EBI Proteomics Services

Abstract

We will provide an overview of recent developments in the tools and resources provided by the EBI Proteomics Services Team.

The IntAct molecular interaction database (http://www.ebi.ac.uk/intact)[1] now offers 163.000 curated binary molecular interactions. Using the Distributed Annotation System (DAS)[2] and DASTY (http://www.ebi.ac.uk/dasty), we are currently enhancing the IntAct molecular view through direct integration with external resources, in particular UniProt and ChEBI. We will provide a detailed view of the process and our experience using DAS for data integration and robust data maintenance.

The PRIDE proteomics identifications database (http://www.ebi.ac.uk/pride) [3] provides more than 500.000 protein identifications, supported by more than 3 million identified peptides. We will report on recent improvements to data submission system and interface, in particular the visualization of PRIDE peptides through DAS, as well as PRIDE protein sets on Reactome pathways.

A major challenge not only, but particularly in proteomics data resources is the efficient management of consistent protein identifiers and controlled vocabularies. We will describe two major tools to address these tasks, the PICR Protein Identifier Cross-Referencing service (http://www.ebi.ac.uk/Tools/picr), and the OLS Ontology Lookup Service (http://www.ebi.ac.uk/ols). PICR provides high quality mapping between protein identifier namespaces, based on a database of more than 15 million unique protein sequences and associated identifiers. OLS provides efficient access to currently almost 700.000 terms from 60 controlled vocabularies in OBO format. Both systems provide interactive as well as web service access, and are publicly available without restrictions.