I spent Sunday morning wandering in and out of the ‘Tools and Resources from EBI’ session here at PAG. Some EBI resources for plant science will be very familiar to some of our community, but the presenters gave accessible talks that included some news and advice, so I thought I’d round them up for you.
Maria Keays presented ArrayExpress and ExpressionAtlas. These are the functional genomics tools from EBI. Keays defined functional genomics as the study of gene expression, gene function and gene regulation – these tools certainly aren’t just for microarray data!
Users submit their data to ArrayExpress via the Annotare submission tool, which encourages inclusion of information about how the samples were grown all the way through to data generation. Keays acknowledged that a user may encounter an error message they can’t get around, and assured us that emails sent to the helpdesk (Arrayexpress@ebi.ac.uk) are responded to quickly. Once submitted, the dataset and associated metadata is checked by a human curator before the user can upload it. The data can stay private until publication because two logins are provided; one for the submitter and one for the reviewer of the paper they hope to publish.
We’ve been encouraging our community to share data on NCBI GEO because it is able to disseminate almost any data type. But for functional genomics data, ArrayExpress is just as acceptable to journals as GEO, and the Annotare submission tool requires more extensive metadata and more stringent standards than GEO. (more…)