Functional Genomics Production Team

The Functional Genomics Production Team manages data content and user interaction for the core EBI databases: the ArrayExpress Archive (Parkinson, 2009), the Gene Expression Atlas (GXA; Kapushesky et al., 2010) and the new Biosamples Database.

All three resources have complex metadata representing experimental types, variables and sample attributes for which we require semantic markup in the form of ontologies. We develop ontologies and software for the annotation of complex biological data, including the Experimental Factor Ontology (EFO) for functional genomics annotation (Malone, 2010), the Software Ontology, the Ontology for Biomedical Investigation and the Vertebrate Anatomy Ontology (VBO). We collaborate with international partners to develop MAGE-TAB- based data management infrastructure and annotation tools for gene expression data.

The team has expanded its remit to deal with the change in technology from arrays to RNA sequencing experiments; this has resulted in collaboration with the EBI databases ENA and EGA to provide data flow and integration between these sequence databases and ArrayExpress.

The Functional Genomics Production Team is headed by Helen Parkinson.

Databases and Services

• ArrayExpress An archive of functional genomics data including gene expression data from RNA-Seq and array technology.
• BioSamples Database (BioSD) A database designed to hold information about biological samples that are referenced from other EBI databases.
• Experimental Factor Ontology (EFO) The Experimental Factor Ontology is an application focused ontology modelling the experimental factors in ArrayExpress

Collaborations

• The Ontology for BioMedical Investigation
• The Annotare project
• Software Ontology Project (JISC)
• FGED (formerly MGED)

Funding

• EMBL Core funds.
• EC FP7 - SLING
• EC FP7 - Gen2Phen
• JISC

Useful Links

• Experimental Factor Ontology