ProteomeBinders is a European consortium proposing to establish a comprehensive infrastructure resource of binding molecules for detection of the human proteome, together with tools for their use and applications in studying proteome function and organisation.
Currently there is no pan-European platform for the systematic development and quality control for these essential reagents. The consortium aims to provide a set of consistently characterised binders, required to detect all the relevant human proteins in tissues and fluids in health and disease. As the size of the human proteome is at least an order of magnitude greater than the ~ 24.000 protein coding genes known to date, and as for many applications several binders against each target are needed, the scale of our project is potentially immense.
The project will coordinate a European resource by integrating existing infrastructures, reviewing technologies and high-throughput production methods, standardising tools and applications, and establishing a database.
In the context of this project, I'm participating as an INRIA post-doc in the NA5 networking activities. The aim of this work package is to provide bioinformatics resources for the project. In particular, I'm involved in the NA5.1 networking activity, which is focused on standards, ontology and database schema for ligand binders information.
Indeed to facilitate sharing of ligand binder information, data must be standardised to provide unambiguous descriptions of binders and targets. The objective is to formalise such descriptions in an ontology of binder properties and a set of binder requirements for data presentation and exchange. In addition, the database schema for a central repository of binders against the human proteome has to be developed, providing basic information on each binder/target pair, with links to distributed resources, such as databases maintained by partners.
My work is more precisely focused on adapting the Intact data model for ProteomeBinders and defining the ligand-binder ontology, as a basis for reasoning on the large amount of data which should soon be available. The middle term goal is to develop web services to assist binder producers and users in their everyday tasks such as: planning binder production according to the importance of molecules in molecular pathways or as missing elements in a high-throughput experimental design, choosing the most adapted binder or binders for particular experimental settings and experimental goals, etc.
A few external resources are worth a look around this topic: