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.

Although we won't be tied to specific a biological domain, one of our goals is to support the Carcinogenomics European project, which addresses the creation of in-silico models for toxicity tests. These will offer an alternative to the employment of animal testing. A relevant part of the project is about the use and development of controlled vocabularies and ontologies.

What am I doing specifically?

At the moment I am mainly working on the submission tool component. The idea is to use a tabular, spreadsheet-like format for the input of multi-omics data. Instances of such a format, which at low level is a set of Tab-Separated Value files (TSV, also called CSV), may be produced by means of spreadsheet applications, like MS Excel or Open Office, or in a programmatic way (e.g.: data exchange puorposes). We plan also to develop an interactive tool, which will probably based on Excel, and which will be inspired by PRIDE-Harvest.

I am currently working on the import code, which parses the TSV files and maps them into our Java object model. In order to do that in a flexible and reusable way, I view the tabular format in a way similar to a relational database, and I am arranging the mapping task in a way similar to Hibernate mapping. More details in this presention.

Click to rate this post!
[Total: 0 Average: 0]

Written by

I'm the owner of this personal site. I'm a geek, I'm specialised in hacking software to deal with heaps of data, especially life science data. I'm interested in data standards, open culture (open source, open data, open everything), IT and society, and more. Further info at

Leave a Reply

Your email address will not be published. Required fields are marked *