.

A few notes from UK Ontology Network 2013

[UK Ontology Network]

A few notes here about the UK Ontology Network Meeting I've attended today. PDF available too.

[Cover]
As their site says:

The UK Ontology Network is an informal and voluntary coordination between people based in the United Kingdom and working in the area of ontology and ontology related technology. Members of the network include people from all areas of science and industry and across all disciplines.

It has been nice to see works in a variety of fields, where clearly there are different approaches and philosopies on designing and applying ontologies.

 

 

Happy Releases with Maven and Bamboo

[Dilbert on Software Versions, courtesy of dilbert.com]
Maven has several nice plug-ins to automate almost all the stages of a release process. Whether it is changing your POM with a new version number, tagging your SCM or updating references in other POMs, you can do it by just a few command lines. Even better, you can put Maven goals into a continuous integration software and release with just a few clicks.

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 (http://www.ebi.ac.uk/arrayexpress) 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.

Every Programmer has its Own Toolbox: jUtils

[Young Worker With his Toolbox - courtesy of http://www.joli-petite.com]My personal lib of utils is now a quite public project, jUtils (part of ISA-Tools) and the code in it doesn't come from myself only any more. In this post, I'd like to give a brief overview of what it offers. Who knows, that bit you were about to code yourself might be described in the next paragraphs.

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.

[graph2tab]

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 http://github.com/ISA-tools/graph2tab.

Contact: brandizi@ebi.ac.uk.

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.

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.

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